---
_id: '14901'
abstract:
- lang: eng
text: Global services like navigation, communication, and Earth observation have
increased dramatically in the 21st century due to advances in outer space industries.
But as orbits become increasingly crowded with both satellites and inevitable
space debris pollution, continued operations become endangered by the heightened
risks of debris collisions in orbit. Kessler Syndrome is the term for when a critical
threshold of orbiting debris triggers a runaway positive feedback loop of debris
collisions, creating debris congestion that can render orbits unusable. As this
potential tipping point becomes more widely recognized, there have been renewed
calls for debris mitigation and removal. Here, we combine complex systems and
social-ecological systems approaches to study how these efforts may affect space
debris accumulation and the likelihood of reaching Kessler Syndrome. Specifically,
we model how debris levels are affected by future launch rates, cleanup activities,
and collisions between extant debris. We contextualize and interpret our dynamic
model within a discussion of existing space debris governance and other social,
economic, and geopolitical factors that may influence effective collective management
of the orbital commons. In line with previous studies, our model finds that debris
congestion may be reached in less than 200 years, though a holistic management
strategy combining removal and mitigation actions can avoid such outcomes while
continuing space activities. Moreover, although active debris removal may be particularly
effective, the current lack of market and governance support may impede its implementation.
Research into these critical dynamics and the multi-faceted variables that influence
debris outcomes can support policymakers in curating impactful governance strategies
and realistic transition pathways to sustaining debris-free orbits. Overall, our
study is useful for communicating about space debris sustainability in policy
and education settings by providing an exploration of policy portfolio options
supported by a simple and clear social-ecological modeling approach.
acknowledgement: The authors would like to thank the special issue co-editors, Marco
Janssen and Xiao-Shan Yap, and the anonymous reviewers for their comments that helped
improve the manuscript. The paper also benefited from suggestions by other author
participants in this special issue. We would also like to thank the 2022 Santa Fe
Institute Complex Systems Summer School for providing space to initiate this study.
article_processing_charge: Yes
article_type: original
author:
- first_name: Keiko
full_name: Nomura, Keiko
last_name: Nomura
- first_name: Simon
full_name: Rella, Simon
id: B4765ACA-AA38-11E9-AC9A-0930E6697425
last_name: Rella
- first_name: Haily
full_name: Merritt, Haily
last_name: Merritt
- first_name: Mathieu
full_name: Baltussen, Mathieu
last_name: Baltussen
- first_name: Darcy
full_name: Bird, Darcy
last_name: Bird
- first_name: Annika
full_name: Tjuka, Annika
last_name: Tjuka
- first_name: Dan
full_name: Falk, Dan
last_name: Falk
citation:
ama: Nomura K, Rella S, Merritt H, et al. Tipping points of space debris in low
earth orbit. International Journal of the Commons. 2024;18(1). doi:10.5334/ijc.1275
apa: Nomura, K., Rella, S., Merritt, H., Baltussen, M., Bird, D., Tjuka, A., &
Falk, D. (2024). Tipping points of space debris in low earth orbit. International
Journal of the Commons. Ubiquity Press. https://doi.org/10.5334/ijc.1275
chicago: Nomura, Keiko, Simon Rella, Haily Merritt, Mathieu Baltussen, Darcy Bird,
Annika Tjuka, and Dan Falk. “Tipping Points of Space Debris in Low Earth Orbit.”
International Journal of the Commons. Ubiquity Press, 2024. https://doi.org/10.5334/ijc.1275.
ieee: K. Nomura et al., “Tipping points of space debris in low earth orbit,”
International Journal of the Commons, vol. 18, no. 1. Ubiquity Press, 2024.
ista: Nomura K, Rella S, Merritt H, Baltussen M, Bird D, Tjuka A, Falk D. 2024.
Tipping points of space debris in low earth orbit. International Journal of the
Commons. 18(1).
mla: Nomura, Keiko, et al. “Tipping Points of Space Debris in Low Earth Orbit.”
International Journal of the Commons, vol. 18, no. 1, Ubiquity Press, 2024,
doi:10.5334/ijc.1275.
short: K. Nomura, S. Rella, H. Merritt, M. Baltussen, D. Bird, A. Tjuka, D. Falk,
International Journal of the Commons 18 (2024).
date_created: 2024-01-30T11:58:02Z
date_published: 2024-01-11T00:00:00Z
date_updated: 2024-02-05T10:10:27Z
day: '11'
ddc:
- '550'
department:
- _id: GradSch
- _id: GaTk
doi: 10.5334/ijc.1275
file:
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checksum: b80ebc889033c365d8f8c05a0c655382
content_type: application/pdf
creator: dernst
date_created: 2024-02-05T10:06:35Z
date_updated: 2024-02-05T10:06:35Z
file_id: '14939'
file_name: 2023_IntJourCommons_Nomura.pdf
file_size: 1305786
relation: main_file
success: 1
file_date_updated: 2024-02-05T10:06:35Z
has_accepted_license: '1'
intvolume: ' 18'
issue: '1'
keyword:
- Sociology and Political Science
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '01'
oa: 1
oa_version: Published Version
publication: International Journal of the Commons
publication_identifier:
issn:
- 1875-0281
publication_status: published
publisher: Ubiquity Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tipping points of space debris in low earth orbit
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2024'
...
---
_id: '15020'
abstract:
- lang: eng
text: "This thesis consists of four distinct pieces of work within theoretical biology,
with two themes in common: the concept of optimization in biological systems,
and the use of information-theoretic tools to quantify biological stochasticity
and statistical uncertainty.\r\nChapter 2 develops a statistical framework for
studying biological systems which we believe to be optimized for a particular
utility function, such as retinal neurons conveying information about visual stimuli.
We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the
expected utility. We explore how such priors aid inference of system parameters
with limited data and enable optimality hypothesis testing: is the utility higher
than by chance?\r\nChapter 3 examines the ultimate biological optimization process:
evolution by natural selection. As some individuals survive and reproduce more
successfully than others, populations evolve towards fitter genotypes and phenotypes.
We formalize this as accumulation of genetic information, and use population genetics
theory to study how much such information can be accumulated per generation and
maintained in the face of random mutation and genetic drift. We identify the population
size and fitness variance as the key quantities that control information accumulation
and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter
3, but from a different perspective: we ask how much genetic information organisms
actually need, in particular in the context of gene regulation. For example, how
much information is needed to bind transcription factors at correct locations
within the genome? Population genetics provides us with a refined answer: with
an increasing population size, populations achieve higher fitness by maintaining
more genetic information. Moreover, regulatory parameters experience selection
pressure to optimize the fitness-information trade-off, i.e. minimize the information
needed for a given fitness. This provides an evolutionary derivation of the optimization
priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information
between a signal and a communication channel output (such as neural activity).
Mutual information is an important utility measure for biological systems, but
its practical use can be difficult due to the large dimensionality of many biological
channels. Sometimes, a lower bound on mutual information is computed by replacing
the high-dimensional channel outputs with decodes (signal estimates). Our result
provides a corresponding upper bound, provided that the decodes are the maximum
posterior estimates of the signal."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
citation:
ama: Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020
apa: Hledik, M. (2024). Genetic information and biological optimization.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020
chicago: Hledik, Michal. “Genetic Information and Biological Optimization.” Institute
of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020.
ieee: M. Hledik, “Genetic information and biological optimization,” Institute of
Science and Technology Austria, 2024.
ista: Hledik M. 2024. Genetic information and biological optimization. Institute
of Science and Technology Austria.
mla: Hledik, Michal. Genetic Information and Biological Optimization. Institute
of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.
short: M. Hledik, Genetic Information and Biological Optimization, Institute of
Science and Technology Austria, 2024.
date_created: 2024-02-23T14:02:04Z
date_published: 2024-02-23T00:00:00Z
date_updated: 2024-03-06T14:22:52Z
day: '23'
ddc:
- '576'
- '519'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
- _id: GaTk
doi: 10.15479/at:ista:15020
ec_funded: 1
file:
- access_level: open_access
checksum: b2d3da47c98d481577a4baf68944fe41
content_type: application/pdf
creator: mhledik
date_created: 2024-02-23T13:50:53Z
date_updated: 2024-02-23T13:50:53Z
file_id: '15021'
file_name: hledik thesis pdfa 2b.pdf
file_size: 7102089
relation: main_file
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content_type: application/zip
creator: mhledik
date_created: 2024-02-23T13:50:54Z
date_updated: 2024-02-23T14:20:16Z
file_id: '15022'
file_name: hledik thesis source.zip
file_size: 14014790
relation: source_file
file_date_updated: 2024-02-23T14:20:16Z
has_accepted_license: '1'
keyword:
- Theoretical biology
- Optimality
- Evolution
- Information
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '158'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 2665AAFE-B435-11E9-9278-68D0E5697425
grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7553'
relation: part_of_dissertation
status: public
- id: '12081'
relation: part_of_dissertation
status: public
- id: '7606'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Genetic information and biological optimization
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...
---
_id: '13127'
abstract:
- lang: eng
text: Cooperative disease defense emerges as group-level collective behavior, yet
how group members make the underlying individual decisions is poorly understood.
Using garden ants and fungal pathogens as an experimental model, we derive the
rules governing individual ant grooming choices and show how they produce colony-level
hygiene. Time-resolved behavioral analysis, pathogen quantification, and probabilistic
modeling reveal that ants increase grooming and preferentially target highly-infectious
individuals when perceiving high pathogen load, but transiently suppress grooming
after having been groomed by nestmates. Ants thus react to both, the infectivity
of others and the social feedback they receive on their own contagiousness. While
inferred solely from momentary ant decisions, these behavioral rules quantitatively
predict hour-long experimental dynamics, and synergistically combine into efficient
colony-wide pathogen removal. Our analyses show that noisy individual decisions
based on only local, incomplete, yet dynamically-updated information on pathogen
threat and social feedback can lead to potent collective disease defense.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: We thank Mike Bidochka for the fungal strains, the ISTA Social Immunity
Team for ant collection, Hanna Leitner for experimental and molecular support, Jennifer
Robb and Lukas Lindorfer for microscopy, and the LabSupport Facility at ISTA for
general laboratory support. We further thank Victor Mireles, Iain Couzin, Fabian
Theis and the Social Immunity Team for continued feedback throughout, and Michael
Sixt, Yuko Ulrich, Koos Boomsma, Erika Dawson, Megan Kutzer and Hinrich Schulenburg
for comments on the manuscript. This project has received funding from the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
program (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency
of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science
Program (Grant No. RGP0065/2012) to GT.
article_number: '3232'
article_processing_charge: Yes
article_type: original
author:
- first_name: Barbara E
full_name: Casillas Perez, Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
- first_name: Katarína
full_name: Bod'Ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'Ová
orcid: 0000-0002-7214-0171
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. Dynamic pathogen
detection and social feedback shape collective hygiene in ants. Nature Communications.
2023;14. doi:10.1038/s41467-023-38947-y
apa: Casillas Perez, B. E., Bodova, K., Grasse, A. V., Tkačik, G., & Cremer,
S. (2023). Dynamic pathogen detection and social feedback shape collective hygiene
in ants. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38947-y
chicago: Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gašper Tkačik,
and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective
Hygiene in Ants.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38947-y.
ieee: B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkačik, and S. Cremer, “Dynamic
pathogen detection and social feedback shape collective hygiene in ants,” Nature
Communications, vol. 14. Springer Nature, 2023.
ista: Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. 2023. Dynamic
pathogen detection and social feedback shape collective hygiene in ants. Nature
Communications. 14, 3232.
mla: Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback
Shape Collective Hygiene in Ants.” Nature Communications, vol. 14, 3232,
Springer Nature, 2023, doi:10.1038/s41467-023-38947-y.
short: B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature
Communications 14 (2023).
date_created: 2023-06-11T22:00:40Z
date_published: 2023-06-03T00:00:00Z
date_updated: 2023-08-07T13:09:09Z
day: '03'
ddc:
- '570'
department:
- _id: SyCr
- _id: GaTk
doi: 10.1038/s41467-023-38947-y
ec_funded: 1
external_id:
isi:
- '001002562700005'
pmid:
- '37270641'
file:
- access_level: open_access
checksum: 4af0393e3ed47b3fc46e68b81c3c1007
content_type: application/pdf
creator: dernst
date_created: 2023-06-13T08:05:46Z
date_updated: 2023-06-13T08:05:46Z
file_id: '13132'
file_name: 2023_NatureComm_CasillasPerez.pdf
file_size: 2358167
relation: main_file
success: 1
file_date_updated: 2023-06-13T08:05:46Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
- _id: 255008E4-B435-11E9-9278-68D0E5697425
grant_number: RGP0065/2012
name: Information processing and computation in fish groups
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '12945'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Dynamic pathogen detection and social feedback shape collective hygiene in
ants
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '12762'
abstract:
- lang: eng
text: Neurons in the brain are wired into adaptive networks that exhibit collective
dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches.
Although existing models account for oscillations and avalanches separately, they
typically do not explain both phenomena, are too complex to analyze analytically
or intractable to infer from data rigorously. Here we propose a feedback-driven
Ising-like class of neural networks that captures avalanches and oscillations
simultaneously and quantitatively. In the simplest yet fully microscopic model
version, we can analytically compute the phase diagram and make direct contact
with human brain resting-state activity recordings via tractable inference of
the model’s two essential parameters. The inferred model quantitatively captures
the dynamics over a broad range of scales, from single sensor oscillations to
collective behaviors of extreme events and neuronal avalanches. Importantly, the
inferred parameters indicate that the co-existence of scale-specific (oscillations)
and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical
point at the onset of self-sustained oscillations.
acknowledgement: This research was funded in whole, or in part, by the Austrian Science
Fund (FWF) (grant no. PT1013M03318 to F.L. and no. P34015 to G.T.). For the purpose
of open access, the author has applied a CC BY public copyright licence to any Author
Accepted Manuscript version arising from this submission. The study was supported
by the European Union Horizon 2020 research and innovation program under the Marie
Sklodowska-Curie action (grant agreement No. 754411 to F.L.).
article_processing_charge: No
article_type: original
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Selver
full_name: Pepic, Selver
id: F93245C4-C3CA-11E9-B4F0-C6F4E5697425
last_name: Pepic
- first_name: Oren
full_name: Shriki, Oren
last_name: Shriki
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling
of adaptive neural networks explains co-existence of avalanches and oscillations
in resting human brain. Nature Computational Science. 2023;3:254-263. doi:10.1038/s43588-023-00410-9
apa: Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., & De Martino, D. (2023).
Statistical modeling of adaptive neural networks explains co-existence of avalanches
and oscillations in resting human brain. Nature Computational Science.
Springer Nature. https://doi.org/10.1038/s43588-023-00410-9
chicago: Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele
De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence
of Avalanches and Oscillations in Resting Human Brain.” Nature Computational
Science. Springer Nature, 2023. https://doi.org/10.1038/s43588-023-00410-9.
ieee: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical
modeling of adaptive neural networks explains co-existence of avalanches and oscillations
in resting human brain,” Nature Computational Science, vol. 3. Springer
Nature, pp. 254–263, 2023.
ista: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling
of adaptive neural networks explains co-existence of avalanches and oscillations
in resting human brain. Nature Computational Science. 3, 254–263.
mla: Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks
Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.”
Nature Computational Science, vol. 3, Springer Nature, 2023, pp. 254–63,
doi:10.1038/s43588-023-00410-9.
short: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational
Science 3 (2023) 254–263.
date_created: 2023-03-26T22:01:08Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2023-08-16T12:41:53Z
day: '20'
ddc:
- '570'
department:
- _id: GaTk
- _id: GradSch
doi: 10.1038/s43588-023-00410-9
ec_funded: 1
external_id:
arxiv:
- '2108.06686'
file:
- access_level: open_access
checksum: 7c63b2b2edfd68aaffe96d70ca6a865a
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T12:39:57Z
date_updated: 2023-08-16T12:39:57Z
file_id: '14073'
file_name: 2023_NatureCompScience_Lombardi.pdf
file_size: 4474284
relation: main_file
success: 1
file_date_updated: 2023-08-16T12:39:57Z
has_accepted_license: '1'
intvolume: ' 3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 254-263
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: eb943429-77a9-11ec-83b8-9f471cdf5c67
grant_number: M03318
name: Functional Advantages of Critical Brain Dynamics
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
publication: Nature Computational Science
publication_identifier:
eissn:
- 2662-8457
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Statistical modeling of adaptive neural networks explains co-existence of avalanches
and oscillations in resting human brain
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2023'
...
---
_id: '14515'
abstract:
- lang: eng
text: Most natural and engineered information-processing systems transmit information
via signals that vary in time. Computing the information transmission rate or
the information encoded in the temporal characteristics of these signals requires
the mutual information between the input and output signals as a function of time,
i.e., between the input and output trajectories. Yet, this is notoriously difficult
because of the high-dimensional nature of the trajectory space, and all existing
techniques require approximations. We present an exact Monte Carlo technique called
path weight sampling (PWS) that, for the first time, makes it possible to compute
the mutual information between input and output trajectories for any stochastic
system that is described by a master equation. The principal idea is to use the
master equation to evaluate the exact conditional probability of an individual
output trajectory for a given input trajectory and average this via Monte Carlo
sampling in trajectory space to obtain the mutual information. We present three
variants of PWS, which all generate the trajectories using the standard stochastic
simulation algorithm. While direct PWS is a brute-force method, Rosenbluth-Rosenbluth
PWS exploits the analogy between signal trajectory sampling and polymer sampling,
and thermodynamic integration PWS is based on a reversible work calculation in
trajectory space. PWS also makes it possible to compute the mutual information
between input and output trajectories for systems with hidden internal states
as well as systems with feedback from output to input. Applying PWS to the bacterial
chemotaxis system, consisting of 182 coupled chemical reactions, demonstrates
not only that the scheme is highly efficient but also that the number of receptor
clusters is much smaller than hitherto believed, while their size is much larger.
acknowledgement: "We thank Bela Mulder, Tom Shimizu, Fotios Avgidis, Peter Bolhuis,
and Daan Frenkel for useful discussions and a careful reading of the manuscript,
and we thank Age Tjalma for support with obtaining the Gaussian approximation of
the chemotaxis system. This work is part of the Dutch Research Council (NWO) and
was performed at the research institute AMOLF. This project has received funding
from the European Research Council (ERC) under the European Union’s Horizon 2020
research and innovation program (Grant Agreement No. 885065) and was\r\nfinancially
supported by NWO through the “Building a Synthetic Cell (BaSyC)” Gravitation Grant
(024.003.019)."
article_number: '041017'
article_processing_charge: Yes
article_type: original
author:
- first_name: Manuel
full_name: Reinhardt, Manuel
last_name: Reinhardt
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Pieter Rein
full_name: Ten Wolde, Pieter Rein
last_name: Ten Wolde
citation:
ama: 'Reinhardt M, Tkačik G, Ten Wolde PR. Path weight sampling: Exact Monte Carlo
computation of the mutual information between stochastic trajectories. Physical
Review X. 2023;13(4). doi:10.1103/PhysRevX.13.041017'
apa: 'Reinhardt, M., Tkačik, G., & Ten Wolde, P. R. (2023). Path weight sampling:
Exact Monte Carlo computation of the mutual information between stochastic trajectories.
Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.13.041017'
chicago: 'Reinhardt, Manuel, Gašper Tkačik, and Pieter Rein Ten Wolde. “Path Weight
Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic
Trajectories.” Physical Review X. American Physical Society, 2023. https://doi.org/10.1103/PhysRevX.13.041017.'
ieee: 'M. Reinhardt, G. Tkačik, and P. R. Ten Wolde, “Path weight sampling: Exact
Monte Carlo computation of the mutual information between stochastic trajectories,”
Physical Review X, vol. 13, no. 4. American Physical Society, 2023.'
ista: 'Reinhardt M, Tkačik G, Ten Wolde PR. 2023. Path weight sampling: Exact Monte
Carlo computation of the mutual information between stochastic trajectories. Physical
Review X. 13(4), 041017.'
mla: 'Reinhardt, Manuel, et al. “Path Weight Sampling: Exact Monte Carlo Computation
of the Mutual Information between Stochastic Trajectories.” Physical Review
X, vol. 13, no. 4, 041017, American Physical Society, 2023, doi:10.1103/PhysRevX.13.041017.'
short: M. Reinhardt, G. Tkačik, P.R. Ten Wolde, Physical Review X 13 (2023).
date_created: 2023-11-12T23:00:55Z
date_published: 2023-10-26T00:00:00Z
date_updated: 2023-11-13T09:03:30Z
day: '26'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.1103/PhysRevX.13.041017
external_id:
arxiv:
- '2203.03461'
file:
- access_level: open_access
checksum: 32574aeebcca7347a4152c611b66b3d5
content_type: application/pdf
creator: dernst
date_created: 2023-11-13T09:00:19Z
date_updated: 2023-11-13T09:00:19Z
file_id: '14522'
file_name: 2023_PhysReviewX_Reinhardt.pdf
file_size: 1595223
relation: main_file
success: 1
file_date_updated: 2023-11-13T09:00:19Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Physical Review X
publication_identifier:
eissn:
- 2160-3308
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Path weight sampling: Exact Monte Carlo computation of the mutual information
between stochastic trajectories'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2023'
...
---
_id: '14656'
abstract:
- lang: eng
text: Although much is known about how single neurons in the hippocampus represent
an animal's position, how circuit interactions contribute to spatial coding is
less well understood. Using a novel statistical estimator and theoretical modeling,
both developed in the framework of maximum entropy models, we reveal highly structured
CA1 cell-cell interactions in male rats during open field exploration. The statistics
of these interactions depend on whether the animal is in a familiar or novel environment.
In both conditions the circuit interactions optimize the encoding of spatial information,
but for regimes that differ in the informativeness of their spatial inputs. This
structure facilitates linear decodability, making the information easy to read
out by downstream circuits. Overall, our findings suggest that the efficient coding
hypothesis is not only applicable to individual neuron properties in the sensory
periphery, but also to neural interactions in the central brain.
acknowledgement: M.N. was supported by the European Union Horizon 2020 Grant 665385.
J.C. was supported by the European Research Council Consolidator Grant 281511. G.T.
was supported by the Austrian Science Fund (FWF) Grant P34015. C.S. was supported
by an Institute of Science and Technology fellow award and by the National Science
Foundation (NSF) Award No. 1922658. We thank Peter Baracskay, Karola Kaefer, and
Hugo Malagon-Vina for the acquisition of the data. We also thank Federico Stella,
Wiktor Młynarski, Dori Derdikman, Colin Bredenberg, Roman Huszar, Heloisa Chiossi,
Lorenzo Posani, and Mohamady El-Gaby for comments on an earlier version of the manuscript.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
citation:
ama: Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1
interactions optimizes spatial coding across experience. The Journal of Neuroscience.
2023;43(48):8140-8156. doi:10.1523/JNEUROSCI.0194-23.2023
apa: Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (2023). The structure
of hippocampal CA1 interactions optimizes spatial coding across experience. The
Journal of Neuroscience. Society of Neuroscience. https://doi.org/10.1523/JNEUROSCI.0194-23.2023
chicago: Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin.
“The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across
Experience.” The Journal of Neuroscience. Society of Neuroscience, 2023.
https://doi.org/10.1523/JNEUROSCI.0194-23.2023.
ieee: M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal
CA1 interactions optimizes spatial coding across experience,” The Journal of
Neuroscience, vol. 43, no. 48. Society of Neuroscience, pp. 8140–8156, 2023.
ista: Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal
CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience.
43(48), 8140–8156.
mla: Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes
Spatial Coding across Experience.” The Journal of Neuroscience, vol. 43,
no. 48, Society of Neuroscience, 2023, pp. 8140–56, doi:10.1523/JNEUROSCI.0194-23.2023.
short: M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience
43 (2023) 8140–8156.
date_created: 2023-12-10T23:00:58Z
date_published: 2023-11-29T00:00:00Z
date_updated: 2023-12-11T11:37:20Z
day: '29'
ddc:
- '570'
department:
- _id: JoCs
- _id: GaTk
doi: 10.1523/JNEUROSCI.0194-23.2023
ec_funded: 1
external_id:
pmid:
- '37758476'
file:
- access_level: closed
checksum: e2503c8f84be1050e28f64320f1d5bd2
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T11:30:37Z
date_updated: 2023-12-11T11:30:37Z
embargo: 2024-06-01
embargo_to: open_access
file_id: '14674'
file_name: 2023_JourNeuroscience_Nardin.pdf
file_size: 2280632
relation: main_file
file_date_updated: 2023-12-11T11:30:37Z
has_accepted_license: '1'
intvolume: ' 43'
issue: '48'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1523/JNEUROSCI.0194-23.2023
month: '11'
oa: 1
oa_version: Published Version
page: 8140-8156
pmid: 1
project:
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: The Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
publication_status: published
publisher: Society of Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: The structure of hippocampal CA1 interactions optimizes spatial coding across
experience
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2023'
...
---
_id: '12487'
abstract:
- lang: eng
text: Sleep plays a key role in preserving brain function, keeping the brain network
in a state that ensures optimal computational capabilities. Empirical evidence
indicates that such a state is consistent with criticality, where scale-free neuronal
avalanches emerge. However, the relationship between sleep, emergent avalanches,
and criticality remains poorly understood. Here we fully characterize the critical
behavior of avalanches during sleep, and study their relationship with the sleep
macro- and micro-architecture, in particular the cyclic alternating pattern (CAP).
We show that avalanche size and duration distributions exhibit robust power laws
with exponents approximately equal to −3/2 e −2, respectively. Importantly, we
find that sizes scale as a power law of the durations, and that all critical exponents
for neuronal avalanches obey robust scaling relations, which are consistent with
the mean-field directed percolation universality class. Our analysis demonstrates
that avalanche dynamics depends on the position within the NREM-REM cycles, with
the avalanche density increasing in the descending phases and decreasing in the
ascending phases of sleep cycles. Moreover, we show that, within NREM sleep, avalanche
occurrence correlates with CAP activation phases, particularly A1, which are the
expression of slow wave sleep propensity and have been proposed to be beneficial
for cognitive processes. The results suggest that neuronal avalanches, and thus
tuning to criticality, actively contribute to sleep development and play a role
in preserving network function. Such findings, alongside characterization of the
universality class for avalanches, open new avenues to the investigation of functional
role of criticality during sleep with potential clinical application.Significance
statementWe fully characterize the critical behavior of neuronal
avalanches during sleep, and show that avalanches follow precise scaling laws
that are consistent with the mean-field directed percolation universality class.
The analysis provides first evidence of a functional relationship between avalanche
occurrence, slow-wave sleep dynamics, sleep stage transitions and occurrence of
CAP phase A during NREM sleep. Because CAP is considered one of the major guardians
of NREM sleep that allows the brain to dynamically react to external perturbation
and contributes to the cognitive consolidation processes occurring in sleep, our
observations suggest that neuronal avalanches at criticality are associated with
flexible response to external inputs and to cognitive processes, a key assumption
of the critical brain hypothesis.
acknowledgement: FL acknowledges support from the European Union’s Horizon 2020 research
and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411,
and from the Austrian Science Fund (FWF) under the Lise Meitner fellowship No. PT1013M03318.
IA acknowledges financial support from the MIUR PRIN 2017WZFTZP.
article_processing_charge: Yes
article_type: original
author:
- first_name: Silvia
full_name: Scarpetta, Silvia
last_name: Scarpetta
- first_name: Niccolò
full_name: Morrisi, Niccolò
last_name: Morrisi
- first_name: Carlotta
full_name: Mutti, Carlotta
last_name: Mutti
- first_name: Nicoletta
full_name: Azzi, Nicoletta
last_name: Azzi
- first_name: Irene
full_name: Trippi, Irene
last_name: Trippi
- first_name: Rosario
full_name: Ciliento, Rosario
last_name: Ciliento
- first_name: Ilenia
full_name: Apicella, Ilenia
last_name: Apicella
- first_name: Giovanni
full_name: Messuti, Giovanni
last_name: Messuti
- first_name: Marianna
full_name: Angiolelli, Marianna
last_name: Angiolelli
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Liborio
full_name: Parrino, Liborio
last_name: Parrino
- first_name: Anna Elisabetta
full_name: Vaudano, Anna Elisabetta
last_name: Vaudano
citation:
ama: Scarpetta S, Morrisi N, Mutti C, et al. Criticality of neuronal avalanches
in human sleep and their relationship with sleep macro- and micro-architecture.
iScience. 2023;26(10):107840. doi:10.1016/j.isci.2023.107840
apa: Scarpetta, S., Morrisi, N., Mutti, C., Azzi, N., Trippi, I., Ciliento, R.,
… Vaudano, A. E. (2023). Criticality of neuronal avalanches in human sleep and
their relationship with sleep macro- and micro-architecture. IScience.
Elsevier. https://doi.org/10.1016/j.isci.2023.107840
chicago: Scarpetta, Silvia, Niccolò Morrisi, Carlotta Mutti, Nicoletta Azzi, Irene
Trippi, Rosario Ciliento, Ilenia Apicella, et al. “Criticality of Neuronal Avalanches
in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.”
IScience. Elsevier, 2023. https://doi.org/10.1016/j.isci.2023.107840.
ieee: S. Scarpetta et al., “Criticality of neuronal avalanches in human sleep
and their relationship with sleep macro- and micro-architecture,” iScience,
vol. 26, no. 10. Elsevier, p. 107840, 2023.
ista: Scarpetta S, Morrisi N, Mutti C, Azzi N, Trippi I, Ciliento R, Apicella I,
Messuti G, Angiolelli M, Lombardi F, Parrino L, Vaudano AE. 2023. Criticality
of neuronal avalanches in human sleep and their relationship with sleep macro-
and micro-architecture. iScience. 26(10), 107840.
mla: Scarpetta, Silvia, et al. “Criticality of Neuronal Avalanches in Human Sleep
and Their Relationship with Sleep Macro- and Micro-Architecture.” IScience,
vol. 26, no. 10, Elsevier, 2023, p. 107840, doi:10.1016/j.isci.2023.107840.
short: S. Scarpetta, N. Morrisi, C. Mutti, N. Azzi, I. Trippi, R. Ciliento, I. Apicella,
G. Messuti, M. Angiolelli, F. Lombardi, L. Parrino, A.E. Vaudano, IScience 26
(2023) 107840.
date_created: 2023-02-02T10:50:17Z
date_published: 2023-10-20T00:00:00Z
date_updated: 2023-12-13T11:11:24Z
day: '20'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1016/j.isci.2023.107840
ec_funded: 1
external_id:
isi:
- '001082331200001'
pmid:
- '37766992'
file:
- access_level: open_access
checksum: f499836af172ecc9865de4bb41fa99d1
content_type: application/pdf
creator: dernst
date_created: 2023-10-09T07:23:46Z
date_updated: 2023-10-09T07:23:46Z
file_id: '14412'
file_name: 2023_iScience_Scarpetta.pdf
file_size: 4872708
relation: main_file
success: 1
file_date_updated: 2023-10-09T07:23:46Z
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '107840'
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: eb943429-77a9-11ec-83b8-9f471cdf5c67
grant_number: M03318
name: Functional Advantages of Critical Brain Dynamics
publication: iScience
publication_identifier:
eissn:
- 2589-0042
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Criticality of neuronal avalanches in human sleep and their relationship with
sleep macro- and micro-architecture
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2023'
...
---
_id: '14862'
article_number: ckad160.597
article_processing_charge: No
author:
- first_name: Simon
full_name: Rella, Simon
id: B4765ACA-AA38-11E9-AC9A-0930E6697425
last_name: Rella
- first_name: Y
full_name: Kulikova, Y
last_name: Kulikova
- first_name: Aygul
full_name: Minnegalieva, Aygul
id: 87DF77F0-1D9A-11EA-B6AE-CE443DDC885E
last_name: Minnegalieva
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: 'Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. Complex vaccination strategies
prevent the emergence of vaccine resistance. In: European Journal of Public
Health. Vol 33. Oxford University Press; 2023. doi:10.1093/eurpub/ckad160.597'
apa: Rella, S., Kulikova, Y., Minnegalieva, A., & Kondrashov, F. (2023). Complex
vaccination strategies prevent the emergence of vaccine resistance. In European
Journal of Public Health (Vol. 33). Oxford University Press. https://doi.org/10.1093/eurpub/ckad160.597
chicago: Rella, Simon, Y Kulikova, Aygul Minnegalieva, and Fyodor Kondrashov. “Complex
Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” In European
Journal of Public Health, Vol. 33. Oxford University Press, 2023. https://doi.org/10.1093/eurpub/ckad160.597.
ieee: S. Rella, Y. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination
strategies prevent the emergence of vaccine resistance,” in European Journal
of Public Health, 2023, vol. 33, no. Supplement_2.
ista: Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. 2023. Complex vaccination
strategies prevent the emergence of vaccine resistance. European Journal of Public
Health. vol. 33, ckad160.597.
mla: Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence
of Vaccine Resistance.” European Journal of Public Health, vol. 33, no.
Supplement_2, ckad160.597, Oxford University Press, 2023, doi:10.1093/eurpub/ckad160.597.
short: S. Rella, Y. Kulikova, A. Minnegalieva, F. Kondrashov, in:, European Journal
of Public Health, Oxford University Press, 2023.
date_created: 2024-01-22T12:02:28Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2024-01-24T11:16:09Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1093/eurpub/ckad160.597
file:
- access_level: open_access
checksum: 98706755bb4cc5d553818ade7660a7d2
content_type: application/pdf
creator: dernst
date_created: 2024-01-24T11:12:33Z
date_updated: 2024-01-24T11:12:33Z
file_id: '14882'
file_name: 2023_EurJourPublicHealth_Rella.pdf
file_size: 71057
relation: main_file
success: 1
file_date_updated: 2024-01-24T11:12:33Z
has_accepted_license: '1'
intvolume: ' 33'
issue: Supplement_2
keyword:
- Public Health
- Environmental and Occupational Health
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '10'
oa: 1
oa_version: Published Version
publication: European Journal of Public Health
publication_identifier:
eissn:
- 1464-360X
issn:
- 1101-1262
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Complex vaccination strategies prevent the emergence of vaccine resistance
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2023'
...
---
_id: '14402'
abstract:
- lang: eng
text: Alpha oscillations are a distinctive feature of the awake resting state of
the human brain. However, their functional role in resting-state neuronal dynamics
remains poorly understood. Here we show that, during resting wakefulness, alpha
oscillations drive an alternation of attenuation and amplification bouts in neural
activity. Our analysis indicates that inhibition is activated in pulses that last
for a single alpha cycle and gradually suppress neural activity, while excitation
is successively enhanced over a few alpha cycles to amplify neural activity. Furthermore,
we show that long-term alpha amplitude fluctuations—the “waxing and waning” phenomenon—are
an attenuation-amplification mechanism described by a power-law decay of the activity
rate in the “waning” phase. Importantly, we do not observe such dynamics during
non-rapid eye movement (NREM) sleep with marginal alpha oscillations. The results
suggest that alpha oscillations modulate neural activity not only through pulses
of inhibition (pulsed inhibition hypothesis) but also by timely enhancement of
excitation (or disinhibition).
acknowledgement: This research was funded in whole or in part by the Austrian Science
Fund (FWF) (grant PT1013M03318 to F.L.). For the purpose of open access, the author
has applied a CC BY public copyright license to any Author Accepted Manuscript version
arising from this submission. The study was supported by the European Union Horizon
2020 Research and Innovation Program under the Marie Sklodowska-Curie action (grant
agreement 754411 to F.L.) and in part by the NextGenerationEU through the grant
TAlent in ReSearch@University of Padua – STARS@UNIPD (to F.L.) (project BRAINCIP
[brain criticality and information processing]). L.d.A. acknowledges support from
the Italian MIUR project PRIN2017WZFTZP and partial support from NEXTGENERATIONEU
(NGEU) funded by the Ministry of University and Research (MUR), National Recovery
and Resilience Plan (NRRP), and project MNESYS (PE0000006)—a multiscale integrated
approach to the study of the nervous system in health and disease (DN. 1553 11.10.2022).
O.S. acknowledges support from the Israel Science Foundation, grant 504/17. The
work was supported in part by DIRP ZIAMH02797 (to D.P.).
article_number: '113162'
article_processing_charge: Yes
article_type: original
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Hans J.
full_name: Herrmann, Hans J.
last_name: Herrmann
- first_name: Liborio
full_name: Parrino, Liborio
last_name: Parrino
- first_name: Dietmar
full_name: Plenz, Dietmar
last_name: Plenz
- first_name: Silvia
full_name: Scarpetta, Silvia
last_name: Scarpetta
- first_name: Anna Elisabetta
full_name: Vaudano, Anna Elisabetta
last_name: Vaudano
- first_name: Lucilla
full_name: De Arcangelis, Lucilla
last_name: De Arcangelis
- first_name: Oren
full_name: Shriki, Oren
last_name: Shriki
citation:
ama: 'Lombardi F, Herrmann HJ, Parrino L, et al. Beyond pulsed inhibition: Alpha
oscillations modulate attenuation and amplification of neural activity in the
awake resting state. Cell Reports. 2023;42(10). doi:10.1016/j.celrep.2023.113162'
apa: 'Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano,
A. E., … Shriki, O. (2023). Beyond pulsed inhibition: Alpha oscillations modulate
attenuation and amplification of neural activity in the awake resting state. Cell
Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.113162'
chicago: 'Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz,
Silvia Scarpetta, Anna Elisabetta Vaudano, Lucilla De Arcangelis, and Oren Shriki.
“Beyond Pulsed Inhibition: Alpha Oscillations Modulate Attenuation and Amplification
of Neural Activity in the Awake Resting State.” Cell Reports. Elsevier,
2023. https://doi.org/10.1016/j.celrep.2023.113162.'
ieee: 'F. Lombardi et al., “Beyond pulsed inhibition: Alpha oscillations
modulate attenuation and amplification of neural activity in the awake resting
state,” Cell Reports, vol. 42, no. 10. Elsevier, 2023.'
ista: 'Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, De
Arcangelis L, Shriki O. 2023. Beyond pulsed inhibition: Alpha oscillations modulate
attenuation and amplification of neural activity in the awake resting state. Cell
Reports. 42(10), 113162.'
mla: 'Lombardi, Fabrizio, et al. “Beyond Pulsed Inhibition: Alpha Oscillations Modulate
Attenuation and Amplification of Neural Activity in the Awake Resting State.”
Cell Reports, vol. 42, no. 10, 113162, Elsevier, 2023, doi:10.1016/j.celrep.2023.113162.'
short: F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano,
L. De Arcangelis, O. Shriki, Cell Reports 42 (2023).
date_created: 2023-10-08T22:01:15Z
date_published: 2023-10-31T00:00:00Z
date_updated: 2024-01-30T14:07:40Z
day: '31'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1016/j.celrep.2023.113162
ec_funded: 1
external_id:
isi:
- '001086695500001'
pmid:
- '37777965'
file:
- access_level: open_access
checksum: 9c71eb2a03aa160415f01ad95f49ceb5
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T14:07:08Z
date_updated: 2024-01-30T14:07:08Z
file_id: '14914'
file_name: 2023_CellReports_Lombardi.pdf
file_size: 5599007
relation: main_file
success: 1
file_date_updated: 2024-01-30T14:07:08Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: eb943429-77a9-11ec-83b8-9f471cdf5c67
grant_number: M03318
name: Functional Advantages of Critical Brain Dynamics
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification
of neural activity in the awake resting state'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...
---
_id: '10821'
abstract:
- lang: eng
text: 'Rhythmical cortical activity has long been recognized as a pillar in the
architecture of brain functions. Yet, the dynamic organization of its underlying
neuronal population activity remains elusive. Here we uncover a unique organizational
principle regulating collective neural dynamics associated with the alpha rhythm
in the awake resting-state. We demonstrate that cascades of neural activity obey
attenuation-amplification dynamics (AAD), with a transition from the attenuation
regime—within alpha cycles—to the amplification regime—across a few alpha cycles—that
correlates with the characteristic frequency of the alpha rhythm. We find that
this short-term AAD is part of a large-scale, size-dependent temporal structure
of neural cascades that obeys the Omori law: Following large cascades, smaller
cascades occur at a rate that decays as a power-law of the time elapsed from such
events—a long-term AAD regulating brain activity over the timescale of seconds.
We show that such an organization corresponds to the "waxing and waning" of the
alpha rhythm. Importantly, we observe that short- and long-term AAD are unique
to the awake resting-state, being absent during NREM sleep. These results provide
a quantitative, dynamical description of the so-far-qualitative notion of the
"waxing and waning" phenomenon, and suggest the AAD as a key principle governing
resting-state dynamics across timescales.'
acknowledgement: FL acknowledges support from the European Union’s Horizon 2020 research
and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411.
LdA acknowledges the Italian MIUR project PRIN2017WZFTZP for financial support and
the project E-PASSION of the program VALERE 2019 funded by the University of Campania,
Italy “L. Vanvitelli”. OS acknowledges support from the Israel Science Foundation,
Grant No. 504/17. Supported in part by DIRP ZIAMH02797 to DP.
article_processing_charge: No
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Hans J.
full_name: Herrmann, Hans J.
last_name: Herrmann
- first_name: Liborio
full_name: Parrino, Liborio
last_name: Parrino
- first_name: Dietmar
full_name: Plenz, Dietmar
last_name: Plenz
- first_name: Silvia
full_name: Scarpetta, Silvia
last_name: Scarpetta
- first_name: Anna Elisabetta
full_name: Vaudano, Anna Elisabetta
last_name: Vaudano
- first_name: Lucilla
full_name: de Arcangelis, Lucilla
last_name: de Arcangelis
- first_name: Oren
full_name: Shriki, Oren
last_name: Shriki
citation:
ama: Lombardi F, Herrmann HJ, Parrino L, et al. Alpha rhythm induces attenuation-amplification
dynamics in neural activity cascades. bioRxiv. 2022. doi:10.1101/2022.03.03.482657
apa: Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano,
A. E., … Shriki, O. (2022). Alpha rhythm induces attenuation-amplification dynamics
in neural activity cascades. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2022.03.03.482657
chicago: Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz, Silvia
Scarpetta, Anna Elisabetta Vaudano, Lucilla de Arcangelis, and Oren Shriki. “Alpha
Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.”
BioRxiv. Cold Spring Harbor Laboratory, 2022. https://doi.org/10.1101/2022.03.03.482657.
ieee: F. Lombardi et al., “Alpha rhythm induces attenuation-amplification
dynamics in neural activity cascades,” bioRxiv. Cold Spring Harbor Laboratory,
2022.
ista: Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, de Arcangelis
L, Shriki O. 2022. Alpha rhythm induces attenuation-amplification dynamics in
neural activity cascades. bioRxiv, 10.1101/2022.03.03.482657.
mla: Lombardi, Fabrizio, et al. “Alpha Rhythm Induces Attenuation-Amplification
Dynamics in Neural Activity Cascades.” BioRxiv, Cold Spring Harbor Laboratory,
2022, doi:10.1101/2022.03.03.482657.
short: F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano,
L. de Arcangelis, O. Shriki, BioRxiv (2022).
date_created: 2022-03-04T22:20:59Z
date_published: 2022-03-04T00:00:00Z
date_updated: 2022-03-07T07:28:34Z
day: '04'
department:
- _id: GaTk
doi: 10.1101/2022.03.03.482657
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2022.03.03.482657
month: '03'
oa: 1
oa_version: Preprint
page: '25'
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: bioRxiv
publication_status: published
publisher: Cold Spring Harbor Laboratory
status: public
title: Alpha rhythm induces attenuation-amplification dynamics in neural activity
cascades
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11638'
abstract:
- lang: eng
text: 'Statistical inference is central to many scientific endeavors, yet how it
works remains unresolved. Answering this requires a quantitative understanding
of the intrinsic interplay between statistical models, inference methods, and
the structure in the data. To this end, we characterize the efficacy of direct
coupling analysis (DCA)—a highly successful method for analyzing amino acid sequence
data—in inferring pairwise interactions from samples of ferromagnetic Ising models
on random graphs. Our approach allows for physically motivated exploration of
qualitatively distinct data regimes separated by phase transitions. We show that
inference quality depends strongly on the nature of data-generating distributions:
optimal accuracy occurs at an intermediate temperature where the detrimental effects
from macroscopic order and thermal noise are minimal. Importantly our results
indicate that DCA does not always outperform its local-statistics-based predecessors;
while DCA excels at low temperatures, it becomes inferior to simple correlation
thresholding at virtually all temperatures when data are limited. Our findings
offer insights into the regime in which DCA operates so successfully, and more
broadly, how inference interacts with the structure in the data.'
acknowledgement: This work was supported in part by the Alfred P. Sloan Foundation,
the Simons Foundation, the National Institutes of Health under Award No. R01EB026943,
and the National Science Foundation, through the Center for the Physics of Biological
Function (PHY-1734030).
article_number: '023240'
article_processing_charge: No
article_type: original
author:
- first_name: Vudtiwat
full_name: Ngampruetikorn, Vudtiwat
last_name: Ngampruetikorn
- first_name: Vedant
full_name: Sachdeva, Vedant
last_name: Sachdeva
- first_name: Johanna
full_name: Torrence, Johanna
last_name: Torrence
- first_name: Jan
full_name: Humplik, Jan
id: 2E9627A8-F248-11E8-B48F-1D18A9856A87
last_name: Humplik
- first_name: David J.
full_name: Schwab, David J.
last_name: Schwab
- first_name: Stephanie E.
full_name: Palmer, Stephanie E.
last_name: Palmer
citation:
ama: Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE.
Inferring couplings in networks across order-disorder phase transitions. Physical
Review Research. 2022;4(2). doi:10.1103/PhysRevResearch.4.023240
apa: Ngampruetikorn, V., Sachdeva, V., Torrence, J., Humplik, J., Schwab, D. J.,
& Palmer, S. E. (2022). Inferring couplings in networks across order-disorder
phase transitions. Physical Review Research. American Physical Society.
https://doi.org/10.1103/PhysRevResearch.4.023240
chicago: Ngampruetikorn, Vudtiwat, Vedant Sachdeva, Johanna Torrence, Jan Humplik,
David J. Schwab, and Stephanie E. Palmer. “Inferring Couplings in Networks across
Order-Disorder Phase Transitions.” Physical Review Research. American Physical
Society, 2022. https://doi.org/10.1103/PhysRevResearch.4.023240.
ieee: V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D. J. Schwab, and
S. E. Palmer, “Inferring couplings in networks across order-disorder phase transitions,”
Physical Review Research, vol. 4, no. 2. American Physical Society, 2022.
ista: Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE.
2022. Inferring couplings in networks across order-disorder phase transitions.
Physical Review Research. 4(2), 023240.
mla: Ngampruetikorn, Vudtiwat, et al. “Inferring Couplings in Networks across Order-Disorder
Phase Transitions.” Physical Review Research, vol. 4, no. 2, 023240, American
Physical Society, 2022, doi:10.1103/PhysRevResearch.4.023240.
short: V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D.J. Schwab, S.E.
Palmer, Physical Review Research 4 (2022).
date_created: 2022-07-24T22:01:42Z
date_published: 2022-06-24T00:00:00Z
date_updated: 2022-07-25T07:52:35Z
day: '24'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.1103/PhysRevResearch.4.023240
external_id:
arxiv:
- '2106.02349'
file:
- access_level: open_access
checksum: ed6fdc2a3a096df785fa5f7b17b716c6
content_type: application/pdf
creator: dernst
date_created: 2022-07-25T07:47:23Z
date_updated: 2022-07-25T07:47:23Z
file_id: '11644'
file_name: 2022_PhysicalReviewResearch_Ngampruetikorn.pdf
file_size: 1379683
relation: main_file
success: 1
file_date_updated: 2022-07-25T07:47:23Z
funded_apc: '1'
has_accepted_license: '1'
intvolume: ' 4'
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inferring couplings in networks across order-disorder phase transitions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2022'
...
---
_id: '12156'
abstract:
- lang: eng
text: Models of transcriptional regulation that assume equilibrium binding of transcription
factors have been less successful at predicting gene expression from sequence
in eukaryotes than in bacteria. This could be due to the non-equilibrium nature
of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium
mechanisms is vast and predominantly uninteresting. The key question is therefore
how this space can be navigated efficiently, to focus on mechanisms and models
that are biologically relevant. In this review, we advocate for the normative
role of theory—theory that prescribes rather than just describes—in providing
such a focus. Theory should expand its remit beyond inferring mechanistic models
from data, towards identifying non-equilibrium gene regulatory schemes that may
have been evolutionarily selected, despite their energy consumption, because they
are precise, reliable, fast, or otherwise outperform regulation at equilibrium.
We illustrate our reasoning by toy examples for which we provide simulation code.
acknowledgement: 'This work was supported through the Center for the Physics of Biological
Function (PHYe1734030) and by National Institutes of Health Grants R01GM097275 and
U01DK127429 (TG). GT acknowledges the support of the Austrian Science Fund grant
FWF P28844 and the Human Frontiers Science Program. '
article_number: '100435'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Benjamin
full_name: Zoller, Benjamin
last_name: Zoller
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: '1'
citation:
ama: Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or
non? Current Opinion in Systems Biology. 2022;31(9). doi:10.1016/j.coisb.2022.100435
apa: Zoller, B., Gregor, T., & Tkačik, G. (2022). Eukaryotic gene regulation
at equilibrium, or non? Current Opinion in Systems Biology. Elsevier. https://doi.org/10.1016/j.coisb.2022.100435
chicago: Zoller, Benjamin, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation
at Equilibrium, or Non?” Current Opinion in Systems Biology. Elsevier,
2022. https://doi.org/10.1016/j.coisb.2022.100435.
ieee: B. Zoller, T. Gregor, and G. Tkačik, “Eukaryotic gene regulation at equilibrium,
or non?,” Current Opinion in Systems Biology, vol. 31, no. 9. Elsevier,
2022.
ista: Zoller B, Gregor T, Tkačik G. 2022. Eukaryotic gene regulation at equilibrium,
or non? Current Opinion in Systems Biology. 31(9), 100435.
mla: Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?”
Current Opinion in Systems Biology, vol. 31, no. 9, 100435, Elsevier, 2022,
doi:10.1016/j.coisb.2022.100435.
short: B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).
date_created: 2023-01-12T12:08:51Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2023-02-13T09:20:34Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1016/j.coisb.2022.100435
file:
- access_level: open_access
checksum: 97ef01e0cc60cdc84f45640a0f248fb0
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T12:14:10Z
date_updated: 2023-01-24T12:14:10Z
file_id: '12362'
file_name: 2022_CurrentBiology_Zoller.pdf
file_size: 2214944
relation: main_file
success: 1
file_date_updated: 2023-01-24T12:14:10Z
has_accepted_license: '1'
intvolume: ' 31'
issue: '9'
keyword:
- Applied Mathematics
- Computer Science Applications
- Drug Discovery
- General Biochemistry
- Genetics and Molecular Biology
- Modeling and Simulation
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Current Opinion in Systems Biology
publication_identifier:
issn:
- 2452-3100
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Eukaryotic gene regulation at equilibrium, or non?
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2022'
...
---
_id: '10530'
abstract:
- lang: eng
text: "Cell dispersion from a confined area is fundamental in a number of biological
processes,\r\nincluding cancer metastasis. To date, a quantitative understanding
of the interplay of single\r\ncell motility, cell proliferation, and intercellular
contacts remains elusive. In particular, the role\r\nof E- and N-Cadherin junctions,
central components of intercellular contacts, is still\r\ncontroversial. Combining
theoretical modeling with in vitro observations, we investigate the\r\ncollective
spreading behavior of colonies of human cancer cells (T24). The spreading of these\r\ncolonies
is driven by stochastic single-cell migration with frequent transient cell-cell
contacts.\r\nWe find that inhibition of E- and N-Cadherin junctions decreases
colony spreading and average\r\nspreading velocities, without affecting the strength
of correlations in spreading velocities of\r\nneighboring cells. Based on a biophysical
simulation model for cell migration, we show that the\r\nbehavioral changes upon
disruption of these junctions can be explained by reduced repulsive\r\nexcluded
volume interactions between cells. This suggests that in cancer cell migration,\r\ncadherin-based
intercellular contacts sharpen cell boundaries leading to repulsive rather than\r\ncohesive
interactions between cells, thereby promoting efficient cell spreading during
collective\r\nmigration.\r\n"
acknowledgement: Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research
Foundation) - Project-ID 201269156 - SFB 1032 (Projects B8 and B12). D.B.B. is supported
in part by a DFG fellowship within the Graduate School of Quantitative Biosciences
Munich (QBM) and by the Joachim Herz Stiftung.
article_processing_charge: No
article_type: original
author:
- first_name: Themistoklis
full_name: Zisis, Themistoklis
last_name: Zisis
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Tom
full_name: Brandstätter, Tom
last_name: Brandstätter
- first_name: Wei Xiong
full_name: Siow, Wei Xiong
last_name: Siow
- first_name: Joseph
full_name: d’Alessandro, Joseph
last_name: d’Alessandro
- first_name: Angelika M.
full_name: Vollmar, Angelika M.
last_name: Vollmar
- first_name: Chase P.
full_name: Broedersz, Chase P.
last_name: Broedersz
- first_name: Stefan
full_name: Zahler, Stefan
last_name: Zahler
citation:
ama: Zisis T, Brückner D, Brandstätter T, et al. Disentangling cadherin-mediated
cell-cell interactions in collective cancer cell migration. Biophysical Journal.
2022;121(1):P44-60. doi:10.1016/j.bpj.2021.12.006
apa: Zisis, T., Brückner, D., Brandstätter, T., Siow, W. X., d’Alessandro, J., Vollmar,
A. M., … Zahler, S. (2022). Disentangling cadherin-mediated cell-cell interactions
in collective cancer cell migration. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2021.12.006
chicago: Zisis, Themistoklis, David Brückner, Tom Brandstätter, Wei Xiong Siow,
Joseph d’Alessandro, Angelika M. Vollmar, Chase P. Broedersz, and Stefan Zahler.
“Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell
Migration.” Biophysical Journal. Elsevier, 2022. https://doi.org/10.1016/j.bpj.2021.12.006.
ieee: T. Zisis et al., “Disentangling cadherin-mediated cell-cell interactions
in collective cancer cell migration,” Biophysical Journal, vol. 121, no.
1. Elsevier, pp. P44-60, 2022.
ista: Zisis T, Brückner D, Brandstätter T, Siow WX, d’Alessandro J, Vollmar AM,
Broedersz CP, Zahler S. 2022. Disentangling cadherin-mediated cell-cell interactions
in collective cancer cell migration. Biophysical Journal. 121(1), P44-60.
mla: Zisis, Themistoklis, et al. “Disentangling Cadherin-Mediated Cell-Cell Interactions
in Collective Cancer Cell Migration.” Biophysical Journal, vol. 121, no.
1, Elsevier, 2022, pp. P44-60, doi:10.1016/j.bpj.2021.12.006.
short: T. Zisis, D. Brückner, T. Brandstätter, W.X. Siow, J. d’Alessandro, A.M.
Vollmar, C.P. Broedersz, S. Zahler, Biophysical Journal 121 (2022) P44-60.
date_created: 2021-12-10T09:48:19Z
date_published: 2022-01-04T00:00:00Z
date_updated: 2023-08-02T13:34:25Z
day: '04'
ddc:
- '570'
department:
- _id: EdHa
- _id: GaTk
doi: 10.1016/j.bpj.2021.12.006
external_id:
isi:
- '000740815400007'
file:
- access_level: open_access
checksum: 1aa7c3478e0c8256b973b632efd1f6b4
content_type: application/pdf
creator: dernst
date_created: 2022-07-29T10:17:10Z
date_updated: 2022-07-29T10:17:10Z
file_id: '11697'
file_name: 2022_BiophysicalJour_Zisis.pdf
file_size: 4475504
relation: main_file
success: 1
file_date_updated: 2022-07-29T10:17:10Z
has_accepted_license: '1'
intvolume: ' 121'
isi: 1
issue: '1'
keyword:
- Biophysics
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: P44-60
project:
- _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A
name: NOMIS Fellowship Program
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Disentangling cadherin-mediated cell-cell interactions in collective cancer
cell migration
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 121
year: '2022'
...
---
_id: '10736'
abstract:
- lang: eng
text: Predicting function from sequence is a central problem of biology. Currently,
this is possible only locally in a narrow mutational neighborhood around a wildtype
sequence rather than globally from any sequence. Using random mutant libraries,
we developed a biophysical model that accounts for multiple features of σ70 binding
bacterial promoters to predict constitutive gene expression levels from any sequence.
We experimentally and theoretically estimated that 10–20% of random sequences
lead to expression and ~80% of non-expressing sequences are one mutation away
from a functional promoter. The potential for generating expression from random
sequences is so pervasive that selection acts against σ70-RNA polymerase binding
sites even within inter-genic, promoter-containing regions. This pervasiveness
of σ70-binding sites implies that emergence of promoters is not the limiting step
in gene regulatory evolution. Ultimately, the inclusion of novel features of promoter
function into a mechanistic model enabled not only more accurate predictions of
gene expression levels, but also identified that promoters evolve more rapidly
than previously thought.
acknowledgement: 'We thank Hande Acar, Nicholas H Barton, Rok Grah, Tiago Paixao,
Maros Pleska, Anna Staron, and Murat Tugrul for insightful comments and input on
the manuscript. This work was supported by: Sir Henry Dale Fellowship jointly funded
by the Wellcome Trust and the Royal Society (grant number 216779/Z/19/Z) to ML;
IPC Grant from IST Austria to ML and SS; European Research Council Funding Programme
7 (2007–2013, grant agreement number 648440) to JPB.'
article_number: e64543
article_processing_charge: No
article_type: original
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Srdjan
full_name: Sarikas, Srdjan
id: 35F0286E-F248-11E8-B48F-1D18A9856A87
last_name: Sarikas
- first_name: Magdalena
full_name: Steinrueck, Magdalena
last_name: Steinrueck
- first_name: David
full_name: Toledo-Aparicio, David
last_name: Toledo-Aparicio
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Lagator M, Sarikas S, Steinrueck M, et al. Predicting bacterial promoter function
and evolution from random sequences. eLife. 2022;11. doi:10.7554/eLife.64543
apa: Lagator, M., Sarikas, S., Steinrueck, M., Toledo-Aparicio, D., Bollback, J.
P., Guet, C. C., & Tkačik, G. (2022). Predicting bacterial promoter function
and evolution from random sequences. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.64543
chicago: Lagator, Mato, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio,
Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter
Function and Evolution from Random Sequences.” ELife. eLife Sciences Publications,
2022. https://doi.org/10.7554/eLife.64543.
ieee: M. Lagator et al., “Predicting bacterial promoter function and evolution
from random sequences,” eLife, vol. 11. eLife Sciences Publications, 2022.
ista: Lagator M, Sarikas S, Steinrueck M, Toledo-Aparicio D, Bollback JP, Guet CC,
Tkačik G. 2022. Predicting bacterial promoter function and evolution from random
sequences. eLife. 11, e64543.
mla: Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution
from Random Sequences.” ELife, vol. 11, e64543, eLife Sciences Publications,
2022, doi:10.7554/eLife.64543.
short: M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback,
C.C. Guet, G. Tkačik, ELife 11 (2022).
date_created: 2022-02-06T23:01:32Z
date_published: 2022-01-26T00:00:00Z
date_updated: 2023-08-02T14:09:02Z
day: '26'
ddc:
- '576'
department:
- _id: CaGu
- _id: GaTk
- _id: NiBa
doi: 10.7554/eLife.64543
ec_funded: 1
external_id:
isi:
- '000751104400001'
pmid:
- '35080492'
file:
- access_level: open_access
checksum: decdcdf600ff51e9a9703b49ca114170
content_type: application/pdf
creator: cchlebak
date_created: 2022-02-07T07:14:09Z
date_updated: 2022-02-07T07:14:09Z
file_id: '10739'
file_name: 2022_ELife_Lagator.pdf
file_size: 5604343
relation: main_file
success: 1
file_date_updated: 2022-02-07T07:14:09Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Predicting bacterial promoter function and evolution from random sequences
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2022'
...
---
_id: '12332'
abstract:
- lang: eng
text: Activity of sensory neurons is driven not only by external stimuli but also
by feedback signals from higher brain areas. Attention is one particularly important
internal signal whose presumed role is to modulate sensory representations such
that they only encode information currently relevant to the organism at minimal
cost. This hypothesis has, however, not yet been expressed in a normative computational
framework. Here, by building on normative principles of probabilistic inference
and efficient coding, we developed a model of dynamic population coding in the
visual cortex. By continuously adapting the sensory code to changing demands of
the perceptual observer, an attention-like modulation emerges. This modulation
can dramatically reduce the amount of neural activity without deteriorating the
accuracy of task-specific inferences. Our results suggest that a range of seemingly
disparate cortical phenomena such as intrinsic gain modulation, attention-related
tuning modulation, and response variability could be manifestations of the same
underlying principles, which combine efficient sensory coding with optimal probabilistic
inference in dynamic environments.
acknowledgement: "We thank Robbe Goris for generously providing figures from his work
and Ann M. Hermundstad for helpful discussions.\r\nGT & WM were supported by the
Austrian Science Fund Standalone Grant P 34015 \"Efficient Coding with Biophysical
Realism\" (https://pf.fwf.ac.at/) WM was additionally supported by the European
Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 754411 (https://ec.europa.eu/research/mariecurieactions/). The
funders had no role in study design, data collection and analysis, decision to publish,
or preparation of the manuscript."
article_processing_charge: No
article_type: original
author:
- first_name: Wiktor F
full_name: Mlynarski, Wiktor F
id: 358A453A-F248-11E8-B48F-1D18A9856A87
last_name: Mlynarski
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: '1'
citation:
ama: Mlynarski WF, Tkačik G. Efficient coding theory of dynamic attentional modulation.
PLoS Biology. 2022;20(12):e3001889. doi:10.1371/journal.pbio.3001889
apa: Mlynarski, W. F., & Tkačik, G. (2022). Efficient coding theory of dynamic
attentional modulation. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3001889
chicago: Mlynarski, Wiktor F, and Gašper Tkačik. “Efficient Coding Theory of Dynamic
Attentional Modulation.” PLoS Biology. Public Library of Science, 2022.
https://doi.org/10.1371/journal.pbio.3001889.
ieee: W. F. Mlynarski and G. Tkačik, “Efficient coding theory of dynamic attentional
modulation,” PLoS Biology, vol. 20, no. 12. Public Library of Science,
p. e3001889, 2022.
ista: Mlynarski WF, Tkačik G. 2022. Efficient coding theory of dynamic attentional
modulation. PLoS Biology. 20(12), e3001889.
mla: Mlynarski, Wiktor F., and Gašper Tkačik. “Efficient Coding Theory of Dynamic
Attentional Modulation.” PLoS Biology, vol. 20, no. 12, Public Library
of Science, 2022, p. e3001889, doi:10.1371/journal.pbio.3001889.
short: W.F. Mlynarski, G. Tkačik, PLoS Biology 20 (2022) e3001889.
date_created: 2023-01-22T23:00:55Z
date_published: 2022-12-21T00:00:00Z
date_updated: 2023-08-03T14:23:49Z
day: '21'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pbio.3001889
ec_funded: 1
external_id:
isi:
- '000925192000001'
file:
- access_level: open_access
checksum: 5d7f1111a87e5f2c1bf92f8886738894
content_type: application/pdf
creator: dernst
date_created: 2023-01-23T08:46:40Z
date_updated: 2023-01-23T08:46:40Z
file_id: '12337'
file_name: 2022_PloSBiology_Mlynarski.pdf
file_size: 4248838
relation: main_file
success: 1
file_date_updated: 2023-01-23T08:46:40Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: e3001889
project:
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: PLoS Biology
publication_identifier:
eissn:
- 1545-7885
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient coding theory of dynamic attentional modulation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 20
year: '2022'
...
---
_id: '12081'
abstract:
- lang: eng
text: 'Selection accumulates information in the genome—it guides stochastically
evolving populations toward states (genotype frequencies) that would be unlikely
under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence
between the actual distribution of genotype frequencies and the corresponding
neutral distribution. First, we show that this population-level information sets
an upper bound on the information at the level of genotype and phenotype, limiting
how precisely they can be specified by selection. Next, we study how the accumulation
and maintenance of information is limited by the cost of selection, measured as
the genetic load or the relative fitness variance, both of which we connect to
the control-theoretic KL cost of control. The information accumulation rate is
upper bounded by the population size times the cost of selection. This bound is
very general, and applies across models (Wright–Fisher, Moran, diffusion) and
to arbitrary forms of selection, mutation, and recombination. Finally, the cost
of maintaining information depends on how it is encoded: Specifying a single allele
out of two is expensive, but one bit encoded among many weakly specified loci
(as in a polygenic trait) is cheap.'
acknowledgement: We thank Ksenia Khudiakova, Wiktor Młynarski, Sean Stankowski, and
two anonymous reviewers for discussions and comments on the manuscript. G.T. and
M.H. acknowledge funding from the Human Frontier Science Program Grant RGP0032/2018.
N.B. acknowledges funding from ERC Grant 250152 “Information and Evolution.”
article_number: e2123152119
article_processing_charge: No
article_type: original
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: '1'
citation:
ama: Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information
in evolution. Proceedings of the National Academy of Sciences. 2022;119(36).
doi:10.1073/pnas.2123152119
apa: Hledik, M., Barton, N. H., & Tkačik, G. (2022). Accumulation and maintenance
of information in evolution. Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2123152119
chicago: Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and
Maintenance of Information in Evolution.” Proceedings of the National Academy
of Sciences. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2123152119.
ieee: M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information
in evolution,” Proceedings of the National Academy of Sciences, vol. 119,
no. 36. Proceedings of the National Academy of Sciences, 2022.
ista: Hledik M, Barton NH, Tkačik G. 2022. Accumulation and maintenance of information
in evolution. Proceedings of the National Academy of Sciences. 119(36), e2123152119.
mla: Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.”
Proceedings of the National Academy of Sciences, vol. 119, no. 36, e2123152119,
Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2123152119.
short: M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of
Sciences 119 (2022).
date_created: 2022-09-11T22:01:55Z
date_published: 2022-08-29T00:00:00Z
date_updated: 2024-03-06T14:22:51Z
day: '29'
ddc:
- '570'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1073/pnas.2123152119
ec_funded: 1
external_id:
isi:
- '000889278400014'
pmid:
- '36037343'
file:
- access_level: open_access
checksum: 6dec51f6567da9039982a571508a8e4d
content_type: application/pdf
creator: dernst
date_created: 2022-09-12T08:08:12Z
date_updated: 2022-09-12T08:08:12Z
file_id: '12091'
file_name: 2022_PNAS_Hledik.pdf
file_size: 2165752
relation: main_file
success: 1
file_date_updated: 2022-09-12T08:08:12Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '36'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 2665AAFE-B435-11E9-9278-68D0E5697425
grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '15020'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Accumulation and maintenance of information in evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 119
year: '2022'
...
---
_id: '10535'
abstract:
- lang: eng
text: Realistic models of biological processes typically involve interacting components
on multiple scales, driven by changing environment and inherent stochasticity.
Such models are often analytically and numerically intractable. We revisit a dynamic
maximum entropy method that combines a static maximum entropy with a quasi-stationary
approximation. This allows us to reduce stochastic non-equilibrium dynamics expressed
by the Fokker-Planck equation to a simpler low-dimensional deterministic dynamics,
without the need to track microscopic details. Although the method has been previously
applied to a few (rather complicated) applications in population genetics, our
main goal here is to explain and to better understand how the method works. We
demonstrate the usefulness of the method for two widely studied stochastic problems,
highlighting its accuracy in capturing important macroscopic quantities even in
rapidly changing non-stationary conditions. For the Ornstein-Uhlenbeck process,
the method recovers the exact dynamics whilst for a stochastic island model with
migration from other habitats, the approximation retains high macroscopic accuracy
under a wide range of scenarios in a dynamic environment.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "Computational resources for the study were provided by the Institute
of Science and Technology, Austria.\r\nKB received funding from the Scientific Grant
Agency of the Slovak Republic under the Grants Nos. 1/0755/19 and 1/0521/20."
article_number: e1009661
article_processing_charge: No
article_type: original
author:
- first_name: Katarína
full_name: Bod'ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'ová
orcid: 0000-0002-7214-0171
- first_name: Eniko
full_name: Szep, Eniko
id: 485BB5A4-F248-11E8-B48F-1D18A9856A87
last_name: Szep
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Bodova K, Szep E, Barton NH. Dynamic maximum entropy provides accurate approximation
of structured population dynamics. PLoS Computational Biology. 2021;17(12).
doi:10.1371/journal.pcbi.1009661
apa: Bodova, K., Szep, E., & Barton, N. H. (2021). Dynamic maximum entropy provides
accurate approximation of structured population dynamics. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009661
chicago: Bodova, Katarina, Eniko Szep, and Nicholas H Barton. “Dynamic Maximum Entropy
Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational
Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009661.
ieee: K. Bodova, E. Szep, and N. H. Barton, “Dynamic maximum entropy provides accurate
approximation of structured population dynamics,” PLoS Computational Biology,
vol. 17, no. 12. Public Library of Science, 2021.
ista: Bodova K, Szep E, Barton NH. 2021. Dynamic maximum entropy provides accurate
approximation of structured population dynamics. PLoS Computational Biology. 17(12),
e1009661.
mla: Bodova, Katarina, et al. “Dynamic Maximum Entropy Provides Accurate Approximation
of Structured Population Dynamics.” PLoS Computational Biology, vol. 17,
no. 12, e1009661, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009661.
short: K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).
date_created: 2021-12-12T23:01:27Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2022-08-01T10:48:04Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1371/journal.pcbi.1009661
external_id:
arxiv:
- '2102.03669'
pmid:
- '34851948'
file:
- access_level: open_access
checksum: dcd185d4f7e0acee25edf1d6537f447e
content_type: application/pdf
creator: dernst
date_created: 2022-05-16T08:53:11Z
date_updated: 2022-05-16T08:53:11Z
file_id: '11383'
file_name: 2021_PLOsComBio_Bodova.pdf
file_size: 2299486
relation: main_file
success: 1
file_date_updated: 2022-05-16T08:53:11Z
has_accepted_license: '1'
intvolume: ' 17'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
issn:
- 1553-734X
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic maximum entropy provides accurate approximation of structured population
dynamics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2021'
...
---
_id: '10912'
abstract:
- lang: eng
text: Brain dynamics display collective phenomena as diverse as neuronal oscillations
and avalanches. Oscillations are rhythmic, with fluctuations occurring at a characteristic
scale, whereas avalanches are scale-free cascades of neural activity. Here we
show that such antithetic features can coexist in a very generic class of adaptive
neural networks. In the most simple yet fully microscopic model from this class
we make direct contact with human brain resting-state activity recordings via
tractable inference of the model's two essential parameters. The inferred model
quantitatively captures the dynamics over a broad range of scales, from single
sensor fluctuations, collective behaviors of nearly-synchronous extreme events
on multiple sensors, to neuronal avalanches unfolding over multiple sensors across
multiple time-bins. Importantly, the inferred parameters correlate with model-independent
signatures of "closeness to criticality", suggesting that the coexistence of scale-specific
(neural oscillations) and scale-free (neuronal avalanches) dynamics in brain activity
occurs close to a non-equilibrium critical point at the onset of self-sustained
oscillations.
acknowledgement: "FL acknowledges support from the European Union’s Horizon 2020 research
and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411.
GT\r\nacknowledges the support of the Austrian Science Fund (FWF) under Stand-Alone
Grant\r\nNo. P34015."
article_processing_charge: No
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Selver
full_name: Pepic, Selver
id: F93245C4-C3CA-11E9-B4F0-C6F4E5697425
last_name: Pepic
- first_name: Oren
full_name: Shriki, Oren
last_name: Shriki
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Daniele
full_name: De Martino, Daniele
last_name: De Martino
citation:
ama: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Quantifying the coexistence
of neuronal oscillations and avalanches. doi:10.48550/ARXIV.2108.06686
apa: Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., & De Martino, D. (n.d.).
Quantifying the coexistence of neuronal oscillations and avalanches. arXiv. https://doi.org/10.48550/ARXIV.2108.06686
chicago: Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele
De Martino. “Quantifying the Coexistence of Neuronal Oscillations and Avalanches.”
arXiv, n.d. https://doi.org/10.48550/ARXIV.2108.06686.
ieee: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Quantifying
the coexistence of neuronal oscillations and avalanches.” arXiv.
ista: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Quantifying the coexistence
of neuronal oscillations and avalanches. 10.48550/ARXIV.2108.06686.
mla: Lombardi, Fabrizio, et al. Quantifying the Coexistence of Neuronal Oscillations
and Avalanches. arXiv, doi:10.48550/ARXIV.2108.06686.
short: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, (n.d.).
date_created: 2022-03-21T11:41:28Z
date_published: 2021-08-17T00:00:00Z
date_updated: 2022-03-22T07:53:18Z
day: '17'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.48550/ARXIV.2108.06686
ec_funded: 1
external_id:
arxiv:
- '2108.06686'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2108.06686
month: '08'
oa: 1
oa_version: Preprint
page: '37'
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
publication_status: submitted
publisher: arXiv
status: public
title: Quantifying the coexistence of neuronal oscillations and avalanches
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10579'
abstract:
- lang: eng
text: 'We consider a totally asymmetric simple exclusion process (TASEP) consisting
of particles on a lattice that require binding by a "token" to move. Using a combination
of theory and simulations, we address the following questions: (i) How token binding
kinetics affects the current-density relation; (ii) How the current-density relation
depends on the scarcity of tokens; (iii) How tokens propagate the effects of the
locally-imposed disorder (such a slow site) over the entire lattice; (iv) How
a shared pool of tokens couples concurrent TASEPs running on multiple lattices;
(v) How our results translate to TASEPs with open boundaries that exchange particles
with the reservoir. Since real particle motion (including in systems that inspired
the standard TASEP model, e.g., protein synthesis or movement of molecular motors)
is often catalyzed, regulated, actuated, or otherwise mediated, the token-driven
TASEP dynamics analyzed in this paper should allow for a better understanding
of real systems and enable a closer match between TASEP theory and experimental
observations.'
acknowledgement: B.K. thanks Stefano Elefante, Simon Rella, and Michal Hledík for
their help with the usage of the cluster. B.K. additionally thanks Călin Guet and
his group for help and advice. We thank M. Hennessey-Wesen for constructive comments
on the manuscript. We thank Ankita Gupta (Indian Institute of Technology) for spotting
a typographical error in Eq. (49) in the preprint version of this paper.
article_number: '2112.13558'
article_processing_charge: No
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Kavcic B, Tkačik G. Token-driven totally asymmetric simple exclusion process.
arXiv. doi:10.48550/arXiv.2112.13558
apa: Kavcic, B., & Tkačik, G. (n.d.). Token-driven totally asymmetric simple
exclusion process. arXiv. https://doi.org/10.48550/arXiv.2112.13558
chicago: Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple
Exclusion Process.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2112.13558.
ieee: B. Kavcic and G. Tkačik, “Token-driven totally asymmetric simple exclusion
process,” arXiv. .
ista: Kavcic B, Tkačik G. Token-driven totally asymmetric simple exclusion process.
arXiv, 2112.13558.
mla: Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion
Process.” ArXiv, 2112.13558, doi:10.48550/arXiv.2112.13558.
short: B. Kavcic, G. Tkačik, ArXiv (n.d.).
date_created: 2021-12-28T06:52:09Z
date_published: 2021-12-27T00:00:00Z
date_updated: 2023-05-03T10:54:05Z
day: '27'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.48550/arXiv.2112.13558
external_id:
arxiv:
- '2112.13558'
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2112.13558
month: '12'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Token-driven totally asymmetric simple exclusion process
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '7463'
abstract:
- lang: eng
text: Resting-state brain activity is characterized by the presence of neuronal
avalanches showing absence of characteristic size. Such evidence has been interpreted
in the context of criticality and associated with the normal functioning of the
brain. A distinctive attribute of systems at criticality is the presence of long-range
correlations. Thus, to verify the hypothesis that the brain operates close to
a critical point and consequently assess deviations from criticality for diagnostic
purposes, it is of primary importance to robustly and reliably characterize correlations
in resting-state brain activity. Recent works focused on the analysis of narrow-band
electroencephalography (EEG) and magnetoencephalography (MEG) signal amplitude
envelope, showing evidence of long-range temporal correlations (LRTC) in neural
oscillations. However, brain activity is a broadband phenomenon, and a significant
piece of information useful to precisely discriminate between normal (critical)
and pathological behavior (non-critical), may be encoded in the broadband spatio-temporal
cortical dynamics. Here we propose to characterize the temporal correlations in
the broadband brain activity through the lens of neuronal avalanches. To this
end, we consider resting-state EEG and long-term MEG recordings, extract the corresponding
neuronal avalanche sequences, and study their temporal correlations. We demonstrate
that the broadband resting-state brain activity consistently exhibits long-range
power-law correlations in both EEG and MEG recordings, with similar values of
the scaling exponents. Importantly, although we observe that the avalanche size
distribution depends on scale parameters, scaling exponents characterizing long-range
correlations are quite robust. In particular, they are independent of the temporal
binning (scale of analysis), indicating that our analysis captures intrinsic characteristics
of the underlying dynamics. Because neuronal avalanches constitute a fundamental
feature of neural systems with universal characteristics, the proposed approach
may serve as a general, systems- and experiment-independent procedure to infer
the existence of underlying long-range correlations in extended neural systems,
and identify pathological behaviors in the complex spatio-temporal interplay of
cortical rhythms.
acknowledgement: LdA would like to acknowledge the financial support from MIUR-PRIN2017
WZFTZP and VALERE:VAnviteLli pEr la RicErca 2019. FL acknowledges support from the
European Union’s Horizon 2020 research and innovation programme under the Marie
Sklodowska-Curie Grant Agreement No. 754411. HJH would like to thank the Agencies
CAPES and FUNCAP for financial support.
article_processing_charge: No
article_type: original
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Oren
full_name: Shriki, Oren
last_name: Shriki
- first_name: Hans J
full_name: Herrmann, Hans J
last_name: Herrmann
- first_name: Lucilla
full_name: de Arcangelis, Lucilla
last_name: de Arcangelis
citation:
ama: Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. Long-range temporal correlations
in the broadband resting state activity of the human brain revealed by neuronal
avalanches. Neurocomputing. 2021;461:657-666. doi:10.1016/j.neucom.2020.05.126
apa: Lombardi, F., Shriki, O., Herrmann, H. J., & de Arcangelis, L. (2021).
Long-range temporal correlations in the broadband resting state activity of the
human brain revealed by neuronal avalanches. Neurocomputing. Elsevier.
https://doi.org/10.1016/j.neucom.2020.05.126
chicago: Lombardi, Fabrizio, Oren Shriki, Hans J Herrmann, and Lucilla de Arcangelis.
“Long-Range Temporal Correlations in the Broadband Resting State Activity of the
Human Brain Revealed by Neuronal Avalanches.” Neurocomputing. Elsevier,
2021. https://doi.org/10.1016/j.neucom.2020.05.126.
ieee: F. Lombardi, O. Shriki, H. J. Herrmann, and L. de Arcangelis, “Long-range
temporal correlations in the broadband resting state activity of the human brain
revealed by neuronal avalanches,” Neurocomputing, vol. 461. Elsevier, pp.
657–666, 2021.
ista: Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. 2021. Long-range temporal
correlations in the broadband resting state activity of the human brain revealed
by neuronal avalanches. Neurocomputing. 461, 657–666.
mla: Lombardi, Fabrizio, et al. “Long-Range Temporal Correlations in the Broadband
Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” Neurocomputing,
vol. 461, Elsevier, 2021, pp. 657–66, doi:10.1016/j.neucom.2020.05.126.
short: F. Lombardi, O. Shriki, H.J. Herrmann, L. de Arcangelis, Neurocomputing 461
(2021) 657–666.
date_created: 2020-02-06T16:09:14Z
date_published: 2021-05-13T00:00:00Z
date_updated: 2023-08-04T10:46:29Z
day: '13'
department:
- _id: GaTk
doi: 10.1016/j.neucom.2020.05.126
ec_funded: 1
external_id:
isi:
- '000704086300015'
intvolume: ' 461'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.02.03.930966
month: '05'
oa: 1
oa_version: Preprint
page: 657-666
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Neurocomputing
publication_identifier:
eissn:
- 1872-8286
issn:
- 0925-2312
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long-range temporal correlations in the broadband resting state activity of
the human brain revealed by neuronal avalanches
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 461
year: '2021'
...
---
_id: '9226'
abstract:
- lang: eng
text: 'Half a century after Lewis Wolpert''s seminal conceptual advance on how cellular
fates distribute in space, we provide a brief historical perspective on how the
concept of positional information emerged and influenced the field of developmental
biology and beyond. We focus on a modern interpretation of this concept in terms
of information theory, largely centered on its application to cell specification
in the early Drosophila embryo. We argue that a true physical variable (position)
is encoded in local concentrations of patterning molecules, that this mapping
is stochastic, and that the processes by which positions and corresponding cell
fates are determined based on these concentrations need to take such stochasticity
into account. With this approach, we shift the focus from biological mechanisms,
molecules, genes and pathways to quantitative systems-level questions: where does
positional information reside, how it is transformed and accessed during development,
and what fundamental limits it is subject to?'
acknowledgement: This work was supported in part by the National Science Foundation,
through the Center for the Physics of Biological Function (PHY-1734030), by the
National Institutes of Health (R01GM097275) and by the Fonds zur Förderung der wissenschaftlichen
Forschung (FWF P28844). Deposited in PMC for release after 12 months.
article_number: dev176065
article_processing_charge: No
article_type: original
author:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
citation:
ama: Tkačik G, Gregor T. The many bits of positional information. Development.
2021;148(2). doi:10.1242/dev.176065
apa: Tkačik, G., & Gregor, T. (2021). The many bits of positional information.
Development. The Company of Biologists. https://doi.org/10.1242/dev.176065
chicago: Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.”
Development. The Company of Biologists, 2021. https://doi.org/10.1242/dev.176065.
ieee: G. Tkačik and T. Gregor, “The many bits of positional information,” Development,
vol. 148, no. 2. The Company of Biologists, 2021.
ista: Tkačik G, Gregor T. 2021. The many bits of positional information. Development.
148(2), dev176065.
mla: Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.”
Development, vol. 148, no. 2, dev176065, The Company of Biologists, 2021,
doi:10.1242/dev.176065.
short: G. Tkačik, T. Gregor, Development 148 (2021).
date_created: 2021-03-07T23:01:25Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2023-08-07T13:57:30Z
day: '01'
department:
- _id: GaTk
doi: 10.1242/dev.176065
external_id:
isi:
- '000613906000007'
pmid:
- '33526425'
intvolume: ' 148'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1242/dev.176065
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Development
publication_identifier:
eissn:
- 1477-9129
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: The many bits of positional information
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 148
year: '2021'
...
---
_id: '9439'
abstract:
- lang: eng
text: The ability to adapt to changes in stimulus statistics is a hallmark of sensory
systems. Here, we developed a theoretical framework that can account for the dynamics
of adaptation from an information processing perspective. We use this framework
to optimize and analyze adaptive sensory codes, and we show that codes optimized
for stationary environments can suffer from prolonged periods of poor performance
when the environment changes. To mitigate the adversarial effects of these environmental
changes, sensory systems must navigate tradeoffs between the ability to accurately
encode incoming stimuli and the ability to rapidly detect and adapt to changes
in the distribution of these stimuli. We derive families of codes that balance
these objectives, and we demonstrate their close match to experimentally observed
neural dynamics during mean and variance adaptation. Our results provide a unifying
perspective on adaptation across a range of sensory systems, environments, and
sensory tasks.
acknowledgement: We thank D. Kastner and T. Münch for generously providing figures
from their work. We also thank V. Jayaraman, M. Noorman, T. Ma, and K. Krishnamurthy
for useful discussions and feedback on the manuscript. W.F.M. was funded by the
European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie
Grant Agreement No. 754411. A.M.H. was supported by the Howard Hughes Medical Institute.
article_processing_charge: No
article_type: original
author:
- first_name: Wiktor F
full_name: Mlynarski, Wiktor F
id: 358A453A-F248-11E8-B48F-1D18A9856A87
last_name: Mlynarski
- first_name: Ann M.
full_name: Hermundstad, Ann M.
last_name: Hermundstad
citation:
ama: Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. Nature
Neuroscience. 2021;24:998-1009. doi:10.1038/s41593-021-00846-0
apa: Mlynarski, W. F., & Hermundstad, A. M. (2021). Efficient and adaptive sensory
codes. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-021-00846-0
chicago: Mlynarski, Wiktor F, and Ann M. Hermundstad. “Efficient and Adaptive Sensory
Codes.” Nature Neuroscience. Springer Nature, 2021. https://doi.org/10.1038/s41593-021-00846-0.
ieee: W. F. Mlynarski and A. M. Hermundstad, “Efficient and adaptive sensory codes,”
Nature Neuroscience, vol. 24. Springer Nature, pp. 998–1009, 2021.
ista: Mlynarski WF, Hermundstad AM. 2021. Efficient and adaptive sensory codes.
Nature Neuroscience. 24, 998–1009.
mla: Mlynarski, Wiktor F., and Ann M. Hermundstad. “Efficient and Adaptive Sensory
Codes.” Nature Neuroscience, vol. 24, Springer Nature, 2021, pp. 998–1009,
doi:10.1038/s41593-021-00846-0.
short: W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009.
date_created: 2021-05-30T22:01:24Z
date_published: 2021-05-20T00:00:00Z
date_updated: 2023-08-08T13:51:14Z
day: '20'
department:
- _id: GaTk
doi: 10.1038/s41593-021-00846-0
ec_funded: 1
external_id:
isi:
- '000652577300003'
intvolume: ' 24'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/669200 '
month: '05'
oa: 1
oa_version: Preprint
page: 998-1009
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature Neuroscience
publication_identifier:
eissn:
- 1546-1726
issn:
- 1097-6256
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient and adaptive sensory codes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 24
year: '2021'
...
---
_id: '9822'
abstract:
- lang: eng
text: Attachment of adhesive molecules on cell culture surfaces to restrict cell
adhesion to defined areas and shapes has been vital for the progress of in vitro
research. In currently existing patterning methods, a combination of pattern properties
such as stability, precision, specificity, high-throughput outcome, and spatiotemporal
control is highly desirable but challenging to achieve. Here, we introduce a versatile
and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent
patterning step and a subsequent functionalization of the pattern via click chemistry.
This two-step process is feasible on arbitrary surfaces and allows for generation
of sustainable patterns and gradients. The method is validated in different biological
systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining
the growth and migration of cells to the designated areas. We then implement a
sequential photopatterning approach by adding a second switchable patterning step,
allowing for spatiotemporal control over two distinct surface patterns. As a proof
of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis.
Our results show that the spatiotemporal control provided by our “sequential photopatterning”
system is essential for mimicking dynamic biological processes and that our innovative
approach has great potential for further applications in cell science.
acknowledgement: We would like to thank Charlott Leu for the production of our chromium
wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh
Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim
Rädler for his valuable scientific guidance.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Themistoklis
full_name: Zisis, Themistoklis
last_name: Zisis
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Miriam
full_name: Balles, Miriam
last_name: Balles
- first_name: Maibritt
full_name: Kretschmer, Maibritt
last_name: Kretschmer
- first_name: Maria
full_name: Nemethova, Maria
id: 34E27F1C-F248-11E8-B48F-1D18A9856A87
last_name: Nemethova
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Janina
full_name: Lange, Janina
last_name: Lange
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-4561-241X
- first_name: Stefan
full_name: Zahler, Stefan
last_name: Zahler
citation:
ama: Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for
studying cellular processes under spatiotemporal control. ACS Applied Materials
and Interfaces. 2021;13(30):35545–35560. doi:10.1021/acsami.1c09850
apa: Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R.
P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular
processes under spatiotemporal control. ACS Applied Materials and Interfaces.
American Chemical Society. https://doi.org/10.1021/acsami.1c09850
chicago: Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria
Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning
for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied
Materials and Interfaces. American Chemical Society, 2021. https://doi.org/10.1021/acsami.1c09850.
ieee: T. Zisis et al., “Sequential and switchable patterning for studying
cellular processes under spatiotemporal control,” ACS Applied Materials and
Interfaces, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021.
ista: Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild
R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning
for studying cellular processes under spatiotemporal control. ACS Applied Materials
and Interfaces. 13(30), 35545–35560.
mla: Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying
Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and
Interfaces, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560,
doi:10.1021/acsami.1c09850.
short: T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait,
R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials
and Interfaces 13 (2021) 35545–35560.
date_created: 2021-08-08T22:01:28Z
date_published: 2021-08-04T00:00:00Z
date_updated: 2023-08-10T14:22:48Z
day: '04'
ddc:
- '620'
- '570'
department:
- _id: MiSi
- _id: GaTk
- _id: Bio
- _id: CaGu
doi: 10.1021/acsami.1c09850
ec_funded: 1
external_id:
isi:
- '000683741400026'
pmid:
- '34283577'
file:
- access_level: open_access
checksum: b043a91d9f9200e467b970b692687ed3
content_type: application/pdf
creator: asandaue
date_created: 2021-08-09T09:44:03Z
date_updated: 2021-08-09T09:44:03Z
file_id: '9833'
file_name: 2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf
file_size: 7123293
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intvolume: ' 13'
isi: 1
issue: '30'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 35545–35560
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
publication: ACS Applied Materials and Interfaces
publication_identifier:
eissn:
- '19448252'
issn:
- '19448244'
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sequential and switchable patterning for studying cellular processes under
spatiotemporal control
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2021'
...
---
_id: '9828'
abstract:
- lang: eng
text: Amplitude demodulation is a classical operation used in signal processing.
For a long time, its effective applications in practice have been limited to narrowband
signals. In this work, we generalize amplitude demodulation to wideband signals.
We pose demodulation as a recovery problem of an oversampled corrupted signal
and introduce special iterative schemes belonging to the family of alternating
projection algorithms to solve it. Sensibly chosen structural assumptions on the
demodulation outputs allow us to reveal the high inferential accuracy of the method
over a rich set of relevant signals. This new approach surpasses current state-of-the-art
demodulation techniques apt to wideband signals in computational efficiency by
up to many orders of magnitude with no sacrifice in quality. Such performance
opens the door for applications of the amplitude demodulation procedure in new
contexts. In particular, the new method makes online and large-scale offline data
processing feasible, including the calculation of modulator-carrier pairs in higher
dimensions and poor sampling conditions, independent of the signal bandwidth.
We illustrate the utility and specifics of applications of the new method in practice
by using natural speech and synthetic signals.
acknowledgement: The author thanks his colleagues K. Huszár and G. Tkačik for valuable
discussions and comments on the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Mantas
full_name: Gabrielaitis, Mantas
id: 4D5B0CBC-F248-11E8-B48F-1D18A9856A87
last_name: Gabrielaitis
orcid: 0000-0002-7758-2016
citation:
ama: Gabrielaitis M. Fast and accurate amplitude demodulation of wideband signals.
IEEE Transactions on Signal Processing. 2021;69:4039-4054. doi:10.1109/TSP.2021.3087899
apa: Gabrielaitis, M. (2021). Fast and accurate amplitude demodulation of wideband
signals. IEEE Transactions on Signal Processing. Institute of Electrical
and Electronics Engineers. https://doi.org/10.1109/TSP.2021.3087899
chicago: Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband
Signals.” IEEE Transactions on Signal Processing. Institute of Electrical
and Electronics Engineers, 2021. https://doi.org/10.1109/TSP.2021.3087899.
ieee: M. Gabrielaitis, “Fast and accurate amplitude demodulation of wideband signals,”
IEEE Transactions on Signal Processing, vol. 69. Institute of Electrical
and Electronics Engineers, pp. 4039–4054, 2021.
ista: Gabrielaitis M. 2021. Fast and accurate amplitude demodulation of wideband
signals. IEEE Transactions on Signal Processing. 69, 4039–4054.
mla: Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband
Signals.” IEEE Transactions on Signal Processing, vol. 69, Institute of
Electrical and Electronics Engineers, 2021, pp. 4039–54, doi:10.1109/TSP.2021.3087899.
short: M. Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 4039–4054.
date_created: 2021-08-08T22:01:31Z
date_published: 2021-06-09T00:00:00Z
date_updated: 2023-08-10T14:19:33Z
day: '09'
department:
- _id: GaTk
doi: 10.1109/TSP.2021.3087899
external_id:
arxiv:
- '2102.04832'
isi:
- '000682123900002'
intvolume: ' 69'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2102.04832
month: '06'
oa: 1
oa_version: Preprint
page: 4039 - 4054
publication: IEEE Transactions on Signal Processing
publication_identifier:
eissn:
- 1941-0476
issn:
- 1053-587X
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast and accurate amplitude demodulation of wideband signals
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 69
year: '2021'
...
---
_id: '9362'
abstract:
- lang: eng
text: A central goal in systems neuroscience is to understand the functions performed
by neural circuits. Previous top-down models addressed this question by comparing
the behaviour of an ideal model circuit, optimised to perform a given function,
with neural recordings. However, this requires guessing in advance what function
is being performed, which may not be possible for many neural systems. To address
this, we propose an inverse reinforcement learning (RL) framework for inferring
the function performed by a neural network from data. We assume that the responses
of each neuron in a network are optimised so as to drive the network towards ‘rewarded’
states, that are desirable for performing a given function. We then show how one
can use inverse RL to infer the reward function optimised by the network from
observing its responses. This inferred reward function can be used to predict
how the neural network should adapt its dynamics to perform the same function
when the external environment or network structure changes. This could lead to
theoretical predictions about how neural network dynamics adapt to deal with cell
death and/or varying sensory stimulus statistics.
acknowledgement: The authors would like to thank Ulisse Ferrari for useful discussions
and feedback.
article_number: e0248940
article_processing_charge: No
article_type: original
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
citation:
ama: Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent
neural network. PLoS ONE. 2021;16(4). doi:10.1371/journal.pone.0248940
apa: Chalk, M. J., Tkačik, G., & Marre, O. (2021). Inferring the function performed
by a recurrent neural network. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0248940
chicago: Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function
Performed by a Recurrent Neural Network.” PLoS ONE. Public Library of Science,
2021. https://doi.org/10.1371/journal.pone.0248940.
ieee: M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by
a recurrent neural network,” PLoS ONE, vol. 16, no. 4. Public Library of
Science, 2021.
ista: Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent
neural network. PLoS ONE. 16(4), e0248940.
mla: Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent
Neural Network.” PLoS ONE, vol. 16, no. 4, e0248940, Public Library of
Science, 2021, doi:10.1371/journal.pone.0248940.
short: M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).
date_created: 2021-05-02T22:01:28Z
date_published: 2021-04-15T00:00:00Z
date_updated: 2023-10-18T08:17:42Z
day: '15'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0248940
external_id:
isi:
- '000641474900072'
pmid:
- '33857170'
file:
- access_level: open_access
checksum: c52da133850307d2031f552d998f00e8
content_type: application/pdf
creator: kschuh
date_created: 2021-05-04T13:22:19Z
date_updated: 2021-05-04T13:22:19Z
file_id: '9371'
file_name: 2021_pone_Chalk.pdf
file_size: 2768282
relation: main_file
success: 1
file_date_updated: 2021-05-04T13:22:19Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS ONE
publication_identifier:
eissn:
- '19326203'
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inferring the function performed by a recurrent neural network
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2021'
...
---
_id: '8997'
abstract:
- lang: eng
text: Phenomenological relations such as Ohm’s or Fourier’s law have a venerable
history in physics but are still scarce in biology. This situation restrains predictive
theory. Here, we build on bacterial “growth laws,” which capture physiological
feedback between translation and cell growth, to construct a minimal biophysical
model for the combined action of ribosome-targeting antibiotics. Our model predicts
drug interactions like antagonism or synergy solely from responses to individual
drugs. We provide analytical results for limiting cases, which agree well with
numerical results. We systematically refine the model by including direct physical
interactions of different antibiotics on the ribosome. In a limiting case, our
model provides a mechanistic underpinning for recent predictions of higher-order
interactions that were derived using entropy maximization. We further refine the
model to include the effects of antibiotics that mimic starvation and the presence
of resistance genes. We describe the impact of a starvation-mimicking antibiotic
on drug interactions analytically and verify it experimentally. Our extended model
suggests a change in the type of drug interaction that depends on the strength
of resistance, which challenges established rescaling paradigms. We experimentally
show that the presence of unregulated resistance genes can lead to altered drug
interaction, which agrees with the prediction of the model. While minimal, the
model is readily adaptable and opens the door to predicting interactions of second
and higher-order in a broad range of biological systems.
acknowledgement: 'This work was supported in part by Tum stipend of Knafelj foundation
(to B.K.), Austrian Science Fund (FWF) standalone grants P 27201-B22 (to T.B.) and
P 28844(to G.T.), HFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation
(DFG) individual grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG)
Collaborative Research Centre (SFB) 1310 (to T.B.). '
article_number: e1008529
article_processing_charge: Yes
article_type: original
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic
action. PLOS Computational Biology. 2021;17. doi:10.1371/journal.pcbi.1008529
apa: Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2021). Minimal biophysical
model of combined antibiotic action. PLOS Computational Biology. Public
Library of Science. https://doi.org/10.1371/journal.pcbi.1008529
chicago: Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical
Model of Combined Antibiotic Action.” PLOS Computational Biology. Public
Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008529.
ieee: B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of
combined antibiotic action,” PLOS Computational Biology, vol. 17. Public
Library of Science, 2021.
ista: Kavcic B, Tkačik G, Bollenbach MT. 2021. Minimal biophysical model of combined
antibiotic action. PLOS Computational Biology. 17, e1008529.
mla: Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.”
PLOS Computational Biology, vol. 17, e1008529, Public Library of Science,
2021, doi:10.1371/journal.pcbi.1008529.
short: B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).
date_created: 2021-01-08T07:16:18Z
date_published: 2021-01-07T00:00:00Z
date_updated: 2024-02-21T12:41:41Z
day: '07'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1008529
external_id:
isi:
- '000608045000010'
file:
- access_level: open_access
checksum: e29f2b42651bef8e034781de8781ffac
content_type: application/pdf
creator: dernst
date_created: 2021-02-04T12:30:48Z
date_updated: 2021-02-04T12:30:48Z
file_id: '9092'
file_name: 2021_PlosComBio_Kavcic.pdf
file_size: 3690053
relation: main_file
success: 1
file_date_updated: 2021-02-04T12:30:48Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
keyword:
- Modelling and Simulation
- Genetics
- Molecular Biology
- Antibiotics
- Drug interactions
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: PLOS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
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relation: earlier_version
status: public
- id: '8930'
relation: research_data
status: public
status: public
title: Minimal biophysical model of combined antibiotic action
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2021'
...
---
_id: '9283'
abstract:
- lang: eng
text: Gene expression levels are influenced by multiple coexisting molecular mechanisms.
Some of these interactions such as those of transcription factors and promoters
have been studied extensively. However, predicting phenotypes of gene regulatory
networks (GRNs) remains a major challenge. Here, we use a well-defined synthetic
GRN to study in Escherichia coli how network phenotypes depend on local genetic
context, i.e. the genetic neighborhood of a transcription factor and its relative
position. We show that one GRN with fixed topology can display not only quantitatively
but also qualitatively different phenotypes, depending solely on the local genetic
context of its components. Transcriptional read-through is the main molecular
mechanism that places one transcriptional unit (TU) within two separate regulons
without the need for complex regulatory sequences. We propose that relative order
of individual TUs, with its potential for combinatorial complexity, plays an important
role in shaping phenotypes of GRNs.
acknowledgement: "We thank J Bollback, L Hurst, M Lagator, C Nizak, O Rivoire, M Savageau,
G Tkacik, and B Vicozo\r\nfor helpful discussions; A Dolinar and A Greshnova for
technical assistance; T Bollenbach for supplying the strain JW0336; C Rusnac, and
members of the Guet lab for comments. The research leading to these results has
received funding from the People Programme (Marie Curie Actions) of the European
Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n˚\r\n628377
(ANS) and an Austrian Science Fund (FWF) grant n˚ I 3901-B32 (CCG)."
article_number: e65993
article_processing_charge: Yes
article_type: original
author:
- first_name: Anna A
full_name: Nagy-Staron, Anna A
id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87
last_name: Nagy-Staron
orcid: 0000-0002-1391-8377
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
- first_name: Caroline
full_name: Caruso Carter, Caroline
last_name: Caruso Carter
- first_name: Elisabeth
full_name: Sonnleitner, Elisabeth
last_name: Sonnleitner
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Tiago
full_name: Paixão, Tiago
last_name: Paixão
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Nagy-Staron AA, Tomasek K, Caruso Carter C, et al. Local genetic context shapes
the function of a gene regulatory network. eLife. 2021;10. doi:10.7554/elife.65993
apa: Nagy-Staron, A. A., Tomasek, K., Caruso Carter, C., Sonnleitner, E., Kavcic,
B., Paixão, T., & Guet, C. C. (2021). Local genetic context shapes the function
of a gene regulatory network. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.65993
chicago: Nagy-Staron, Anna A, Kathrin Tomasek, Caroline Caruso Carter, Elisabeth
Sonnleitner, Bor Kavcic, Tiago Paixão, and Calin C Guet. “Local Genetic Context
Shapes the Function of a Gene Regulatory Network.” ELife. eLife Sciences
Publications, 2021. https://doi.org/10.7554/elife.65993.
ieee: A. A. Nagy-Staron et al., “Local genetic context shapes the function
of a gene regulatory network,” eLife, vol. 10. eLife Sciences Publications,
2021.
ista: Nagy-Staron AA, Tomasek K, Caruso Carter C, Sonnleitner E, Kavcic B, Paixão
T, Guet CC. 2021. Local genetic context shapes the function of a gene regulatory
network. eLife. 10, e65993.
mla: Nagy-Staron, Anna A., et al. “Local Genetic Context Shapes the Function of
a Gene Regulatory Network.” ELife, vol. 10, e65993, eLife Sciences Publications,
2021, doi:10.7554/elife.65993.
short: A.A. Nagy-Staron, K. Tomasek, C. Caruso Carter, E. Sonnleitner, B. Kavcic,
T. Paixão, C.C. Guet, ELife 10 (2021).
date_created: 2021-03-23T10:11:46Z
date_published: 2021-03-08T00:00:00Z
date_updated: 2024-02-21T12:41:57Z
day: '08'
ddc:
- '570'
department:
- _id: GaTk
- _id: CaGu
doi: 10.7554/elife.65993
ec_funded: 1
external_id:
isi:
- '000631050900001'
file:
- access_level: open_access
checksum: 3c2f44058c2dd45a5a1027f09d263f8e
content_type: application/pdf
creator: bkavcic
date_created: 2021-03-23T10:12:58Z
date_updated: 2021-03-23T10:12:58Z
file_id: '9284'
file_name: elife-65993-v2.pdf
file_size: 1390469
relation: main_file
success: 1
file_date_updated: 2021-03-23T10:12:58Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
keyword:
- Genetics and Molecular Biology
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 2517526A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '628377'
name: 'The Systems Biology of Transcriptional Read-Through in Bacteria: from Synthetic
Networks to Genomic Studies'
- _id: 268BFA92-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03901
name: 'CyberCircuits: Cybergenetic circuits to test composability of gene networks'
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
record:
- id: '8951'
relation: research_data
status: public
status: public
title: Local genetic context shapes the function of a gene regulatory network
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '7553'
abstract:
- lang: eng
text: Normative theories and statistical inference provide complementary approaches
for the study of biological systems. A normative theory postulates that organisms
have adapted to efficiently solve essential tasks, and proceeds to mathematically
work out testable consequences of such optimality; parameters that maximize the
hypothesized organismal function can be derived ab initio, without reference to
experimental data. In contrast, statistical inference focuses on efficient utilization
of data to learn model parameters, without reference to any a priori notion of
biological function, utility, or fitness. Traditionally, these two approaches
were developed independently and applied separately. Here we unify them in a coherent
Bayesian framework that embeds a normative theory into a family of maximum-entropy
“optimization priors.” This family defines a smooth interpolation between a data-rich
inference regime (characteristic of “bottom-up” statistical models), and a data-limited
ab inito prediction regime (characteristic of “top-down” normative theory). We
demonstrate the applicability of our framework using data from the visual cortex,
and argue that the flexibility it affords is essential to address a number of
fundamental challenges relating to inference and prediction in complex, high-dimensional
biological problems.
acknowledgement: The authors thank Dario Ringach for providing the V1 receptive fields
and Olivier Marre for providing the retinal receptive fields. W.M. was funded by
the European Union’s Horizon 2020 research and innovation programme under the Marie
Skłodowska-Curie grant agreement no. 754411. M.H. was funded in part by Human Frontiers
Science grant no. HFSP RGP0032/2018.
article_processing_charge: No
author:
- first_name: Wiktor F
full_name: Mlynarski, Wiktor F
id: 358A453A-F248-11E8-B48F-1D18A9856A87
last_name: Mlynarski
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality
of neural systems. Neuron. 2021;109(7):1227-1241.e5. doi:10.1016/j.neuron.2021.01.020
apa: Mlynarski, W. F., Hledik, M., Sokolowski, T. R., & Tkačik, G. (2021). Statistical
analysis and optimality of neural systems. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2021.01.020
chicago: Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik.
“Statistical Analysis and Optimality of Neural Systems.” Neuron. Cell Press,
2021. https://doi.org/10.1016/j.neuron.2021.01.020.
ieee: W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical
analysis and optimality of neural systems,” Neuron, vol. 109, no. 7. Cell
Press, p. 1227–1241.e5, 2021.
ista: Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. 2021. Statistical analysis
and optimality of neural systems. Neuron. 109(7), 1227–1241.e5.
mla: Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural
Systems.” Neuron, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:10.1016/j.neuron.2021.01.020.
short: W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021)
1227–1241.e5.
date_created: 2020-02-28T11:00:12Z
date_published: 2021-04-07T00:00:00Z
date_updated: 2024-03-06T14:22:51Z
day: '07'
department:
- _id: GaTk
doi: 10.1016/j.neuron.2021.01.020
ec_funded: 1
external_id:
isi:
- '000637809600006'
intvolume: ' 109'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/848374
month: '04'
oa: 1
oa_version: Preprint
page: 1227-1241.e5
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Neuron
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/can-evolution-be-predicted/
record:
- id: '15020'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Statistical analysis and optimality of neural systems
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 109
year: '2021'
...
---
_id: '10077'
abstract:
- lang: eng
text: Although much is known about how single neurons in the hippocampus represent
an animal’s position, how cell-cell interactions contribute to spatial coding
remains poorly understood. Using a novel statistical estimator and theoretical
modeling, both developed in the framework of maximum entropy models, we reveal
highly structured cell-to-cell interactions whose statistics depend on familiar
vs. novel environment. In both conditions the circuit interactions optimize the
encoding of spatial information, but for regimes that differ in the signal-to-noise
ratio of their spatial inputs. Moreover, the topology of the interactions facilitates
linear decodability, making the information easy to read out by downstream circuits.
These findings suggest that the efficient coding hypothesis is not applicable
only to individual neuron properties in the sensory periphery, but also to neural
interactions in the central brain.
acknowledgement: We thank Peter Baracskay, Karola Kaefer and Hugo Malagon-Vina for
the acquisition of the data. We thank Federico Stella for comments on an earlier
version of the manuscript. MN was supported by European Union Horizon 2020 grant
665385, JC was supported by European Research Council consolidator grant 281511,
GT was supported by the Austrian Science Fund (FWF) grant P34015, CS was supported
by an IST fellow grant, National Institute of Mental Health Award 1R01MH125571-01,
by the National Science Foundation under NSF Award No. 1922658 and a Google faculty
award.
article_processing_charge: No
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
citation:
ama: Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1
interactions optimizes spatial coding across experience. bioRxiv. doi:10.1101/2021.09.28.460602
apa: Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (n.d.). The structure
of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv.
Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.09.28.460602
chicago: Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin.
“The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across
Experience.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.09.28.460602.
ieee: M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal
CA1 interactions optimizes spatial coding across experience,” bioRxiv.
Cold Spring Harbor Laboratory.
ista: Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1
interactions optimizes spatial coding across experience. bioRxiv, 10.1101/2021.09.28.460602.
mla: Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes
Spatial Coding across Experience.” BioRxiv, Cold Spring Harbor Laboratory,
doi:10.1101/2021.09.28.460602.
short: M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.).
date_created: 2021-10-04T06:23:34Z
date_published: 2021-09-29T00:00:00Z
date_updated: 2024-03-28T23:30:16Z
day: '29'
department:
- _id: GradSch
- _id: JoCs
- _id: GaTk
doi: 10.1101/2021.09.28.460602
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2021.09.28.460602
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
publication: bioRxiv
publication_status: submitted
publisher: Cold Spring Harbor Laboratory
related_material:
record:
- id: '11932'
relation: dissertation_contains
status: public
status: public
title: The structure of hippocampal CA1 interactions optimizes spatial coding across
experience
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '8105'
abstract:
- lang: eng
text: Physical and biological systems often exhibit intermittent dynamics with bursts
or avalanches (active states) characterized by power-law size and duration distributions.
These emergent features are typical of systems at the critical point of continuous
phase transitions, and have led to the hypothesis that such systems may self-organize
at criticality, i.e. without any fine tuning of parameters. Since the introduction
of the Bak-Tang-Wiesenfeld (BTW) model, the paradigm of self-organized criticality
(SOC) has been very fruitful for the analysis of emergent collective behaviors
in a number of systems, including the brain. Although considerable effort has
been devoted in identifying and modeling scaling features of burst and avalanche
statistics, dynamical aspects related to the temporal organization of bursts remain
often poorly understood or controversial. Of crucial importance to understand
the mechanisms responsible for emergent behaviors is the relationship between
active and quiet periods, and the nature of the correlations. Here we investigate
the dynamics of active (θ-bursts) and quiet states (δ-bursts) in brain activity
during the sleep-wake cycle. We show the duality of power-law (θ, active phase)
and exponential-like (δ, quiescent phase) duration distributions, typical of SOC,
jointly emerge with power-law temporal correlations and anti-correlated coupling
between active and quiet states. Importantly, we demonstrate that such temporal
organization shares important similarities with earthquake dynamics, and propose
that specific power-law correlations and coupling between active and quiet states
are distinctive characteristics of a class of systems with self-organization at
criticality.
article_number: '00005'
article_processing_charge: No
article_type: original
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Jilin W.J.L.
full_name: Wang, Jilin W.J.L.
last_name: Wang
- first_name: Xiyun
full_name: Zhang, Xiyun
last_name: Zhang
- first_name: Plamen Ch
full_name: Ivanov, Plamen Ch
last_name: Ivanov
citation:
ama: Lombardi F, Wang JWJL, Zhang X, Ivanov PC. Power-law correlations and coupling
of active and quiet states underlie a class of complex systems with self-organization
at criticality. EPJ Web of Conferences. 2020;230. doi:10.1051/epjconf/202023000005
apa: Lombardi, F., Wang, J. W. J. L., Zhang, X., & Ivanov, P. C. (2020). Power-law
correlations and coupling of active and quiet states underlie a class of complex
systems with self-organization at criticality. EPJ Web of Conferences.
EDP Sciences. https://doi.org/10.1051/epjconf/202023000005
chicago: Lombardi, Fabrizio, Jilin W.J.L. Wang, Xiyun Zhang, and Plamen Ch Ivanov.
“Power-Law Correlations and Coupling of Active and Quiet States Underlie a Class
of Complex Systems with Self-Organization at Criticality.” EPJ Web of Conferences.
EDP Sciences, 2020. https://doi.org/10.1051/epjconf/202023000005.
ieee: F. Lombardi, J. W. J. L. Wang, X. Zhang, and P. C. Ivanov, “Power-law correlations
and coupling of active and quiet states underlie a class of complex systems with
self-organization at criticality,” EPJ Web of Conferences, vol. 230. EDP
Sciences, 2020.
ista: Lombardi F, Wang JWJL, Zhang X, Ivanov PC. 2020. Power-law correlations and
coupling of active and quiet states underlie a class of complex systems with self-organization
at criticality. EPJ Web of Conferences. 230, 00005.
mla: Lombardi, Fabrizio, et al. “Power-Law Correlations and Coupling of Active and
Quiet States Underlie a Class of Complex Systems with Self-Organization at Criticality.”
EPJ Web of Conferences, vol. 230, 00005, EDP Sciences, 2020, doi:10.1051/epjconf/202023000005.
short: F. Lombardi, J.W.J.L. Wang, X. Zhang, P.C. Ivanov, EPJ Web of Conferences
230 (2020).
date_created: 2020-07-12T16:20:33Z
date_published: 2020-03-11T00:00:00Z
date_updated: 2021-01-12T08:16:55Z
day: '11'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.1051/epjconf/202023000005
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-07-22T06:17:11Z
date_updated: 2020-07-22T06:17:11Z
file_id: '8144'
file_name: 2020_EPJWebConf_Lombardi.pdf
file_size: 2197543
relation: main_file
success: 1
file_date_updated: 2020-07-22T06:17:11Z
has_accepted_license: '1'
intvolume: ' 230'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: EPJ Web of Conferences
publication_identifier:
issn:
- 2100-014X
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
status: public
title: Power-law correlations and coupling of active and quiet states underlie a class
of complex systems with self-organization at criticality
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 230
year: '2020'
...
---
_id: '7490'
abstract:
- lang: eng
text: In plants, clathrin mediated endocytosis (CME) represents the major route
for cargo internalisation from the cell surface. It has been assumed to operate
in an evolutionary conserved manner as in yeast and animals. Here we report characterisation
of ultrastructure, dynamics and mechanisms of plant CME as allowed by our advancement
in electron microscopy and quantitative live imaging techniques. Arabidopsis CME
appears to follow the constant curvature model and the bona fide CME population
generates vesicles of a predominantly hexagonal-basket type; larger and with faster
kinetics than in other models. Contrary to the existing paradigm, actin is dispensable
for CME events at the plasma membrane but plays a unique role in collecting endocytic
vesicles, sorting of internalised cargos and directional endosome movement that
itself actively promote CME events. Internalized vesicles display a strongly delayed
and sequential uncoating. These unique features highlight the independent evolution
of the plant CME mechanism during the autonomous rise of multicellularity in eukaryotes.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
article_number: e52067
article_processing_charge: No
article_type: original
author:
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Barbara E
full_name: Casillas Perez, Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Narasimhan M, Johnson AJ, Prizak R, et al. Evolutionarily unique mechanistic
framework of clathrin-mediated endocytosis in plants. eLife. 2020;9. doi:10.7554/eLife.52067
apa: Narasimhan, M., Johnson, A. J., Prizak, R., Kaufmann, W., Tan, S., Casillas
Perez, B. E., & Friml, J. (2020). Evolutionarily unique mechanistic framework
of clathrin-mediated endocytosis in plants. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.52067
chicago: Narasimhan, Madhumitha, Alexander J Johnson, Roshan Prizak, Walter Kaufmann,
Shutang Tan, Barbara E Casillas Perez, and Jiří Friml. “Evolutionarily Unique
Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.” ELife.
eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.52067.
ieee: M. Narasimhan et al., “Evolutionarily unique mechanistic framework
of clathrin-mediated endocytosis in plants,” eLife, vol. 9. eLife Sciences
Publications, 2020.
ista: Narasimhan M, Johnson AJ, Prizak R, Kaufmann W, Tan S, Casillas Perez BE,
Friml J. 2020. Evolutionarily unique mechanistic framework of clathrin-mediated
endocytosis in plants. eLife. 9, e52067.
mla: Narasimhan, Madhumitha, et al. “Evolutionarily Unique Mechanistic Framework
of Clathrin-Mediated Endocytosis in Plants.” ELife, vol. 9, e52067, eLife
Sciences Publications, 2020, doi:10.7554/eLife.52067.
short: M. Narasimhan, A.J. Johnson, R. Prizak, W. Kaufmann, S. Tan, B.E. Casillas
Perez, J. Friml, ELife 9 (2020).
date_created: 2020-02-16T23:00:50Z
date_published: 2020-01-23T00:00:00Z
date_updated: 2023-08-18T06:33:07Z
day: '23'
ddc:
- '570'
- '580'
department:
- _id: JiFr
- _id: GaTk
- _id: EM-Fac
- _id: SyCr
doi: 10.7554/eLife.52067
ec_funded: 1
external_id:
isi:
- '000514104100001'
pmid:
- '31971511'
file:
- access_level: open_access
checksum: 2052daa4be5019534f3a42f200a09f32
content_type: application/pdf
creator: dernst
date_created: 2020-02-18T07:21:16Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7494'
file_name: 2020_eLife_Narasimhan.pdf
file_size: 7247468
relation: main_file
file_date_updated: 2020-07-14T12:47:59Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis
in plants
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2020'
...
---
_id: '9779'
article_processing_charge: No
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: Tamar
full_name: Friedlander, Tamar
last_name: Friedlander
citation:
ama: Grah R, Friedlander T. Distribution of crosstalk values. 2020. doi:10.1371/journal.pcbi.1007642.s003
apa: Grah, R., & Friedlander, T. (2020). Distribution of crosstalk values. Public
Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s003
chicago: Grah, Rok, and Tamar Friedlander. “Distribution of Crosstalk Values.” Public
Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s003.
ieee: R. Grah and T. Friedlander, “Distribution of crosstalk values.” Public Library
of Science, 2020.
ista: Grah R, Friedlander T. 2020. Distribution of crosstalk values, Public Library
of Science, 10.1371/journal.pcbi.1007642.s003.
mla: Grah, Rok, and Tamar Friedlander. Distribution of Crosstalk Values.
Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s003.
short: R. Grah, T. Friedlander, (2020).
date_created: 2021-08-06T07:24:37Z
date_published: 2020-02-25T00:00:00Z
date_updated: 2023-08-18T06:47:47Z
day: '25'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1007642.s003
month: '02'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '7569'
relation: research_data
status: public
status: public
title: Distribution of crosstalk values
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
_id: '9776'
article_processing_charge: No
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: Tamar
full_name: Friedlander, Tamar
last_name: Friedlander
citation:
ama: Grah R, Friedlander T. Supporting information. 2020. doi:10.1371/journal.pcbi.1007642.s001
apa: Grah, R., & Friedlander, T. (2020). Supporting information. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1007642.s001
chicago: Grah, Rok, and Tamar Friedlander. “Supporting Information.” Public Library
of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s001.
ieee: R. Grah and T. Friedlander, “Supporting information.” Public Library of Science,
2020.
ista: Grah R, Friedlander T. 2020. Supporting information, Public Library of Science,
10.1371/journal.pcbi.1007642.s001.
mla: Grah, Rok, and Tamar Friedlander. Supporting Information. Public Library
of Science, 2020, doi:10.1371/journal.pcbi.1007642.s001.
short: R. Grah, T. Friedlander, (2020).
date_created: 2021-08-06T07:15:04Z
date_published: 2020-02-25T00:00:00Z
date_updated: 2023-08-18T06:47:47Z
day: '25'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1007642.s001
month: '02'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '7569'
relation: used_in_publication
status: public
status: public
title: Supporting information
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
_id: '7656'
abstract:
- lang: eng
text: 'We propose that correlations among neurons are generically strong enough
to organize neural activity patterns into a discrete set of clusters, which can
each be viewed as a population codeword. Our reasoning starts with the analysis
of retinal ganglion cell data using maximum entropy models, showing that the population
is robustly in a frustrated, marginally sub-critical, or glassy, state. This leads
to an argument that neural populations in many other brain areas might share this
structure. Next, we use latent variable models to show that this glassy state
possesses well-defined clusters of neural activity. Clusters have three appealing
properties: (i) clusters exhibit error correction, i.e., they are reproducibly
elicited by the same stimulus despite variability at the level of constituent
neurons; (ii) clusters encode qualitatively different visual features than their
constituent neurons; and (iii) clusters can be learned by downstream neural circuits
in an unsupervised fashion. We hypothesize that these properties give rise to
a “learnable” neural code which the cortical hierarchy uses to extract increasingly
complex features without supervision or reinforcement.'
article_number: '20'
article_processing_charge: No
article_type: original
author:
- first_name: Michael J.
full_name: Berry, Michael J.
last_name: Berry
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: 'Berry MJ, Tkačik G. Clustering of neural activity: A design principle for
population codes. Frontiers in Computational Neuroscience. 2020;14. doi:10.3389/fncom.2020.00020'
apa: 'Berry, M. J., & Tkačik, G. (2020). Clustering of neural activity: A design
principle for population codes. Frontiers in Computational Neuroscience.
Frontiers. https://doi.org/10.3389/fncom.2020.00020'
chicago: 'Berry, Michael J., and Gašper Tkačik. “Clustering of Neural Activity:
A Design Principle for Population Codes.” Frontiers in Computational Neuroscience.
Frontiers, 2020. https://doi.org/10.3389/fncom.2020.00020.'
ieee: 'M. J. Berry and G. Tkačik, “Clustering of neural activity: A design principle
for population codes,” Frontiers in Computational Neuroscience, vol. 14.
Frontiers, 2020.'
ista: 'Berry MJ, Tkačik G. 2020. Clustering of neural activity: A design principle
for population codes. Frontiers in Computational Neuroscience. 14, 20.'
mla: 'Berry, Michael J., and Gašper Tkačik. “Clustering of Neural Activity: A Design
Principle for Population Codes.” Frontiers in Computational Neuroscience,
vol. 14, 20, Frontiers, 2020, doi:10.3389/fncom.2020.00020.'
short: M.J. Berry, G. Tkačik, Frontiers in Computational Neuroscience 14 (2020).
date_created: 2020-04-12T22:00:40Z
date_published: 2020-03-13T00:00:00Z
date_updated: 2023-08-18T10:30:11Z
day: '13'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.3389/fncom.2020.00020
external_id:
isi:
- '000525543200001'
pmid:
- '32231528'
file:
- access_level: open_access
checksum: 2b1da23823eae9cedbb42d701945b61e
content_type: application/pdf
creator: dernst
date_created: 2020-04-14T12:20:39Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7659'
file_name: 2020_Frontiers_Berry.pdf
file_size: 4082937
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Computational Neuroscience
publication_identifier:
eissn:
- '16625188'
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Clustering of neural activity: A design principle for population codes'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2020'
...
---
_id: '8698'
abstract:
- lang: eng
text: The brain represents and reasons probabilistically about complex stimuli and
motor actions using a noisy, spike-based neural code. A key building block for
such neural computations, as well as the basis for supervised and unsupervised
learning, is the ability to estimate the surprise or likelihood of incoming high-dimensional
neural activity patterns. Despite progress in statistical modeling of neural responses
and deep learning, current approaches either do not scale to large neural populations
or cannot be implemented using biologically realistic mechanisms. Inspired by
the sparse and random connectivity of real neuronal circuits, we present a model
for neural codes that accurately estimates the likelihood of individual spiking
patterns and has a straightforward, scalable, efficient, learnable, and realistic
neural implementation. This model’s performance on simultaneously recorded spiking
activity of >100 neurons in the monkey visual and prefrontal cortices is comparable
with or better than that of state-of-the-art models. Importantly, the model can
be learned using a small number of samples and using a local learning rule that
utilizes noise intrinsic to neural circuits. Slower, structural changes in random
connectivity, consistent with rewiring and pruning processes, further improve
the efficiency and sparseness of the resulting neural representations. Our results
merge insights from neuroanatomy, machine learning, and theoretical neuroscience
to suggest random sparse connectivity as a key design principle for neuronal computation.
acknowledgement: We thank Udi Karpas, Roy Harpaz, Tal Tamir, Adam Haber, and Amir
Bar for discussions and suggestions; and especially Oren Forkosh and Walter Senn
for invaluable discussions of the learning rule. This work was supported by European
Research Council Grant 311238 (to E.S.) and Israel Science Foundation Grant 1629/12
(to E.S.); as well as research support from Martin Kushner Schnur and Mr. and Mrs.
Lawrence Feis (E.S.); National Institute of Mental Health Grant R01MH109180 (to
R.K.); a Pew Scholarship in Biomedical Sciences (to R.K.); Simons Collaboration
on the Global Brain Grant 542997 (to R.K. and E.S.); and a CRCNS (Collaborative
Research in Computational Neuroscience) grant (to R.K. and E.S.).
article_processing_charge: No
article_type: original
author:
- first_name: Ori
full_name: Maoz, Ori
last_name: Maoz
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Mohamad Saleh
full_name: Esteki, Mohamad Saleh
last_name: Esteki
- first_name: Roozbeh
full_name: Kiani, Roozbeh
last_name: Kiani
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
citation:
ama: Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. Learning probabilistic
neural representations with randomly connected circuits. Proceedings of the
National Academy of Sciences of the United States of America. 2020;117(40):25066-25073.
doi:10.1073/pnas.1912804117
apa: Maoz, O., Tkačik, G., Esteki, M. S., Kiani, R., & Schneidman, E. (2020).
Learning probabilistic neural representations with randomly connected circuits.
Proceedings of the National Academy of Sciences of the United States of America.
National Academy of Sciences. https://doi.org/10.1073/pnas.1912804117
chicago: Maoz, Ori, Gašper Tkačik, Mohamad Saleh Esteki, Roozbeh Kiani, and Elad
Schneidman. “Learning Probabilistic Neural Representations with Randomly Connected
Circuits.” Proceedings of the National Academy of Sciences of the United States
of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1912804117.
ieee: O. Maoz, G. Tkačik, M. S. Esteki, R. Kiani, and E. Schneidman, “Learning probabilistic
neural representations with randomly connected circuits,” Proceedings of the
National Academy of Sciences of the United States of America, vol. 117, no.
40. National Academy of Sciences, pp. 25066–25073, 2020.
ista: Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. 2020. Learning probabilistic
neural representations with randomly connected circuits. Proceedings of the National
Academy of Sciences of the United States of America. 117(40), 25066–25073.
mla: Maoz, Ori, et al. “Learning Probabilistic Neural Representations with Randomly
Connected Circuits.” Proceedings of the National Academy of Sciences of the
United States of America, vol. 117, no. 40, National Academy of Sciences,
2020, pp. 25066–73, doi:10.1073/pnas.1912804117.
short: O. Maoz, G. Tkačik, M.S. Esteki, R. Kiani, E. Schneidman, Proceedings of
the National Academy of Sciences of the United States of America 117 (2020) 25066–25073.
date_created: 2020-10-25T23:01:16Z
date_published: 2020-10-06T00:00:00Z
date_updated: 2023-08-22T12:11:23Z
day: '06'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1073/pnas.1912804117
external_id:
isi:
- '000579045200012'
pmid:
- '32948691'
file:
- access_level: open_access
checksum: c6a24fdecf3f28faf447078e7a274a88
content_type: application/pdf
creator: cziletti
date_created: 2020-10-27T14:57:50Z
date_updated: 2020-10-27T14:57:50Z
file_id: '8713'
file_name: 2020_PNAS_Maoz.pdf
file_size: 1755359
relation: main_file
success: 1
file_date_updated: 2020-10-27T14:57:50Z
has_accepted_license: '1'
intvolume: ' 117'
isi: 1
issue: '40'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 25066-25073
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- '10916490'
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Learning probabilistic neural representations with randomly connected circuits
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 117
year: '2020'
...
---
_id: '8955'
abstract:
- lang: eng
text: Skeletal muscle activity is continuously modulated across physiologic states
to provide coordination, flexibility and responsiveness to body tasks and external
inputs. Despite the central role the muscular system plays in facilitating vital
body functions, the network of brain-muscle interactions required to control hundreds
of muscles and synchronize their activation in relation to distinct physiologic
states has not been investigated. Recent approaches have focused on general associations
between individual brain rhythms and muscle activation during movement tasks.
However, the specific forms of coupling, the functional network of cortico-muscular
coordination, and how network structure and dynamics are modulated by autonomic
regulation across physiologic states remains unknown. To identify and quantify
the cortico-muscular interaction network and uncover basic features of neuro-autonomic
control of muscle function, we investigate the coupling between synchronous bursts
in cortical rhythms and peripheral muscle activation during sleep and wake. Utilizing
the concept of time delay stability and a novel network physiology approach, we
find that the brain-muscle network exhibits complex dynamic patterns of communication
involving multiple brain rhythms across cortical locations and different electromyographic
frequency bands. Moreover, our results show that during each physiologic state
the cortico-muscular network is characterized by a specific profile of network
links strength, where particular brain rhythms play role of main mediators of
interaction and control. Further, we discover a hierarchical reorganization in
network structure across physiologic states, with high connectivity and network
link strength during wake, intermediate during REM and light sleep, and low during
deep sleep, a sleep-stage stratification that demonstrates a unique association
between physiologic states and cortico-muscular network structure. The reported
empirical observations are consistent across individual subjects, indicating universal
behavior in network structure and dynamics, and high sensitivity of cortico-muscular
control to changes in autonomic regulation, even at low levels of physical activity
and muscle tone during sleep. Our findings demonstrate previously unrecognized
basic principles of brain-muscle network communication and control, and provide
new perspectives on the regulatory mechanisms of brain dynamics and locomotor
activation, with potential clinical implications for neurodegenerative, movement
and sleep disorders, and for developing efficient treatment strategies.
acknowledgement: We acknowledge support from the W. M. Keck Foundation, National Institutes
of Health (NIH Grant 1R01-HL098437), the US-Israel Binational Science Foundation
(BSF Grant 2012219), and the Office of Naval Research (ONR Grant 000141010078).
FL acknowledges support also from the European Union's Horizon 2020 research and
innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411.
article_number: '558070'
article_processing_charge: No
article_type: original
author:
- first_name: Rossella
full_name: Rizzo, Rossella
last_name: Rizzo
- first_name: Xiyun
full_name: Zhang, Xiyun
last_name: Zhang
- first_name: Jilin W.J.L.
full_name: Wang, Jilin W.J.L.
last_name: Wang
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Plamen Ch
full_name: Ivanov, Plamen Ch
last_name: Ivanov
citation:
ama: Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. Network physiology of cortico–muscular
interactions. Frontiers in Physiology. 2020;11. doi:10.3389/fphys.2020.558070
apa: Rizzo, R., Zhang, X., Wang, J. W. J. L., Lombardi, F., & Ivanov, P. C.
(2020). Network physiology of cortico–muscular interactions. Frontiers in Physiology.
Frontiers. https://doi.org/10.3389/fphys.2020.558070
chicago: Rizzo, Rossella, Xiyun Zhang, Jilin W.J.L. Wang, Fabrizio Lombardi, and
Plamen Ch Ivanov. “Network Physiology of Cortico–Muscular Interactions.” Frontiers
in Physiology. Frontiers, 2020. https://doi.org/10.3389/fphys.2020.558070.
ieee: R. Rizzo, X. Zhang, J. W. J. L. Wang, F. Lombardi, and P. C. Ivanov, “Network
physiology of cortico–muscular interactions,” Frontiers in Physiology,
vol. 11. Frontiers, 2020.
ista: Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. 2020. Network physiology
of cortico–muscular interactions. Frontiers in Physiology. 11, 558070.
mla: Rizzo, Rossella, et al. “Network Physiology of Cortico–Muscular Interactions.”
Frontiers in Physiology, vol. 11, 558070, Frontiers, 2020, doi:10.3389/fphys.2020.558070.
short: R. Rizzo, X. Zhang, J.W.J.L. Wang, F. Lombardi, P.C. Ivanov, Frontiers in
Physiology 11 (2020).
date_created: 2020-12-20T23:01:18Z
date_published: 2020-11-26T00:00:00Z
date_updated: 2023-08-24T11:00:45Z
day: '26'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.3389/fphys.2020.558070
ec_funded: 1
external_id:
isi:
- '000596849400001'
pmid:
- '33324233'
file:
- access_level: open_access
checksum: ef9515b28c5619b7126c0f347958bcb3
content_type: application/pdf
creator: dernst
date_created: 2020-12-21T10:37:50Z
date_updated: 2020-12-21T10:37:50Z
file_id: '8961'
file_name: 2020_Frontiers_Rizzo.pdf
file_size: 13380030
relation: main_file
success: 1
file_date_updated: 2020-12-21T10:37:50Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Frontiers in Physiology
publication_identifier:
eissn:
- 1664042X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Network physiology of cortico–muscular interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2020'
...
---
_id: '9000'
abstract:
- lang: eng
text: 'In prokaryotes, thermodynamic models of gene regulation provide a highly
quantitative mapping from promoter sequences to gene-expression levels that is
compatible with in vivo and in vitro biophysical measurements. Such concordance
has not been achieved for models of enhancer function in eukaryotes. In equilibrium
models, it is difficult to reconcile the reported short transcription factor (TF)
residence times on the DNA with the high specificity of regulation. In nonequilibrium
models, progress is difficult due to an explosion in the number of parameters.
Here, we navigate this complexity by looking for minimal nonequilibrium enhancer
models that yield desired regulatory phenotypes: low TF residence time, high specificity,
and tunable cooperativity. We find that a single extra parameter, interpretable
as the “linking rate,” by which bound TFs interact with Mediator components, enables
our models to escape equilibrium bounds and access optimal regulatory phenotypes,
while remaining consistent with the reported phenomenology and simple enough to
be inferred from upcoming experiments. We further find that high specificity in
nonequilibrium models is in a trade-off with gene-expression noise, predicting
bursty dynamics—an experimentally observed hallmark of eukaryotic transcription.
By drastically reducing the vast parameter space of nonequilibrium enhancer models
to a much smaller subspace that optimally realizes biological function, we deliver
a rich class of models that could be tractably inferred from data in the near
future.'
acknowledgement: G.T. was supported by Human Frontiers Science Program Grant RGP0034/2018.
R.G. was supported by the Austrian Academy of Sciences DOC Fellowship. R.G. thanks
S. Avvakumov for helpful discussions.
article_processing_charge: No
article_type: original
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: Benjamin
full_name: Zoller, Benjamin
last_name: Zoller
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Grah R, Zoller B, Tkačik G. Nonequilibrium models of optimal enhancer function.
PNAS. 2020;117(50):31614-31622. doi:10.1073/pnas.2006731117
apa: Grah, R., Zoller, B., & Tkačik, G. (2020). Nonequilibrium models of optimal
enhancer function. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.2006731117
chicago: Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Nonequilibrium Models of
Optimal Enhancer Function.” PNAS. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2006731117.
ieee: R. Grah, B. Zoller, and G. Tkačik, “Nonequilibrium models of optimal enhancer
function,” PNAS, vol. 117, no. 50. National Academy of Sciences, pp. 31614–31622,
2020.
ista: Grah R, Zoller B, Tkačik G. 2020. Nonequilibrium models of optimal enhancer
function. PNAS. 117(50), 31614–31622.
mla: Grah, Rok, et al. “Nonequilibrium Models of Optimal Enhancer Function.” PNAS,
vol. 117, no. 50, National Academy of Sciences, 2020, pp. 31614–22, doi:10.1073/pnas.2006731117.
short: R. Grah, B. Zoller, G. Tkačik, PNAS 117 (2020) 31614–31622.
date_created: 2021-01-10T23:01:17Z
date_published: 2020-12-15T00:00:00Z
date_updated: 2023-08-24T11:10:22Z
day: '15'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1073/pnas.2006731117
external_id:
isi:
- '000600608300015'
pmid:
- '33268497'
file:
- access_level: open_access
checksum: 69039cd402a571983aa6cb4815ffa863
content_type: application/pdf
creator: dernst
date_created: 2021-01-11T08:37:31Z
date_updated: 2021-01-11T08:37:31Z
file_id: '9004'
file_name: 2020_PNAS_Grah.pdf
file_size: 1199247
relation: main_file
success: 1
file_date_updated: 2021-01-11T08:37:31Z
has_accepted_license: '1'
intvolume: ' 117'
isi: 1
issue: '50'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 31614-31622
pmid: 1
project:
- _id: 2665AAFE-B435-11E9-9278-68D0E5697425
grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
- _id: 267C84F4-B435-11E9-9278-68D0E5697425
name: Biophysically realistic genotype-phenotype maps for regulatory networks
publication: PNAS
publication_identifier:
eissn:
- '10916490'
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-compact-model-for-gene-regulation-in-higher-organisms/
scopus_import: '1'
status: public
title: Nonequilibrium models of optimal enhancer function
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 117
year: '2020'
...
---
_id: '8084'
abstract:
- lang: eng
text: Origin and functions of intermittent transitions among sleep stages, including
brief awakenings and arousals, constitute a challenge to the current homeostatic
framework for sleep regulation, focusing on factors modulating sleep over large
time scales. Here we propose that the complex micro-architecture characterizing
sleep on scales of seconds and minutes results from intrinsic non-equilibrium
critical dynamics. We investigate θ- and δ-wave dynamics in control rats and in
rats where the sleep-promoting ventrolateral preoptic nucleus (VLPO) is lesioned
(male Sprague-Dawley rats). We demonstrate that bursts in θ and δ cortical rhythms
exhibit complex temporal organization, with long-range correlations and robust
duality of power-law (θ-bursts, active phase) and exponential-like (δ-bursts,
quiescent phase) duration distributions, features typical of non-equilibrium systems
self-organizing at criticality. We show that such non-equilibrium behavior relates
to anti-correlated coupling between θ- and δ-bursts, persists across a range of
time scales, and is independent of the dominant physiologic state; indications
of a basic principle in sleep regulation. Further, we find that VLPO lesions lead
to a modulation of cortical dynamics resulting in altered dynamical parameters
of θ- and δ-bursts and significant reduction in θ–δ coupling. Our empirical findings
and model simulations demonstrate that θ–δ coupling is essential for the emerging
non-equilibrium critical dynamics observed across the sleep–wake cycle, and indicate
that VLPO neurons may have dual role for both sleep and arousal/brief wake activation.
The uncovered critical behavior in sleep- and wake-related cortical rhythms indicates
a mechanism essential for the micro-architecture of spontaneous sleep-stage and
arousal transitions within a novel, non-homeostatic paradigm of sleep regulation.
article_processing_charge: No
article_type: original
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Manuel
full_name: Gómez-Extremera, Manuel
last_name: Gómez-Extremera
- first_name: Pedro
full_name: Bernaola-Galván, Pedro
last_name: Bernaola-Galván
- first_name: Ramalingam
full_name: Vetrivelan, Ramalingam
last_name: Vetrivelan
- first_name: Clifford B.
full_name: Saper, Clifford B.
last_name: Saper
- first_name: Thomas E.
full_name: Scammell, Thomas E.
last_name: Scammell
- first_name: Plamen Ch.
full_name: Ivanov, Plamen Ch.
last_name: Ivanov
citation:
ama: Lombardi F, Gómez-Extremera M, Bernaola-Galván P, et al. Critical dynamics
and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism
for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake.
Journal of Neuroscience. 2020;40(1):171-190. doi:10.1523/jneurosci.1278-19.2019
apa: Lombardi, F., Gómez-Extremera, M., Bernaola-Galván, P., Vetrivelan, R., Saper,
C. B., Scammell, T. E., & Ivanov, P. C. (2020). Critical dynamics and coupling
in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage
transitions and dual role of VLPO neurons in both sleep and wake. Journal of
Neuroscience. Society for Neuroscience. https://doi.org/10.1523/jneurosci.1278-19.2019
chicago: Lombardi, Fabrizio, Manuel Gómez-Extremera, Pedro Bernaola-Galván, Ramalingam
Vetrivelan, Clifford B. Saper, Thomas E. Scammell, and Plamen Ch. Ivanov. “Critical
Dynamics and Coupling in Bursts of Cortical Rhythms Indicate Non-Homeostatic Mechanism
for Sleep-Stage Transitions and Dual Role of VLPO Neurons in Both Sleep and Wake.”
Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/jneurosci.1278-19.2019.
ieee: F. Lombardi et al., “Critical dynamics and coupling in bursts of cortical
rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual
role of VLPO neurons in both sleep and wake,” Journal of Neuroscience,
vol. 40, no. 1. Society for Neuroscience, pp. 171–190, 2020.
ista: Lombardi F, Gómez-Extremera M, Bernaola-Galván P, Vetrivelan R, Saper CB,
Scammell TE, Ivanov PC. 2020. Critical dynamics and coupling in bursts of cortical
rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual
role of VLPO neurons in both sleep and wake. Journal of Neuroscience. 40(1), 171–190.
mla: Lombardi, Fabrizio, et al. “Critical Dynamics and Coupling in Bursts of Cortical
Rhythms Indicate Non-Homeostatic Mechanism for Sleep-Stage Transitions and Dual
Role of VLPO Neurons in Both Sleep and Wake.” Journal of Neuroscience,
vol. 40, no. 1, Society for Neuroscience, 2020, pp. 171–90, doi:10.1523/jneurosci.1278-19.2019.
short: F. Lombardi, M. Gómez-Extremera, P. Bernaola-Galván, R. Vetrivelan, C.B.
Saper, T.E. Scammell, P.C. Ivanov, Journal of Neuroscience 40 (2020) 171–190.
date_created: 2020-07-05T15:24:51Z
date_published: 2020-01-02T00:00:00Z
date_updated: 2023-09-05T14:02:55Z
day: '02'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1523/jneurosci.1278-19.2019
ec_funded: 1
external_id:
isi:
- '000505167600016'
pmid:
- '31694962'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-07-22T11:44:48Z
date_updated: 2020-07-22T11:44:48Z
file_id: '8150'
file_name: 2020_JournNeuroscience_Lombardi.pdf
file_size: 6646046
relation: main_file
success: 1
file_date_updated: 2020-07-22T11:44:48Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 171-190
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
issn:
- 0270-6474
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic
mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep
and wake
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 40
year: '2020'
...
---
_id: '8155'
abstract:
- lang: eng
text: "In the thesis we focus on the interplay of the biophysics and evolution of
gene regulation. We start by addressing how the type of prokaryotic gene regulation
– activation and repression – affects spurious binding to DNA, also known as\r\ntranscriptional
crosstalk. We propose that regulatory interference caused by excess regulatory
proteins in the dense cellular medium – global crosstalk – could be a factor in
determining which type of gene regulatory network is evolutionarily preferred.
Next,we use a normative approach in eukaryotic gene regulation to describe minimal\r\nnon-equilibrium
enhancer models that optimize so-called regulatory phenotypes. We find a class
of models that differ from standard thermodynamic equilibrium models by a single
parameter that notably increases the regulatory performance. Next chapter addresses
the question of genotype-phenotype-fitness maps of higher dimensional phenotypes.
We show that our biophysically realistic approach allows us to understand how
the mechanisms of promoter function constrain genotypephenotype maps, and how
they affect the evolutionary trajectories of promoters.\r\nIn the last chapter
we ask whether the intrinsic instability of gene duplication and amplification
provides a generic alternative to canonical gene regulation. Using mathematical
modeling, we show that amplifications can tune gene expression in many environments,
including those where transcription factor-based schemes are\r\nhard to evolve
or maintain. "
acknowledgement: For the duration of his PhD, Rok was a recipient of a DOC fellowship
of the Austrian Academy of Sciences.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
citation:
ama: Grah R. Gene regulation across scales – how biophysical constraints shape evolution.
2020. doi:10.15479/AT:ISTA:8155
apa: Grah, R. (2020). Gene regulation across scales – how biophysical constraints
shape evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8155
chicago: Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints
Shape Evolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8155.
ieee: R. Grah, “Gene regulation across scales – how biophysical constraints shape
evolution,” Institute of Science and Technology Austria, 2020.
ista: Grah R. 2020. Gene regulation across scales – how biophysical constraints
shape evolution. Institute of Science and Technology Austria.
mla: Grah, Rok. Gene Regulation across Scales – How Biophysical Constraints Shape
Evolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8155.
short: R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape
Evolution, Institute of Science and Technology Austria, 2020.
date_created: 2020-07-23T09:51:28Z
date_published: 2020-07-24T00:00:00Z
date_updated: 2023-09-07T13:13:27Z
day: '24'
ddc:
- '530'
- '570'
degree_awarded: PhD
department:
- _id: CaGu
- _id: GaTk
doi: 10.15479/AT:ISTA:8155
file:
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content_type: application/pdf
creator: rgrah
date_created: 2020-07-27T12:00:07Z
date_updated: 2020-07-27T12:00:07Z
file_id: '8176'
file_name: Thesis_RokGrah_200727_convertedNew.pdf
file_size: 16638998
relation: main_file
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content_type: application/zip
creator: rgrah
date_created: 2020-07-27T12:02:23Z
date_updated: 2020-07-30T13:04:55Z
file_id: '8177'
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language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '310'
project:
- _id: 267C84F4-B435-11E9-9278-68D0E5697425
name: Biophysically realistic genotype-phenotype maps for regulatory networks
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
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relation: part_of_dissertation
status: public
- id: '7569'
relation: part_of_dissertation
status: public
- id: '7652'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Gene regulation across scales – how biophysical constraints shape evolution
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7675'
abstract:
- lang: eng
text: 'In prokaryotes, thermodynamic models of gene regulation provide a highly
quantitative mapping from promoter sequences to gene expression levels that is
compatible with in vivo and in vitro bio-physical measurements. Such concordance
has not been achieved for models of enhancer function in eukaryotes. In equilibrium
models, it is difficult to reconcile the reported short transcription factor (TF)
residence times on the DNA with the high specificity of regulation. In non-equilibrium
models, progress is difficult due to an explosion in the number of parameters.
Here, we navigate this complexity by looking for minimal non-equilibrium enhancer
models that yield desired regulatory phenotypes: low TF residence time, high specificity
and tunable cooperativity. We find that a single extra parameter, interpretable
as the “linking rate” by which bound TFs interact with Mediator components, enables
our models to escape equilibrium bounds and access optimal regulatory phenotypes,
while remaining consistent with the reported phenomenology and simple enough to
be inferred from upcoming experiments. We further find that high specificity in
non-equilibrium models is in a tradeoff with gene expression noise, predicting
bursty dynamics — an experimentally-observed hallmark of eukaryotic transcription.
By drastically reducing the vast parameter space to a much smaller subspace that
optimally realizes biological function prior to inference from data, our normative
approach holds promise for mathematical models in systems biology.'
article_processing_charge: No
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: Benjamin
full_name: Zoller, Benjamin
last_name: Zoller
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Grah R, Zoller B, Tkačik G. Normative models of enhancer function. bioRxiv.
2020. doi:10.1101/2020.04.08.029405
apa: Grah, R., Zoller, B., & Tkačik, G. (2020). Normative models of enhancer
function. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.04.08.029405
chicago: Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer
Function.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.04.08.029405.
ieee: R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,”
bioRxiv. Cold Spring Harbor Laboratory, 2020.
ista: Grah R, Zoller B, Tkačik G. 2020. Normative models of enhancer function. bioRxiv,
10.1101/2020.04.08.029405.
mla: Grah, Rok, et al. “Normative Models of Enhancer Function.” BioRxiv,
Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.08.029405.
short: R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020).
date_created: 2020-04-23T10:12:51Z
date_published: 2020-04-09T00:00:00Z
date_updated: 2023-09-07T13:13:26Z
day: '09'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1101/2020.04.08.029405
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/2020.04.08.029405 '
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 2665AAFE-B435-11E9-9278-68D0E5697425
grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
- _id: 267C84F4-B435-11E9-9278-68D0E5697425
name: Biophysically realistic genotype-phenotype maps for regulatory networks
publication: bioRxiv
publication_status: published
publisher: Cold Spring Harbor Laboratory
related_material:
record:
- id: '8155'
relation: dissertation_contains
status: public
status: public
title: Normative models of enhancer function
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7569'
abstract:
- lang: eng
text: 'Genes differ in the frequency at which they are expressed and in the form
of regulation used to control their activity. In particular, positive or negative
regulation can lead to activation of a gene in response to an external signal.
Previous works proposed that the form of regulation of a gene correlates with
its frequency of usage: positive regulation when the gene is frequently expressed
and negative regulation when infrequently expressed. Such network design means
that, in the absence of their regulators, the genes are found in their least required
activity state, hence regulatory intervention is often necessary. Due to the multitude
of genes and regulators, spurious binding and unbinding events, called “crosstalk”,
could occur. To determine how the form of regulation affects the global crosstalk
in the network, we used a mathematical model that includes multiple regulators
and multiple target genes. We found that crosstalk depends non-monotonically on
the availability of regulators. Our analysis showed that excess use of regulation
entailed by the formerly suggested network design caused high crosstalk levels
in a large part of the parameter space. We therefore considered the opposite ‘idle’
design, where the default unregulated state of genes is their frequently required
activity state. We found, that ‘idle’ design minimized the use of regulation and
thus minimized crosstalk. In addition, we estimated global crosstalk of S. cerevisiae
using transcription factors binding data. We demonstrated that even partial network
data could suffice to estimate its global crosstalk, suggesting its applicability
to additional organisms. We found that S. cerevisiae estimated crosstalk is lower
than that of a random network, suggesting that natural selection reduces crosstalk.
In summary, our study highlights a new type of protein production cost which is
typically overlooked: that of regulatory interference caused by the presence of
excess regulators in the cell. It demonstrates the importance of whole-network
descriptions, which could show effects missed by single-gene models.'
article_number: e1007642
article_processing_charge: No
article_type: original
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: Tamar
full_name: Friedlander, Tamar
last_name: Friedlander
citation:
ama: Grah R, Friedlander T. The relation between crosstalk and gene regulation form
revisited. PLOS Computational Biology. 2020;16(2). doi:10.1371/journal.pcbi.1007642
apa: Grah, R., & Friedlander, T. (2020). The relation between crosstalk and
gene regulation form revisited. PLOS Computational Biology. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1007642
chicago: Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene
Regulation Form Revisited.” PLOS Computational Biology. Public Library
of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.
ieee: R. Grah and T. Friedlander, “The relation between crosstalk and gene regulation
form revisited,” PLOS Computational Biology, vol. 16, no. 2. Public Library
of Science, 2020.
ista: Grah R, Friedlander T. 2020. The relation between crosstalk and gene regulation
form revisited. PLOS Computational Biology. 16(2), e1007642.
mla: Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene
Regulation Form Revisited.” PLOS Computational Biology, vol. 16, no. 2,
e1007642, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.
short: R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020).
date_created: 2020-03-06T07:39:38Z
date_published: 2020-02-25T00:00:00Z
date_updated: 2023-09-12T11:02:24Z
day: '25'
ddc:
- '000'
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department:
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pcbi.1007642
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publisher: Public Library of Science
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scopus_import: '1'
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title: The relation between crosstalk and gene regulation form revisited
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
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...
---
_id: '9777'
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author:
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full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: Tamar
full_name: Friedlander, Tamar
last_name: Friedlander
citation:
ama: Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:10.1371/journal.pcbi.1007642.s002
apa: Grah, R., & Friedlander, T. (2020). Maximizing crosstalk. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1007642.s002
chicago: Grah, Rok, and Tamar Friedlander. “Maximizing Crosstalk.” Public Library
of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s002.
ieee: R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science,
2020.
ista: Grah R, Friedlander T. 2020. Maximizing crosstalk, Public Library of Science,
10.1371/journal.pcbi.1007642.s002.
mla: Grah, Rok, and Tamar Friedlander. Maximizing Crosstalk. Public Library
of Science, 2020, doi:10.1371/journal.pcbi.1007642.s002.
short: R. Grah, T. Friedlander, (2020).
date_created: 2021-08-06T07:21:51Z
date_published: 2020-02-25T00:00:00Z
date_updated: 2023-09-12T11:02:25Z
day: '25'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1007642.s002
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oa: 1
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title: Maximizing crosstalk
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year: '2020'
...
---
_id: '8657'
abstract:
- lang: eng
text: "Synthesis of proteins – translation – is a fundamental process of life. Quantitative
studies anchor translation into the context of bacterial physiology and reveal
several mathematical relationships, called “growth laws,” which capture physiological
feedbacks between protein synthesis and cell growth. Growth laws describe the
dependency of the ribosome abundance as a function of growth rate, which can change
depending on the growth conditions. Perturbations of translation reveal that bacteria
employ a compensatory strategy in which the reduced translation capability results
in increased expression of the translation machinery.\r\nPerturbations of translation
are achieved in various ways; clinically interesting is the application of translation-targeting
antibiotics – translation inhibitors. The antibiotic effects on bacterial physiology
are often poorly understood. Bacterial responses to two or more simultaneously
applied antibiotics are even more puzzling. The combined antibiotic effect determines
the type of drug interaction, which ranges from synergy (the effect is stronger
than expected) to antagonism (the effect is weaker) and suppression (one of the
drugs loses its potency).\r\nIn the first part of this work, we systematically
measure the pairwise interaction network for translation inhibitors that interfere
with different steps in translation. We find that the interactions are surprisingly
diverse and tend to be more antagonistic. To explore the underlying mechanisms,
we begin with a minimal biophysical model of combined antibiotic action. We base
this model on the kinetics of antibiotic uptake and binding together with the
physiological response described by the growth laws. The biophysical model explains
some drug interactions, but not all; it specifically fails to predict suppression.\r\nIn
the second part of this work, we hypothesize that elusive suppressive drug interactions
result from the interplay between ribosomes halted in different stages of translation.
To elucidate this putative mechanism of drug interactions between translation
inhibitors, we generate translation bottlenecks genetically using in- ducible
control of translation factors that regulate well-defined translation cycle steps.
These perturbations accurately mimic antibiotic action and drug interactions,
supporting that the interplay of different translation bottlenecks partially causes
these interactions.\r\nWe extend this approach by varying two translation bottlenecks
simultaneously. This approach reveals the suppression of translocation inhibition
by inhibited translation. We rationalize this effect by modeling dense traffic
of ribosomes that move on transcripts in a translation factor-mediated manner.
This model predicts a dissolution of traffic jams caused by inhibited translocation
when the density of ribosome traffic is reduced by lowered initiation. We base
this model on the growth laws and quantitative relationships between different
translation and growth parameters.\r\nIn the final part of this work, we describe
a set of tools aimed at quantification of physiological and translation parameters.
We further develop a simple model that directly connects the abundance of a translation
factor with the growth rate, which allows us to extract physiological parameters
describing initiation. We demonstrate the development of tools for measuring translation
rate.\r\nThis thesis showcases how a combination of high-throughput growth rate
mea- surements, genetics, and modeling can reveal mechanisms of drug interactions.
Furthermore, by a gradual transition from combinations of antibiotics to precise
genetic interventions, we demonstrated the equivalency between genetic and chemi-
cal perturbations of translation. These findings tile the path for quantitative
studies of antibiotic combinations and illustrate future approaches towards the
quantitative description of translation."
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
acknowledgement: I thank Life Science Facilities for their continuous support with
providing top-notch laboratory materials, keeping the devices humming, and coordinating
the repairs and building of custom-designed laboratory equipment with the MIBA Machine
shop.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
citation:
ama: 'Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics
and physiology. 2020. doi:10.15479/AT:ISTA:8657'
apa: 'Kavcic, B. (2020). Perturbations of protein synthesis: from antibiotics
to genetics and physiology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8657'
chicago: 'Kavcic, Bor. “Perturbations of Protein Synthesis: From Antibiotics to
Genetics and Physiology.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8657.'
ieee: 'B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics
and physiology,” Institute of Science and Technology Austria, 2020.'
ista: 'Kavcic B. 2020. Perturbations of protein synthesis: from antibiotics to genetics
and physiology. Institute of Science and Technology Austria.'
mla: 'Kavcic, Bor. Perturbations of Protein Synthesis: From Antibiotics to Genetics
and Physiology. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8657.'
short: 'B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics
and Physiology, Institute of Science and Technology Austria, 2020.'
date_created: 2020-10-13T16:46:14Z
date_published: 2020-10-14T00:00:00Z
date_updated: 2023-09-07T13:20:48Z
day: '14'
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- '530'
- '570'
degree_awarded: PhD
department:
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doi: 10.15479/AT:ISTA:8657
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date_updated: 2021-10-07T22:30:03Z
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supervisor:
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full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
title: 'Perturbations of protein synthesis: from antibiotics to genetics and physiology'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8250'
abstract:
- lang: eng
text: 'Antibiotics that interfere with translation, when combined, interact in diverse
and difficult-to-predict ways. Here, we explain these interactions by “translation
bottlenecks”: points in the translation cycle where antibiotics block ribosomal
progression. To elucidate the underlying mechanisms of drug interactions between
translation inhibitors, we generate translation bottlenecks genetically using
inducible control of translation factors that regulate well-defined translation
cycle steps. These perturbations accurately mimic antibiotic action and drug interactions,
supporting that the interplay of different translation bottlenecks causes these
interactions. We further show that growth laws, combined with drug uptake and
binding kinetics, enable the direct prediction of a large fraction of observed
interactions, yet fail to predict suppression. However, varying two translation
bottlenecks simultaneously supports that dense traffic of ribosomes and competition
for translation factors account for the previously unexplained suppression. These
results highlight the importance of “continuous epistasis” in bacterial physiology.'
acknowledgement: "We thank M. Hennessey-Wesen, I. Tomanek, K. Jain, A. Staron, K.
Tomasek, M. Scott,\r\nK.C. Huang, and Z. Gitai for reading the manuscript and constructive
comments. B.K. is\r\nindebted to C. Guet for additional guidance and generous support,
which rendered this\r\nwork possible. B.K. thanks all members of Guet group for
many helpful discussions and\r\nsharing of resources. B.K. additionally acknowledges
the tremendous support from A.\r\nAngermayr and K. Mitosch with experimental work.
We further thank E. Brown for\r\nhelpful comments regarding lamotrigine, and A.
Buskirk for valuable suggestions\r\nregarding the ribosome footprint size. This
work was supported in part by Austrian\r\nScience Fund (FWF) standalone grants P
27201-B22 (to T.B.) and P 28844 (to G.T.),\r\nHFSP program Grant RGP0042/2013 (to
T.B.), German Research Foundation (DFG)\r\nstandalone grant BO 3502/2-1 (to T.B.),
and German Research Foundation (DFG)\r\nCollaborative Research Centre (SFB) 1310
(to T.B.). Open access funding provided by\r\nProjekt DEAL."
article_number: '4013'
article_processing_charge: No
article_type: original
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Kavcic B, Tkačik G, Bollenbach MT. Mechanisms of drug interactions between
translation-inhibiting antibiotics. Nature Communications. 2020;11. doi:10.1038/s41467-020-17734-z
apa: Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). Mechanisms of drug
interactions between translation-inhibiting antibiotics. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-020-17734-z
chicago: Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Mechanisms of
Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications.
Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17734-z.
ieee: B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Mechanisms of drug interactions
between translation-inhibiting antibiotics,” Nature Communications, vol.
11. Springer Nature, 2020.
ista: Kavcic B, Tkačik G, Bollenbach MT. 2020. Mechanisms of drug interactions between
translation-inhibiting antibiotics. Nature Communications. 11, 4013.
mla: Kavcic, Bor, et al. “Mechanisms of Drug Interactions between Translation-Inhibiting
Antibiotics.” Nature Communications, vol. 11, 4013, Springer Nature, 2020,
doi:10.1038/s41467-020-17734-z.
short: B. Kavcic, G. Tkačik, M.T. Bollenbach, Nature Communications 11 (2020).
date_created: 2020-08-12T09:13:50Z
date_published: 2020-08-11T00:00:00Z
date_updated: 2024-03-28T23:30:08Z
day: '11'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1038/s41467-020-17734-z
external_id:
isi:
- '000562769300008'
file:
- access_level: open_access
checksum: 986bebb308850a55850028d3d2b5b664
content_type: application/pdf
creator: dernst
date_created: 2020-08-17T07:36:57Z
date_updated: 2020-08-17T07:36:57Z
file_id: '8275'
file_name: 2020_NatureComm_Kavcic.pdf
file_size: 1965672
relation: main_file
success: 1
file_date_updated: 2020-08-17T07:36:57Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8657'
relation: dissertation_contains
status: public
status: public
title: Mechanisms of drug interactions between translation-inhibiting antibiotics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2020'
...
---
_id: '7673'
abstract:
- lang: eng
text: Combining drugs can improve the efficacy of treatments. However, predicting
the effect of drug combinations is still challenging. The combined potency of
drugs determines the drug interaction, which is classified as synergistic, additive,
antagonistic, or suppressive. While probabilistic, non-mechanistic models exist,
there is currently no biophysical model that can predict antibiotic interactions.
Here, we present a physiologically relevant model of the combined action of antibiotics
that inhibit protein synthesis by targeting the ribosome. This model captures
the kinetics of antibiotic binding and transport, and uses bacterial growth laws
to predict growth in the presence of antibiotic combinations. We find that this
biophysical model can produce all drug interaction types except suppression. We
show analytically that antibiotics which cannot bind to the ribosome simultaneously
generally act as substitutes for one another, leading to additive drug interactions.
Previously proposed null expectations for higher-order drug interactions follow
as a limiting case of our model. We further extend the model to include the effects
of direct physical or allosteric interactions between individual drugs on the
ribosome. Notably, such direct interactions profoundly change the combined drug
effect, depending on the kinetic parameters of the drugs used. The model makes
additional predictions for the effects of resistance genes on drug interactions
and for interactions between ribosome-targeting antibiotics and antibiotics with
other targets. These findings enhance our understanding of the interplay between
drug action and cell physiology and are a key step toward a general framework
for predicting drug interactions.
article_processing_charge: No
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Kavcic B, Tkačik G, Bollenbach MT. A minimal biophysical model of combined
antibiotic action. bioRxiv. 2020. doi:10.1101/2020.04.18.047886
apa: Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). A minimal biophysical
model of combined antibiotic action. bioRxiv. Cold Spring Harbor Laboratory.
https://doi.org/10.1101/2020.04.18.047886
chicago: Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “A Minimal Biophysical
Model of Combined Antibiotic Action.” BioRxiv. Cold Spring Harbor Laboratory,
2020. https://doi.org/10.1101/2020.04.18.047886.
ieee: B. Kavcic, G. Tkačik, and M. T. Bollenbach, “A minimal biophysical model of
combined antibiotic action,” bioRxiv. Cold Spring Harbor Laboratory, 2020.
ista: Kavcic B, Tkačik G, Bollenbach MT. 2020. A minimal biophysical model of combined
antibiotic action. bioRxiv, 10.1101/2020.04.18.047886.
mla: Kavcic, Bor, et al. “A Minimal Biophysical Model of Combined Antibiotic Action.”
BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.18.047886.
short: B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020).
date_created: 2020-04-22T08:27:56Z
date_published: 2020-04-18T00:00:00Z
date_updated: 2024-03-28T23:30:08Z
day: '18'
department:
- _id: GaTk
doi: 10.1101/2020.04.18.047886
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/2020.04.18.047886 '
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: bioRxiv
publication_status: published
publisher: Cold Spring Harbor Laboratory
related_material:
record:
- id: '8997'
relation: later_version
status: public
- id: '8657'
relation: dissertation_contains
status: public
status: public
title: A minimal biophysical model of combined antibiotic action
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7652'
abstract:
- lang: eng
text: Organisms cope with change by taking advantage of transcriptional regulators.
However, when faced with rare environments, the evolution of transcriptional regulators
and their promoters may be too slow. Here, we investigate whether the intrinsic
instability of gene duplication and amplification provides a generic alternative
to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations
in Escherichia coli, we show that gene duplications and amplifications enable
adaptation to fluctuating environments by rapidly generating copy-number and,
therefore, expression-level polymorphisms. This amplification-mediated gene expression
tuning (AMGET) occurs on timescales that are similar to canonical gene regulation
and can respond to rapid environmental changes. Mathematical modelling shows that
amplifications also tune gene expression in stochastic environments in which transcription-factor-based
schemes are hard to evolve or maintain. The fleeting nature of gene amplifications
gives rise to a generic population-level mechanism that relies on genetic heterogeneity
to rapidly tune the expression of any gene, without leaving any genomic signature.
acknowledgement: We thank L. Hurst, N. Barton, M. Pleska, M. Steinrück, B. Kavcic
and A. Staron for input on the manuscript, and To. Bergmiller and R. Chait for help
with microfluidics experiments. I.T. is a recipient the OMV fellowship. R.G. is
a recipient of a DOC (Doctoral Fellowship Programme of the Austrian Academy of Sciences)
Fellowship of the Austrian Academy of Sciences.
article_processing_charge: No
article_type: original
author:
- first_name: Isabella
full_name: Tomanek, Isabella
id: 3981F020-F248-11E8-B48F-1D18A9856A87
last_name: Tomanek
orcid: 0000-0001-6197-363X
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: M.
full_name: Lagator, M.
last_name: Lagator
- first_name: A. M. C.
full_name: Andersson, A. M. C.
last_name: Andersson
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level
gene expression regulation. Nature Ecology & Evolution. 2020;4(4):612-625.
doi:10.1038/s41559-020-1132-7
apa: Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik,
G., & Guet, C. C. (2020). Gene amplification as a form of population-level
gene expression regulation. Nature Ecology & Evolution. Springer Nature.
https://doi.org/10.1038/s41559-020-1132-7
chicago: Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P
Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level
Gene Expression Regulation.” Nature Ecology & Evolution. Springer Nature,
2020. https://doi.org/10.1038/s41559-020-1132-7.
ieee: I. Tomanek et al., “Gene amplification as a form of population-level
gene expression regulation,” Nature Ecology & Evolution, vol. 4, no.
4. Springer Nature, pp. 612–625, 2020.
ista: Tomanek I, Grah R, Lagator M, Andersson AMC, Bollback JP, Tkačik G, Guet CC.
2020. Gene amplification as a form of population-level gene expression regulation.
Nature Ecology & Evolution. 4(4), 612–625.
mla: Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level
Gene Expression Regulation.” Nature Ecology & Evolution, vol. 4, no.
4, Springer Nature, 2020, pp. 612–25, doi:10.1038/s41559-020-1132-7.
short: I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkačik,
C.C. Guet, Nature Ecology & Evolution 4 (2020) 612–625.
date_created: 2020-04-08T15:20:53Z
date_published: 2020-04-01T00:00:00Z
date_updated: 2024-03-28T23:30:37Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
- _id: CaGu
doi: 10.1038/s41559-020-1132-7
external_id:
isi:
- '000519008300005'
file:
- access_level: open_access
checksum: ef3bbf42023e30b2c24a6278025d2040
content_type: application/pdf
creator: dernst
date_created: 2020-10-09T09:56:01Z
date_updated: 2020-10-09T09:56:01Z
file_id: '8640'
file_name: 2020_NatureEcolEvo_Tomanek.pdf
file_size: 745242
relation: main_file
success: 1
file_date_updated: 2020-10-09T09:56:01Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 612-625
project:
- _id: 267C84F4-B435-11E9-9278-68D0E5697425
name: Biophysically realistic genotype-phenotype maps for regulatory networks
publication: Nature Ecology & Evolution
publication_identifier:
issn:
- 2397-334X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/
record:
- id: '8155'
relation: dissertation_contains
status: public
- id: '7383'
relation: research_data
status: public
- id: '7016'
relation: research_data
status: public
- id: '8653'
relation: used_in_publication
status: public
scopus_import: '1'
status: public
title: Gene amplification as a form of population-level gene expression regulation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 4
year: '2020'
...
---
_id: '7552'
abstract:
- lang: eng
text: 'There is increasing evidence that protein binding to specific sites along
DNA can activate the reading out of genetic information without coming into direct
physical contact with the gene. There also is evidence that these distant but
interacting sites are embedded in a liquid droplet of proteins which condenses
out of the surrounding solution. We argue that droplet-mediated interactions can
account for crucial features of gene regulation only if the droplet is poised
at a non-generic point in its phase diagram. We explore a minimal model that embodies
this idea, show that this model has a natural mechanism for self-tuning, and suggest
direct experimental tests. '
article_processing_charge: No
author:
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation.
arXiv:191208579.
apa: Bialek, W., Gregor, T., & Tkačik, G. (n.d.). Action at a distance in transcriptional
regulation. arXiv:1912.08579. ArXiv.
chicago: Bialek, William, Thomas Gregor, and Gašper Tkačik. “Action at a Distance
in Transcriptional Regulation.” ArXiv:1912.08579. ArXiv, n.d.
ieee: W. Bialek, T. Gregor, and G. Tkačik, “Action at a distance in transcriptional
regulation,” arXiv:1912.08579. ArXiv.
ista: Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation.
arXiv:1912.08579, .
mla: Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.”
ArXiv:1912.08579, ArXiv.
short: W. Bialek, T. Gregor, G. Tkačik, ArXiv:1912.08579 (n.d.).
date_created: 2020-02-28T10:57:08Z
date_published: 2019-12-18T00:00:00Z
date_updated: 2021-01-12T08:14:09Z
day: '18'
department:
- _id: GaTk
external_id:
arxiv:
- '1912.08579'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1912.08579
month: '12'
oa: 1
oa_version: Preprint
page: '5'
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: arXiv:1912.08579
publication_status: submitted
publisher: ArXiv
status: public
title: Action at a distance in transcriptional regulation
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '5945'
abstract:
- lang: eng
text: In developing organisms, spatially prescribed cell identities are thought
to be determined by the expression levels of multiple genes. Quantitative tests
of this idea, however, require a theoretical framework capable of exposing the
rules and precision of cell specification over developmental time. We use the
gap gene network in the early fly embryo as an example to show how expression
levels of the four gap genes can be jointly decoded into an optimal specification
of position with 1% accuracy. The decoder correctly predicts, with no free parameters,
the dynamics of pair-rule expression patterns at different developmental time
points and in various mutant backgrounds. Precise cellular identities are thus
available at the earliest stages of development, contrasting the prevailing view
of positional information being slowly refined across successive layers of the
patterning network. Our results suggest that developmental enhancers closely approximate
a mathematically optimal decoding strategy.
article_processing_charge: No
article_type: original
author:
- first_name: Mariela D.
full_name: Petkova, Mariela D.
last_name: Petkova
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Eric F.
full_name: Wieschaus, Eric F.
last_name: Wieschaus
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
citation:
ama: Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. Optimal decoding of
cellular identities in a genetic network. Cell. 2019;176(4):844-855.e15.
doi:10.1016/j.cell.2019.01.007
apa: Petkova, M. D., Tkačik, G., Bialek, W., Wieschaus, E. F., & Gregor, T.
(2019). Optimal decoding of cellular identities in a genetic network. Cell.
Cell Press. https://doi.org/10.1016/j.cell.2019.01.007
chicago: Petkova, Mariela D., Gašper Tkačik, William Bialek, Eric F. Wieschaus,
and Thomas Gregor. “Optimal Decoding of Cellular Identities in a Genetic Network.”
Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.01.007.
ieee: M. D. Petkova, G. Tkačik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal
decoding of cellular identities in a genetic network,” Cell, vol. 176,
no. 4. Cell Press, p. 844–855.e15, 2019.
ista: Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. 2019. Optimal decoding
of cellular identities in a genetic network. Cell. 176(4), 844–855.e15.
mla: Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic
Network.” Cell, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:10.1016/j.cell.2019.01.007.
short: M.D. Petkova, G. Tkačik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019)
844–855.e15.
date_created: 2019-02-10T22:59:16Z
date_published: 2019-02-07T00:00:00Z
date_updated: 2023-08-24T14:42:47Z
day: '07'
department:
- _id: GaTk
doi: 10.1016/j.cell.2019.01.007
external_id:
isi:
- '000457969200015'
pmid:
- '30712870'
intvolume: ' 176'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2019.01.007
month: '02'
oa: 1
oa_version: Published Version
page: 844-855.e15
pmid: 1
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Cell
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/cells-find-their-identity-using-a-mathematically-optimal-strategy/
scopus_import: '1'
status: public
title: Optimal decoding of cellular identities in a genetic network
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 176
year: '2019'
...
---
_id: '6049'
abstract:
- lang: eng
text: 'In this article it is shown that large systems with many interacting units
endowing multiple phases display self-oscillations in the presence of linear feedback
between the control and order parameters, where an Andronov–Hopf bifurcation takes
over the phase transition. This is simply illustrated through the mean field Landau
theory whose feedback dynamics turn out to be described by the Van der Pol equation
and it is then validated for the fully connected Ising model following heat bath
dynamics. Despite its simplicity, this theory accounts potentially for a rich
range of phenomena: here it is applied to describe in a stylized way (i) excess
demand-price cycles due to strong herding in a simple agent-based market model;
(ii) congestion waves in queuing networks triggered by user feedback to delays
in overloaded conditions; and (iii) metabolic network oscillations resulting from
cell growth control in a bistable phenotypic landscape.'
article_number: '045002'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: 'De Martino D. Feedback-induced self-oscillations in large interacting systems
subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical.
2019;52(4). doi:10.1088/1751-8121/aaf2dd'
apa: 'De Martino, D. (2019). Feedback-induced self-oscillations in large interacting
systems subjected to phase transitions. Journal of Physics A: Mathematical
and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/aaf2dd'
chicago: 'De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting
Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical
and Theoretical. IOP Publishing, 2019. https://doi.org/10.1088/1751-8121/aaf2dd.'
ieee: 'D. De Martino, “Feedback-induced self-oscillations in large interacting systems
subjected to phase transitions,” Journal of Physics A: Mathematical and Theoretical,
vol. 52, no. 4. IOP Publishing, 2019.'
ista: 'De Martino D. 2019. Feedback-induced self-oscillations in large interacting
systems subjected to phase transitions. Journal of Physics A: Mathematical and
Theoretical. 52(4), 045002.'
mla: 'De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting
Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical
and Theoretical, vol. 52, no. 4, 045002, IOP Publishing, 2019, doi:10.1088/1751-8121/aaf2dd.'
short: 'D. De Martino, Journal of Physics A: Mathematical and Theoretical 52 (2019).'
date_created: 2019-02-24T22:59:19Z
date_published: 2019-01-07T00:00:00Z
date_updated: 2023-08-24T14:49:23Z
day: '07'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1088/1751-8121/aaf2dd
ec_funded: 1
external_id:
isi:
- '000455379500001'
file:
- access_level: open_access
checksum: 1112304ad363a6d8afaeccece36473cf
content_type: application/pdf
creator: kschuh
date_created: 2019-04-19T12:18:57Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6344'
file_name: 2019_IOP_DeMartino.pdf
file_size: 1804557
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
intvolume: ' 52'
isi: 1
issue: '4'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: 'Journal of Physics A: Mathematical and Theoretical'
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Feedback-induced self-oscillations in large interacting systems subjected to
phase transitions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 52
year: '2019'
...
---
_id: '6046'
abstract:
- lang: eng
text: Sudden stress often triggers diverse, temporally structured gene expression
responses in microbes, but it is largely unknown how variable in time such responses
are and if genes respond in the same temporal order in every single cell. Here,
we quantified timing variability of individual promoters responding to sublethal
antibiotic stress using fluorescent reporters, microfluidics, and time‐lapse microscopy.
We identified lower and upper bounds that put definite constraints on timing variability,
which varies strongly among promoters and conditions. Timing variability can be
interpreted using results from statistical kinetics, which enable us to estimate
the number of rate‐limiting molecular steps underlying different responses. We
found that just a few critical steps control some responses while others rely
on dozens of steps. To probe connections between different stress responses, we
then tracked the temporal order and response time correlations of promoter pairs
in individual cells. Our results support that, when bacteria are exposed to the
antibiotic nitrofurantoin, the ensuing oxidative stress and SOS responses are
part of the same causal chain of molecular events. In contrast, under trimethoprim,
the acid stress response and the SOS response are part of different chains of
events running in parallel. Our approach reveals fundamental constraints on gene
expression timing and provides new insights into the molecular events that underlie
the timing of stress responses.
acknowledged_ssus:
- _id: Bio
article_number: e8470
article_processing_charge: No
author:
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
- first_name: Georg
full_name: Rieckh, Georg
id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87
last_name: Rieckh
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Mitosch K, Rieckh G, Bollenbach MT. Temporal order and precision of complex
stress responses in individual bacteria. Molecular systems biology. 2019;15(2).
doi:10.15252/msb.20188470
apa: Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2019). Temporal order and
precision of complex stress responses in individual bacteria. Molecular Systems
Biology. Embo Press. https://doi.org/10.15252/msb.20188470
chicago: Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Temporal Order
and Precision of Complex Stress Responses in Individual Bacteria.” Molecular
Systems Biology. Embo Press, 2019. https://doi.org/10.15252/msb.20188470.
ieee: K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Temporal order and precision
of complex stress responses in individual bacteria,” Molecular systems biology,
vol. 15, no. 2. Embo Press, 2019.
ista: Mitosch K, Rieckh G, Bollenbach MT. 2019. Temporal order and precision of
complex stress responses in individual bacteria. Molecular systems biology. 15(2),
e8470.
mla: Mitosch, Karin, et al. “Temporal Order and Precision of Complex Stress Responses
in Individual Bacteria.” Molecular Systems Biology, vol. 15, no. 2, e8470,
Embo Press, 2019, doi:10.15252/msb.20188470.
short: K. Mitosch, G. Rieckh, M.T. Bollenbach, Molecular Systems Biology 15 (2019).
date_created: 2019-02-24T22:59:18Z
date_published: 2019-02-14T00:00:00Z
date_updated: 2023-08-24T14:49:53Z
day: '14'
department:
- _id: GaTk
doi: 10.15252/msb.20188470
external_id:
isi:
- '000459628300003'
pmid:
- '30765425'
intvolume: ' 15'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30765425
month: '02'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
publication: Molecular systems biology
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Temporal order and precision of complex stress responses in individual bacteria
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2019'
...
---
_id: '6784'
abstract:
- lang: eng
text: Mathematical models have been used successfully at diverse scales of biological
organization, ranging from ecology and population dynamics to stochastic reaction
events occurring between individual molecules in single cells. Generally, many
biological processes unfold across multiple scales, with mutations being the best
studied example of how stochasticity at the molecular scale can influence outcomes
at the population scale. In many other contexts, however, an analogous link between
micro- and macro-scale remains elusive, primarily due to the challenges involved
in setting up and analyzing multi-scale models. Here, we employ such a model to
investigate how stochasticity propagates from individual biochemical reaction
events in the bacterial innate immune system to the ecology of bacteria and bacterial
viruses. We show analytically how the dynamics of bacterial populations are shaped
by the activities of immunity-conferring enzymes in single cells and how the ecological
consequences imply optimal bacterial defense strategies against viruses. Our results
suggest that bacterial populations in the presence of viruses can either optimize
their initial growth rate or their population size, with the first strategy favoring
simple immunity featuring a single restriction modification system and the second
strategy favoring complex bacterial innate immunity featuring several simultaneously
active restriction modification systems.
article_number: e1007168
article_processing_charge: No
article_type: original
author:
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Ruess J, Pleska M, Guet CC, Tkačik G. Molecular noise of innate immunity shapes
bacteria-phage ecologies. PLoS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007168
apa: Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Molecular noise
of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007168
chicago: Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Molecular
Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational
Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.
ieee: J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Molecular noise of innate
immunity shapes bacteria-phage ecologies,” PLoS Computational Biology,
vol. 15, no. 7. Public Library of Science, 2019.
ista: Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Molecular noise of innate immunity
shapes bacteria-phage ecologies. PLoS Computational Biology. 15(7), e1007168.
mla: Ruess, Jakob, et al. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage
Ecologies.” PLoS Computational Biology, vol. 15, no. 7, e1007168, Public
Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.
short: J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, PLoS Computational Biology 15
(2019).
date_created: 2019-08-11T21:59:19Z
date_published: 2019-07-02T00:00:00Z
date_updated: 2023-08-29T07:10:06Z
day: '02'
ddc:
- '570'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pcbi.1007168
external_id:
isi:
- '000481577700032'
file:
- access_level: open_access
checksum: 7ded4721b41c2a0fc66a1c634540416a
content_type: application/pdf
creator: dernst
date_created: 2019-08-12T12:27:26Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6803'
file_name: 2019_PlosComputBiology_Ruess.pdf
file_size: 2200003
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 251D65D8-B435-11E9-9278-68D0E5697425
grant_number: '24210'
name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems
at the Single-Cell Level
- _id: 251BCBEC-B435-11E9-9278-68D0E5697425
grant_number: RGY0079/2011
name: Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification
Systems
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '9786'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Molecular noise of innate immunity shapes bacteria-phage ecologies
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2019'
...
---
_id: '9786'
article_processing_charge: No
author:
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Ruess J, Pleska M, Guet CC, Tkačik G. Supporting text and results. 2019. doi:10.1371/journal.pcbi.1007168.s001
apa: Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Supporting text
and results. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007168.s001
chicago: Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Supporting
Text and Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.s001.
ieee: J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Supporting text and results.”
Public Library of Science, 2019.
ista: Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Supporting text and results, Public
Library of Science, 10.1371/journal.pcbi.1007168.s001.
mla: Ruess, Jakob, et al. Supporting Text and Results. Public Library of
Science, 2019, doi:10.1371/journal.pcbi.1007168.s001.
short: J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, (2019).
date_created: 2021-08-06T08:23:43Z
date_published: 2019-07-02T00:00:00Z
date_updated: 2023-08-29T07:10:05Z
day: '02'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pcbi.1007168.s001
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '6784'
relation: used_in_publication
status: public
status: public
title: Supporting text and results
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '7422'
abstract:
- lang: eng
text: Biochemical reactions often occur at low copy numbers but at once in crowded
and diverse environments. Space and stochasticity therefore play an essential
role in biochemical networks. Spatial-stochastic simulations have become a prominent
tool for understanding how stochasticity at the microscopic level influences the
macroscopic behavior of such systems. While particle-based models guarantee the
level of detail necessary to accurately describe the microscopic dynamics at very
low copy numbers, the algorithms used to simulate them typically imply trade-offs
between computational efficiency and biochemical accuracy. eGFRD (enhanced Green’s
Function Reaction Dynamics) is an exact algorithm that evades such trade-offs
by partitioning the N-particle system into M ≤ N analytically tractable one- and
two-particle systems; the analytical solutions (Green’s functions) then are used
to implement an event-driven particle-based scheme that allows particles to make
large jumps in time and space while retaining access to their state variables
at arbitrary simulation times. Here we present “eGFRD2,” a new eGFRD version that
implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based
simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on
2D planes representing membranes, and on 1D elongated cylinders representative
of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion
used to model active transport. We find that, for low particle densities, eGFRD2
is up to 6 orders of magnitude faster than conventional Brownian dynamics. We
exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1
gradient formation, which involves 3D diffusion, active transport on microtubules,
and autophosphorylation on the membrane, confirming recent experimental and theoretical
results on this system to hold under genuinely stochastic conditions.
article_number: '054108'
article_processing_charge: No
article_type: original
author:
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Joris
full_name: Paijmans, Joris
last_name: Paijmans
- first_name: Laurens
full_name: Bossen, Laurens
last_name: Bossen
- first_name: Thomas
full_name: Miedema, Thomas
last_name: Miedema
- first_name: Martijn
full_name: Wehrens, Martijn
last_name: Wehrens
- first_name: Nils B.
full_name: Becker, Nils B.
last_name: Becker
- first_name: Kazunari
full_name: Kaizu, Kazunari
last_name: Kaizu
- first_name: Koichi
full_name: Takahashi, Koichi
last_name: Takahashi
- first_name: Marileen
full_name: Dogterom, Marileen
last_name: Dogterom
- first_name: Pieter Rein
full_name: ten Wolde, Pieter Rein
last_name: ten Wolde
citation:
ama: Sokolowski TR, Paijmans J, Bossen L, et al. eGFRD in all dimensions. The
Journal of Chemical Physics. 2019;150(5). doi:10.1063/1.5064867
apa: Sokolowski, T. R., Paijmans, J., Bossen, L., Miedema, T., Wehrens, M., Becker,
N. B., … ten Wolde, P. R. (2019). eGFRD in all dimensions. The Journal of Chemical
Physics. AIP Publishing. https://doi.org/10.1063/1.5064867
chicago: Sokolowski, Thomas R, Joris Paijmans, Laurens Bossen, Thomas Miedema, Martijn
Wehrens, Nils B. Becker, Kazunari Kaizu, Koichi Takahashi, Marileen Dogterom,
and Pieter Rein ten Wolde. “EGFRD in All Dimensions.” The Journal of Chemical
Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5064867.
ieee: T. R. Sokolowski et al., “eGFRD in all dimensions,” The Journal
of Chemical Physics, vol. 150, no. 5. AIP Publishing, 2019.
ista: Sokolowski TR, Paijmans J, Bossen L, Miedema T, Wehrens M, Becker NB, Kaizu
K, Takahashi K, Dogterom M, ten Wolde PR. 2019. eGFRD in all dimensions. The Journal
of Chemical Physics. 150(5), 054108.
mla: Sokolowski, Thomas R., et al. “EGFRD in All Dimensions.” The Journal of
Chemical Physics, vol. 150, no. 5, 054108, AIP Publishing, 2019, doi:10.1063/1.5064867.
short: T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker,
K. Kaizu, K. Takahashi, M. Dogterom, P.R. ten Wolde, The Journal of Chemical Physics
150 (2019).
date_created: 2020-01-30T10:34:36Z
date_published: 2019-02-07T00:00:00Z
date_updated: 2023-09-06T14:59:28Z
day: '07'
department:
- _id: GaTk
doi: 10.1063/1.5064867
external_id:
arxiv:
- '1708.09364'
isi:
- '000458109300009'
intvolume: ' 150'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.09364
month: '02'
oa: 1
oa_version: Preprint
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
status: public
title: eGFRD in all dimensions
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 150
year: '2019'
...
---
_id: '6900'
abstract:
- lang: eng
text: Across diverse biological systems—ranging from neural networks to intracellular
signaling and genetic regulatory networks—the information about changes in the
environment is frequently encoded in the full temporal dynamics of the network
nodes. A pressing data-analysis challenge has thus been to efficiently estimate
the amount of information that these dynamics convey from experimental data. Here
we develop and evaluate decoding-based estimation methods to lower bound the mutual
information about a finite set of inputs, encoded in single-cell high-dimensional
time series data. For biological reaction networks governed by the chemical Master
equation, we derive model-based information approximations and analytical upper
bounds, against which we benchmark our proposed model-free decoding estimators.
In contrast to the frequently-used k-nearest-neighbor estimator, decoding-based
estimators robustly extract a large fraction of the available information from
high-dimensional trajectories with a realistic number of data samples. We apply
these estimators to previously published data on Erk and Ca2+ signaling in mammalian
cells and to yeast stress-response, and find that substantial amount of information
about environmental state can be encoded by non-trivial response statistics even
in stationary signals. We argue that these single-cell, decoding-based information
estimates, rather than the commonly-used tests for significant differences between
selected population response statistics, provide a proper and unbiased measure
for the performance of biological signaling networks.
article_processing_charge: No
author:
- first_name: Sarah A
full_name: Cepeda Humerez, Sarah A
id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87
last_name: Cepeda Humerez
- first_name: Jakob
full_name: Ruess, Jakob
last_name: Ruess
orcid: 0000-0003-1615-3282
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Cepeda Humerez SA, Ruess J, Tkačik G. Estimating information in time-varying
signals. PLoS computational biology. 2019;15(9):e1007290. doi:10.1371/journal.pcbi.1007290
apa: Cepeda Humerez, S. A., Ruess, J., & Tkačik, G. (2019). Estimating information
in time-varying signals. PLoS Computational Biology. Public Library of
Science. https://doi.org/10.1371/journal.pcbi.1007290
chicago: Cepeda Humerez, Sarah A, Jakob Ruess, and Gašper Tkačik. “Estimating Information
in Time-Varying Signals.” PLoS Computational Biology. Public Library of
Science, 2019. https://doi.org/10.1371/journal.pcbi.1007290.
ieee: S. A. Cepeda Humerez, J. Ruess, and G. Tkačik, “Estimating information in
time-varying signals,” PLoS computational biology, vol. 15, no. 9. Public
Library of Science, p. e1007290, 2019.
ista: Cepeda Humerez SA, Ruess J, Tkačik G. 2019. Estimating information in time-varying
signals. PLoS computational biology. 15(9), e1007290.
mla: Cepeda Humerez, Sarah A., et al. “Estimating Information in Time-Varying Signals.”
PLoS Computational Biology, vol. 15, no. 9, Public Library of Science,
2019, p. e1007290, doi:10.1371/journal.pcbi.1007290.
short: S.A. Cepeda Humerez, J. Ruess, G. Tkačik, PLoS Computational Biology 15 (2019)
e1007290.
date_created: 2019-09-22T22:00:37Z
date_published: 2019-09-03T00:00:00Z
date_updated: 2023-09-07T12:55:21Z
day: '03'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1007290
external_id:
isi:
- '000489741800021'
pmid:
- '31479447'
file:
- access_level: open_access
checksum: 81bdce1361c9aa8395d6fa635fb6ab47
content_type: application/pdf
creator: kschuh
date_created: 2019-10-01T10:53:45Z
date_updated: 2020-07-14T12:47:44Z
file_id: '6925'
file_name: 2019_PLoS_Cepeda-Humerez.pdf
file_size: 3081855
relation: main_file
file_date_updated: 2020-07-14T12:47:44Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: e1007290
pmid: 1
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: PLoS computational biology
publication_identifier:
eissn:
- '15537358'
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '6473'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Estimating information in time-varying signals
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2019'
...
---
_id: '196'
abstract:
- lang: eng
text: 'The abelian sandpile serves as a model to study self-organized criticality,
a phenomenon occurring in biological, physical and social processes. The identity
of the abelian group is a fractal composed of self-similar patches, and its limit
is subject of extensive collaborative research. Here, we analyze the evolution
of the sandpile identity under harmonic fields of different orders. We show that
this evolution corresponds to periodic cycles through the abelian group characterized
by the smooth transformation and apparent conservation of the patches constituting
the identity. The dynamics induced by second and third order harmonics resemble
smooth stretchings, respectively translations, of the identity, while the ones
induced by fourth order harmonics resemble magnifications and rotations. Starting
with order three, the dynamics pass through extended regions of seemingly random
configurations which spontaneously reassemble into accentuated patterns. We show
that the space of harmonic functions projects to the extended analogue of the
sandpile group, thus providing a set of universal coordinates identifying configurations
between different domains. Since the original sandpile group is a subgroup of
the extended one, this directly implies that it admits a natural renormalization.
Furthermore, we show that the harmonic fields can be induced by simple Markov
processes, and that the corresponding stochastic dynamics show remarkable robustness
over hundreds of periods. Finally, we encode information into seemingly random
configurations, and decode this information with an algorithm requiring minimal
prior knowledge. Our results suggest that harmonic fields might split the sandpile
group into sub-sets showing different critical coefficients, and that it might
be possible to extend the fractal structure of the identity beyond the boundaries
of its domain. '
acknowledgement: "M.L. is grateful to the members of the C Guet and G Tkacik groups
for valuable comments and support. M.S. is grateful to Nikita Kalinin for inspiring
communications.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Mikhail
full_name: Shkolnikov, Mikhail
id: 35084A62-F248-11E8-B48F-1D18A9856A87
last_name: Shkolnikov
orcid: 0000-0002-4310-178X
citation:
ama: Lang M, Shkolnikov M. Harmonic dynamics of the Abelian sandpile. Proceedings
of the National Academy of Sciences. 2019;116(8):2821-2830. doi:10.1073/pnas.1812015116
apa: Lang, M., & Shkolnikov, M. (2019). Harmonic dynamics of the Abelian sandpile.
Proceedings of the National Academy of Sciences. National Academy of Sciences.
https://doi.org/10.1073/pnas.1812015116
chicago: Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian
Sandpile.” Proceedings of the National Academy of Sciences. National Academy
of Sciences, 2019. https://doi.org/10.1073/pnas.1812015116.
ieee: M. Lang and M. Shkolnikov, “Harmonic dynamics of the Abelian sandpile,” Proceedings
of the National Academy of Sciences, vol. 116, no. 8. National Academy of
Sciences, pp. 2821–2830, 2019.
ista: Lang M, Shkolnikov M. 2019. Harmonic dynamics of the Abelian sandpile. Proceedings
of the National Academy of Sciences. 116(8), 2821–2830.
mla: Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.”
Proceedings of the National Academy of Sciences, vol. 116, no. 8, National
Academy of Sciences, 2019, pp. 2821–30, doi:10.1073/pnas.1812015116.
short: M. Lang, M. Shkolnikov, Proceedings of the National Academy of Sciences 116
(2019) 2821–2830.
date_created: 2018-12-11T11:45:08Z
date_published: 2019-02-19T00:00:00Z
date_updated: 2023-09-11T14:09:34Z
day: '19'
department:
- _id: CaGu
- _id: GaTk
- _id: TaHa
doi: 10.1073/pnas.1812015116
external_id:
arxiv:
- '1806.10823'
isi:
- '000459074400013'
pmid:
- ' 30728300'
intvolume: ' 116'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1812015116
month: '02'
oa: 1
oa_version: Published Version
page: 2821-2830
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/famous-sandpile-model-shown-to-move-like-a-traveling-sand-dune/
scopus_import: '1'
status: public
title: Harmonic dynamics of the Abelian sandpile
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 116
year: '2019'
...
---
_id: '5817'
abstract:
- lang: eng
text: We theoretically study the shapes of lipid vesicles confined to a spherical
cavity, elaborating a framework based on the so-called limiting shapes constructed
from geometrically simple structural elements such as double-membrane walls and
edges. Partly inspired by numerical results, the proposed non-compartmentalized
and compartmentalized limiting shapes are arranged in the bilayer-couple phase
diagram which is then compared to its free-vesicle counterpart. We also compute
the area-difference-elasticity phase diagram of the limiting shapes and we use
it to interpret shape transitions experimentally observed in vesicles confined
within another vesicle. The limiting-shape framework may be generalized to theoretically
investigate the structure of certain cell organelles such as the mitochondrion.
article_processing_charge: No
article_type: original
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: A.
full_name: Sakashita, A.
last_name: Sakashita
- first_name: H.
full_name: Noguchi, H.
last_name: Noguchi
- first_name: P.
full_name: Ziherl, P.
last_name: Ziherl
citation:
ama: Kavcic B, Sakashita A, Noguchi H, Ziherl P. Limiting shapes of confined lipid
vesicles. Soft Matter. 2019;15(4):602-614. doi:10.1039/c8sm01956h
apa: Kavcic, B., Sakashita, A., Noguchi, H., & Ziherl, P. (2019). Limiting shapes
of confined lipid vesicles. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c8sm01956h
chicago: Kavcic, Bor, A. Sakashita, H. Noguchi, and P. Ziherl. “Limiting Shapes
of Confined Lipid Vesicles.” Soft Matter. Royal Society of Chemistry, 2019.
https://doi.org/10.1039/c8sm01956h.
ieee: B. Kavcic, A. Sakashita, H. Noguchi, and P. Ziherl, “Limiting shapes of confined
lipid vesicles,” Soft Matter, vol. 15, no. 4. Royal Society of Chemistry,
pp. 602–614, 2019.
ista: Kavcic B, Sakashita A, Noguchi H, Ziherl P. 2019. Limiting shapes of confined
lipid vesicles. Soft Matter. 15(4), 602–614.
mla: Kavcic, Bor, et al. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter,
vol. 15, no. 4, Royal Society of Chemistry, 2019, pp. 602–14, doi:10.1039/c8sm01956h.
short: B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614.
date_created: 2019-01-11T07:37:47Z
date_published: 2019-01-10T00:00:00Z
date_updated: 2023-09-13T08:47:16Z
day: '10'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.1039/c8sm01956h
external_id:
isi:
- '000457329700003'
pmid:
- '30629082'
file:
- access_level: open_access
checksum: 614c337d6424ccd3d48d1b1f9513510d
content_type: application/pdf
creator: bkavcic
date_created: 2020-10-09T11:00:05Z
date_updated: 2020-10-09T11:00:05Z
file_id: '8641'
file_name: lmt_sftmtr_V8.pdf
file_size: 5370762
relation: main_file
success: 1
file_date_updated: 2020-10-09T11:00:05Z
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isi: 1
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language:
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license: https://creativecommons.org/licenses/by-nc-nd/3.0/
month: '01'
oa: 1
oa_version: Submitted Version
page: 602-614
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Limiting shapes of confined lipid vesicles
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND
3.0)
short: CC BY-NC-ND (3.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 15
year: '2019'
...
---
_id: '6473'
abstract:
- lang: eng
text: "Single cells are constantly interacting with their environment and each other,
more importantly, the accurate perception of environmental cues is crucial for
growth, survival, and reproduction. This communication between cells and their
environment can be formalized in mathematical terms and be quantified as the information
flow between them, as prescribed by information theory. \r\nThe recent availability
of real–time dynamical patterns of signaling molecules in single cells has allowed
us to identify encoding about the identity of the environment in the time–series.
However, efficient estimation of the information transmitted by these signals
has been a data–analysis challenge due to the high dimensionality of the trajectories
and the limited number of samples. In the first part of this thesis, we develop
and evaluate decoding–based estimation methods to lower bound the mutual information
and derive model–based precise information estimates for biological reaction networks
governed by the chemical master equation. This is followed by applying the decoding-based
methods to study the intracellular representation of extracellular changes in
budding yeast, by observing the transient dynamics of nuclear translocation of
10 transcription factors in response to 3 stress conditions. Additionally, we
apply these estimators to previously published data on ERK and Ca2+ signaling
and yeast stress response. We argue that this single cell decoding-based measure
of information provides an unbiased, quantitative and interpretable measure for
the fidelity of biological signaling processes. \r\nFinally, in the last section,
we deal with gene regulation which is primarily controlled by transcription factors
(TFs) that bind to the DNA to activate gene expression. The possibility that non-cognate
TFs activate transcription diminishes the accuracy of regulation with potentially
disastrous effects for the cell. This ’crosstalk’ acts as a previously unexplored
source of noise in biochemical networks and puts a strong constraint on their
performance. To mitigate erroneous initiation we propose an out of equilibrium
scheme that implements kinetic proofreading. We show that such architectures are
favored over their equilibrium counterparts for complex organisms despite introducing
noise in gene expression. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sarah A
full_name: Cepeda Humerez, Sarah A
id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87
last_name: Cepeda Humerez
citation:
ama: Cepeda Humerez SA. Estimating information flow in single cells. 2019. doi:10.15479/AT:ISTA:6473
apa: Cepeda Humerez, S. A. (2019). Estimating information flow in single cells.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6473
chicago: Cepeda Humerez, Sarah A. “Estimating Information Flow in Single Cells.”
Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6473.
ieee: S. A. Cepeda Humerez, “Estimating information flow in single cells,” Institute
of Science and Technology Austria, 2019.
ista: Cepeda Humerez SA. 2019. Estimating information flow in single cells. Institute
of Science and Technology Austria.
mla: Cepeda Humerez, Sarah A. Estimating Information Flow in Single Cells.
Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6473.
short: S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, Institute
of Science and Technology Austria, 2019.
date_created: 2019-05-21T00:11:23Z
date_published: 2019-05-23T00:00:00Z
date_updated: 2023-09-19T15:13:26Z
day: '23'
ddc:
- '004'
degree_awarded: PhD
department:
- _id: GaTk
doi: 10.15479/AT:ISTA:6473
file:
- access_level: closed
checksum: 75f9184c1346e10a5de5f9cc7338309a
content_type: application/zip
creator: scepeda
date_created: 2019-05-23T11:18:16Z
date_updated: 2020-07-14T12:47:31Z
file_id: '6480'
file_name: Thesis_Cepeda.zip
file_size: 23937464
relation: source_file
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checksum: afdc0633ddbd71d5b13550d7fb4f4454
content_type: application/pdf
creator: scepeda
date_created: 2019-05-23T11:18:13Z
date_updated: 2020-07-14T12:47:31Z
file_id: '6481'
file_name: CepedaThesis.pdf
file_size: 16646985
relation: main_file
file_date_updated: 2020-07-14T12:47:31Z
has_accepted_license: '1'
keyword:
- Information estimation
- Time-series
- data analysis
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '135'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1576'
relation: dissertation_contains
status: public
- id: '6900'
relation: dissertation_contains
status: public
- id: '281'
relation: dissertation_contains
status: public
- id: '2016'
relation: dissertation_contains
status: public
status: public
supervisor:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Estimating information flow in single cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6071'
abstract:
- lang: eng
text: 'Transcription factors, by binding to specific sequences on the DNA, control
the precise spatio-temporal expression of genes inside a cell. However, this specificity
is limited, leading to frequent incorrect binding of transcription factors that
might have deleterious consequences on the cell. By constructing a biophysical
model of TF-DNA binding in the context of gene regulation, I will first explore
how regulatory constraints can strongly shape the distribution of a population
in sequence space. Then, by directly linking this to a picture of multiple types
of transcription factors performing their functions simultaneously inside the
cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions
between transcription factors and binding sites that lead to erroneous regulatory
states -- and understand the constraints this places on the design of regulatory
systems. I will then develop a generic theoretical framework to investigate the
coevolution of multiple transcription factors and multiple binding sites, in the
context of a gene regulatory network that performs a certain function. As a particular
tractable version of this problem, I will consider the evolution of two transcription
factors when they transmit upstream signals to downstream target genes. Specifically,
I will describe the evolutionary steady states and the evolutionary pathways involved,
along with their timescales, of a system that initially undergoes a transcription
factor duplication event. To connect this important theoretical model to the prominent
biological event of transcription factor duplication giving rise to paralogous
families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription
factors, a major family in humans, and focus on the patterns of evolution that
paralogs have undergone in their various protein domains in the recent past. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
citation:
ama: Prizak R. Coevolution of transcription factors and their binding sites in sequence
space. 2019. doi:10.15479/at:ista:th6071
apa: Prizak, R. (2019). Coevolution of transcription factors and their binding
sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071
chicago: Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding
Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071.
ieee: R. Prizak, “Coevolution of transcription factors and their binding sites in
sequence space,” Institute of Science and Technology Austria, 2019.
ista: Prizak R. 2019. Coevolution of transcription factors and their binding sites
in sequence space. Institute of Science and Technology Austria.
mla: Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites
in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071.
short: R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in
Sequence Space, Institute of Science and Technology Austria, 2019.
date_created: 2019-03-06T16:16:10Z
date_published: 2019-03-11T00:00:00Z
date_updated: 2023-09-22T10:00:48Z
day: '11'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GaTk
- _id: NiBa
doi: 10.15479/at:ista:th6071
file:
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checksum: e60a72de35d270b31f1a23d50f224ec0
content_type: application/pdf
creator: rprizak
date_created: 2019-03-06T16:05:07Z
date_updated: 2020-07-14T12:47:18Z
file_id: '6072'
file_name: Thesis_final_PDFA_RoshanPrizak.pdf
file_size: 20995465
relation: main_file
- access_level: closed
checksum: 67c2630333d05ebafef5f018863a8465
content_type: application/zip
creator: rprizak
date_created: 2019-03-06T16:09:39Z
date_updated: 2020-07-14T12:47:18Z
file_id: '6073'
file_name: thesis_v2_merge.zip
file_size: 85705272
relation: source_file
title: Latex files
file_date_updated: 2020-07-14T12:47:18Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '189'
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1358'
relation: part_of_dissertation
status: public
- id: '955'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Coevolution of transcription factors and their binding sites in sequence space
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '7103'
abstract:
- lang: eng
text: Origin and functions of intermittent transitions among sleep stages, including
short awakenings and arousals, constitute a challenge to the current homeostatic
framework for sleep regulation, focusing on factors modulating sleep over large
time scales. Here we propose that the complex micro-architecture characterizing
the sleep-wake cycle results from an underlying non-equilibrium critical dynamics,
bridging collective behaviors across spatio-temporal scales. We investigate θ
and δ wave dynamics in control rats and in rats with lesions of sleep-promoting
neurons in the parafacial zone. We demonstrate that intermittent bursts in θ and
δ rhythms exhibit a complex temporal organization, with long-range power-law correlations
and a robust duality of power law (θ-bursts, active phase) and exponential-like
(δ-bursts, quiescent phase) duration distributions, typical features of non-equilibrium
systems self-organizing at criticality. Crucially, such temporal organization
relates to anti-correlated coupling between θ- and δ-bursts, and is independent
of the dominant physiologic state and lesions, a solid indication of a basic principle
in sleep dynamics.
article_number: e1007268
article_processing_charge: No
article_type: original
author:
- first_name: Jilin W. J. L.
full_name: Wang, Jilin W. J. L.
last_name: Wang
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Xiyun
full_name: Zhang, Xiyun
last_name: Zhang
- first_name: Christelle
full_name: Anaclet, Christelle
last_name: Anaclet
- first_name: Plamen Ch.
full_name: Ivanov, Plamen Ch.
last_name: Ivanov
citation:
ama: Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. Non-equilibrium critical
dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and
wake micro-architecture. PLoS Computational Biology. 2019;15(11). doi:10.1371/journal.pcbi.1007268
apa: Wang, J. W. J. L., Lombardi, F., Zhang, X., Anaclet, C., & Ivanov, P. C.
(2019). Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental
characteristic of sleep and wake micro-architecture. PLoS Computational Biology.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007268
chicago: Wang, Jilin W. J. L., Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet,
and Plamen Ch. Ivanov. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ
Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” PLoS
Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007268.
ieee: J. W. J. L. Wang, F. Lombardi, X. Zhang, C. Anaclet, and P. C. Ivanov, “Non-equilibrium
critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of
sleep and wake micro-architecture,” PLoS Computational Biology, vol. 15,
no. 11. Public Library of Science, 2019.
ista: Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. 2019. Non-equilibrium
critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of
sleep and wake micro-architecture. PLoS Computational Biology. 15(11), e1007268.
mla: Wang, Jilin W. J. L., et al. “Non-Equilibrium Critical Dynamics of Bursts in
θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.”
PLoS Computational Biology, vol. 15, no. 11, e1007268, Public Library of
Science, 2019, doi:10.1371/journal.pcbi.1007268.
short: J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational
Biology 15 (2019).
date_created: 2019-11-25T08:20:47Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-10-17T12:30:07Z
day: '01'
ddc:
- '570'
- '000'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1007268
ec_funded: 1
external_id:
isi:
- '000500976100014'
pmid:
- '31725712'
file:
- access_level: open_access
checksum: 2a096a9c6dcc6eaa94077b2603bc6c12
content_type: application/pdf
creator: dernst
date_created: 2019-11-25T08:24:01Z
date_updated: 2020-07-14T12:47:49Z
file_id: '7104'
file_name: 2019_PLOSComBio_Wang.pdf
file_size: 3982516
relation: main_file
file_date_updated: 2020-07-14T12:47:49Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: PLoS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental
characteristic of sleep and wake micro-architecture
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2019'
...
---
_id: '6090'
abstract:
- lang: eng
text: Cells need to reliably sense external ligand concentrations to achieve various
biological functions such as chemotaxis or signaling. The molecular recognition
of ligands by surface receptors is degenerate in many systems, leading to crosstalk
between ligand-receptor pairs. Crosstalk is often thought of as a deviation from
optimal specific recognition, as the binding of noncognate ligands can interfere
with the detection of the receptor's cognate ligand, possibly leading to a false
triggering of a downstream signaling pathway. Here we quantify the optimal precision
of sensing the concentrations of multiple ligands by a collection of promiscuous
receptors. We demonstrate that crosstalk can improve precision in concentration
sensing and discrimination tasks. To achieve superior precision, the additional
information about ligand concentrations contained in short binding events of the
noncognate ligand should be exploited. We present a proofreading scheme to realize
an approximate estimation of multiple ligand concentrations that reaches a precision
close to the derived optimal bounds. Our results help rationalize the observed
ubiquity of receptor crosstalk in molecular sensing.
article_number: '022423'
article_processing_charge: No
author:
- first_name: Martín
full_name: Carballo-Pacheco, Martín
last_name: Carballo-Pacheco
- first_name: Jonathan
full_name: Desponds, Jonathan
last_name: Desponds
- first_name: Tatyana
full_name: Gavrilchenko, Tatyana
last_name: Gavrilchenko
- first_name: Andreas
full_name: Mayer, Andreas
last_name: Mayer
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Gautam
full_name: Reddy, Gautam
last_name: Reddy
- first_name: Ilya
full_name: Nemenman, Ilya
last_name: Nemenman
- first_name: Thierry
full_name: Mora, Thierry
last_name: Mora
citation:
ama: Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves
concentration sensing of multiple ligands. Physical Review E. 2019;99(2).
doi:10.1103/PhysRevE.99.022423
apa: Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R.,
Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing
of multiple ligands. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423
chicago: Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas
Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor
Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review
E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423.
ieee: M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration
sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American
Physical Society, 2019.
ista: Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G,
Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of
multiple ligands. Physical Review E. 99(2), 022423.
mla: Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration
Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423,
American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423.
short: M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G.
Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).
date_created: 2019-03-10T22:59:20Z
date_published: 2019-02-26T00:00:00Z
date_updated: 2024-02-28T13:12:06Z
day: '26'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1103/PhysRevE.99.022423
external_id:
isi:
- '000459916500007'
intvolume: ' 99'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/448118v1.abstract
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review E
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Receptor crosstalk improves concentration sensing of multiple ligands
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2019'
...
---
_id: '7606'
abstract:
- lang: eng
text: We derive a tight lower bound on equivocation (conditional entropy), or equivalently
a tight upper bound on mutual information between a signal variable and channel
outputs. The bound is in terms of the joint distribution of the signals and maximum
a posteriori decodes (most probable signals given channel output). As part of
our derivation, we describe the key properties of the distribution of signals,
channel outputs and decodes, that minimizes equivocation and maximizes mutual
information. This work addresses a problem in data analysis, where mutual information
between signals and decodes is sometimes used to lower bound the mutual information
between signals and channel outputs. Our result provides a corresponding upper
bound.
article_number: '8989292'
article_processing_charge: No
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: 'Hledik M, Sokolowski TR, Tkačik G. A tight upper bound on mutual information.
In: IEEE Information Theory Workshop, ITW 2019. IEEE; 2019. doi:10.1109/ITW44776.2019.8989292'
apa: 'Hledik, M., Sokolowski, T. R., & Tkačik, G. (2019). A tight upper bound
on mutual information. In IEEE Information Theory Workshop, ITW 2019. Visby,
Sweden: IEEE. https://doi.org/10.1109/ITW44776.2019.8989292'
chicago: Hledik, Michal, Thomas R Sokolowski, and Gašper Tkačik. “A Tight Upper
Bound on Mutual Information.” In IEEE Information Theory Workshop, ITW 2019.
IEEE, 2019. https://doi.org/10.1109/ITW44776.2019.8989292.
ieee: M. Hledik, T. R. Sokolowski, and G. Tkačik, “A tight upper bound on mutual
information,” in IEEE Information Theory Workshop, ITW 2019, Visby, Sweden,
2019.
ista: Hledik M, Sokolowski TR, Tkačik G. 2019. A tight upper bound on mutual information.
IEEE Information Theory Workshop, ITW 2019. Information Theory Workshop, 8989292.
mla: Hledik, Michal, et al. “A Tight Upper Bound on Mutual Information.” IEEE
Information Theory Workshop, ITW 2019, 8989292, IEEE, 2019, doi:10.1109/ITW44776.2019.8989292.
short: M. Hledik, T.R. Sokolowski, G. Tkačik, in:, IEEE Information Theory Workshop,
ITW 2019, IEEE, 2019.
conference:
end_date: 2019-08-28
location: Visby, Sweden
name: Information Theory Workshop
start_date: 2019-08-25
date_created: 2020-03-22T23:00:47Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2024-03-06T14:22:51Z
day: '01'
department:
- _id: GaTk
doi: 10.1109/ITW44776.2019.8989292
ec_funded: 1
external_id:
arxiv:
- '1812.01475'
isi:
- '000540384500015'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1812.01475
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: IEEE Information Theory Workshop, ITW 2019
publication_identifier:
isbn:
- '9781538669006'
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '15020'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A tight upper bound on mutual information
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '306'
abstract:
- lang: eng
text: A cornerstone of statistical inference, the maximum entropy framework is being
increasingly applied to construct descriptive and predictive models of biological
systems, especially complex biological networks, from large experimental data
sets. Both its broad applicability and the success it obtained in different contexts
hinge upon its conceptual simplicity and mathematical soundness. Here we try to
concisely review the basic elements of the maximum entropy principle, starting
from the notion of ‘entropy’, and describe its usefulness for the analysis of
biological systems. As examples, we focus specifically on the problem of reconstructing
gene interaction networks from expression data and on recent work attempting to
expand our system-level understanding of bacterial metabolism. Finally, we highlight
some extensions and potential limitations of the maximum entropy approach, and
point to more recent developments that are likely to play a key role in the upcoming
challenges of extracting structures and information from increasingly rich, high-throughput
biological data.
article_number: e00596
author:
- first_name: Andrea
full_name: De Martino, Andrea
last_name: De Martino
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: De Martino A, De Martino D. An introduction to the maximum entropy approach
and its application to inference problems in biology. Heliyon. 2018;4(4).
doi:10.1016/j.heliyon.2018.e00596
apa: De Martino, A., & De Martino, D. (2018). An introduction to the maximum
entropy approach and its application to inference problems in biology. Heliyon.
Elsevier. https://doi.org/10.1016/j.heliyon.2018.e00596
chicago: De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum
Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon.
Elsevier, 2018. https://doi.org/10.1016/j.heliyon.2018.e00596.
ieee: A. De Martino and D. De Martino, “An introduction to the maximum entropy approach
and its application to inference problems in biology,” Heliyon, vol. 4,
no. 4. Elsevier, 2018.
ista: De Martino A, De Martino D. 2018. An introduction to the maximum entropy approach
and its application to inference problems in biology. Heliyon. 4(4), e00596.
mla: De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum
Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon,
vol. 4, no. 4, e00596, Elsevier, 2018, doi:10.1016/j.heliyon.2018.e00596.
short: A. De Martino, D. De Martino, Heliyon 4 (2018).
date_created: 2018-12-11T11:45:44Z
date_published: 2018-04-01T00:00:00Z
date_updated: 2021-01-12T07:40:46Z
day: '01'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.1016/j.heliyon.2018.e00596
ec_funded: 1
file:
- access_level: open_access
checksum: 67010cf5e3b3e0637c659371714a715a
content_type: application/pdf
creator: dernst
date_created: 2019-02-06T07:36:24Z
date_updated: 2020-07-14T12:45:59Z
file_id: '5929'
file_name: 2018_Heliyon_DeMartino.pdf
file_size: 994490
relation: main_file
file_date_updated: 2020-07-14T12:45:59Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Heliyon
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: 1
status: public
title: An introduction to the maximum entropy approach and its application to inference
problems in biology
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2018'
...
---
_id: '305'
abstract:
- lang: eng
text: The hanging-drop network (HDN) is a technology platform based on a completely
open microfluidic network at the bottom of an inverted, surface-patterned substrate.
The platform is predominantly used for the formation, culturing, and interaction
of self-assembled spherical microtissues (spheroids) under precisely controlled
flow conditions. Here, we describe design, fabrication, and operation of microfluidic
hanging-drop networks.
acknowledgement: This work was financially supported by FP7 of the EU through the
project “Body on a chip,” ICT-FET-296257, and the ERC Advanced Grant “NeuroCMOS”
(contract 267351), as well as by an individual Ambizione Grant 142440 from the Swiss
National Science Foundation for Olivier Frey. The research leading to these results
also received funding from the People Programme (Marie Curie Actions) of the European
Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no.
[291734]. We would like to thank Alexander Stettler, ETH Zurich for his expertise
and support in the cleanroom, and we acknowledge the Single Cell Unit of D-BSSE,
ETH Zurich for assistance in microscopy issues. M.L. is grateful to the members
of the Guet and Tkačik groups, IST Austria, for valuable comments and support.
alternative_title:
- MIMB
author:
- first_name: Patrick
full_name: Misun, Patrick
last_name: Misun
- first_name: Axel
full_name: Birchler, Axel
last_name: Birchler
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Andreas
full_name: Hierlemann, Andreas
last_name: Hierlemann
- first_name: Olivier
full_name: Frey, Olivier
last_name: Frey
citation:
ama: Misun P, Birchler A, Lang M, Hierlemann A, Frey O. Fabrication and operation
of microfluidic hanging drop networks. Methods in Molecular Biology. 2018;1771:183-202.
doi:10.1007/978-1-4939-7792-5_15
apa: Misun, P., Birchler, A., Lang, M., Hierlemann, A., & Frey, O. (2018). Fabrication
and operation of microfluidic hanging drop networks. Methods in Molecular Biology.
Springer. https://doi.org/10.1007/978-1-4939-7792-5_15
chicago: Misun, Patrick, Axel Birchler, Moritz Lang, Andreas Hierlemann, and Olivier
Frey. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods
in Molecular Biology. Springer, 2018. https://doi.org/10.1007/978-1-4939-7792-5_15.
ieee: P. Misun, A. Birchler, M. Lang, A. Hierlemann, and O. Frey, “Fabrication and
operation of microfluidic hanging drop networks,” Methods in Molecular Biology,
vol. 1771. Springer, pp. 183–202, 2018.
ista: Misun P, Birchler A, Lang M, Hierlemann A, Frey O. 2018. Fabrication and operation
of microfluidic hanging drop networks. Methods in Molecular Biology. 1771, 183–202.
mla: Misun, Patrick, et al. “Fabrication and Operation of Microfluidic Hanging Drop
Networks.” Methods in Molecular Biology, vol. 1771, Springer, 2018, pp.
183–202, doi:10.1007/978-1-4939-7792-5_15.
short: P. Misun, A. Birchler, M. Lang, A. Hierlemann, O. Frey, Methods in Molecular
Biology 1771 (2018) 183–202.
date_created: 2018-12-11T11:45:43Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2021-01-12T07:40:42Z
day: '01'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1007/978-1-4939-7792-5_15
ec_funded: 1
intvolume: ' 1771'
language:
- iso: eng
month: '01'
oa_version: None
page: 183 - 202
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Methods in Molecular Biology
publication_status: published
publisher: Springer
publist_id: '7574'
quality_controlled: '1'
scopus_import: 1
status: public
title: Fabrication and operation of microfluidic hanging drop networks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1771
year: '2018'
...
---
_id: '281'
abstract:
- lang: eng
text: 'Although cells respond specifically to environments, how environmental identity
is encoded intracellularly is not understood. Here, we study this organization
of information in budding yeast by estimating the mutual information between environmental
transitions and the dynamics of nuclear translocation for 10 transcription factors.
Our method of estimation is general, scalable, and based on decoding from single
cells. The dynamics of the transcription factors are necessary to encode the highest
amounts of extracellular information, and we show that information is transduced
through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can
encode the nature of multiple stresses, but only if stress is high; specialists
(Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly
and for a wider range of magnitudes. In particular, Dot6 encodes almost as much
information as Msn2, the master regulator of the environmental stress response.
Each transcription factor reports differently, and it is only their collective
behavior that distinguishes between multiple environmental states. Changes in
the dynamics of the localization of transcription factors thus constitute a precise,
distributed internal representation of extracellular change. We predict that such
multidimensional representations are common in cellular decision-making.'
acknowledgement: This work was supported by the Biotechnology and Biological Sciences
Research Council (J.M.J.P., I.F., and P.S.S.), the Engineering and Physical Sciences
Research Council (EPSRC) (A.A.G.), and Austrian Science Fund Grant FWF P28844 (to
G.T.).
article_processing_charge: No
article_type: original
author:
- first_name: Alejandro
full_name: Granados, Alejandro
last_name: Granados
- first_name: Julian
full_name: Pietsch, Julian
last_name: Pietsch
- first_name: Sarah A
full_name: Cepeda Humerez, Sarah A
id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87
last_name: Cepeda Humerez
- first_name: Isebail
full_name: Farquhar, Isebail
last_name: Farquhar
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Peter
full_name: Swain, Peter
last_name: Swain
citation:
ama: Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed
and dynamic intracellular organization of extracellular information. PNAS.
2018;115(23):6088-6093. doi:10.1073/pnas.1716659115
apa: Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkačik, G.,
& Swain, P. (2018). Distributed and dynamic intracellular organization of
extracellular information. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1716659115
chicago: Granados, Alejandro, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar,
Gašper Tkačik, and Peter Swain. “Distributed and Dynamic Intracellular Organization
of Extracellular Information.” PNAS. National Academy of Sciences, 2018.
https://doi.org/10.1073/pnas.1716659115.
ieee: A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkačik, and
P. Swain, “Distributed and dynamic intracellular organization of extracellular
information,” PNAS, vol. 115, no. 23. National Academy of Sciences, pp.
6088–6093, 2018.
ista: Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. 2018.
Distributed and dynamic intracellular organization of extracellular information.
PNAS. 115(23), 6088–6093.
mla: Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization
of Extracellular Information.” PNAS, vol. 115, no. 23, National Academy
of Sciences, 2018, pp. 6088–93, doi:10.1073/pnas.1716659115.
short: A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P.
Swain, PNAS 115 (2018) 6088–6093.
date_created: 2018-12-11T11:45:35Z
date_published: 2018-06-05T00:00:00Z
date_updated: 2023-09-11T12:58:24Z
day: '05'
department:
- _id: GaTk
doi: 10.1073/pnas.1716659115
external_id:
isi:
- '000434114900071'
pmid:
- '29784812'
intvolume: ' 115'
isi: 1
issue: '23'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/early/2017/09/21/192039
month: '06'
oa: 1
oa_version: Preprint
page: 6088 - 6093
pmid: 1
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '7618'
quality_controlled: '1'
related_material:
record:
- id: '6473'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Distributed and dynamic intracellular organization of extracellular information
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '316'
abstract:
- lang: eng
text: 'Self-incompatibility (SI) is a genetically based recognition system that
functions to prevent self-fertilization and mating among related plants. An enduring
puzzle in SI is how the high diversity observed in nature arises and is maintained.
Based on the underlying recognition mechanism, SI can be classified into two main
groups: self- and non-self recognition. Most work has focused on diversification
within self-recognition systems despite expected differences between the two groups
in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic
population genetic model and stochastic simulations to investigate how novel S-haplotypes
evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI
system. For this model the pathways for diversification involve either the maintenance
or breakdown of SI and can vary in the order of mutations of the female (SRNase)
and male (SLF) components. We show analytically that diversification can occur
with high inbreeding depression and self-pollination, but this varies with evolutionary
pathway and level of completeness (which determines the number of potential mating
partners in the population), and in general is more likely for lower haplotype
number. The conditions for diversification are broader in stochastic simulations
of finite population size. However, the number of haplotypes observed under high
inbreeding and moderate to high self-pollination is less than that commonly observed
in nature. Diversification was observed through pathways that maintain SI as well
as through self-compatible intermediates. Yet the lifespan of diversified haplotypes
was sensitive to their level of completeness. By examining diversification in
a non-self recognition SI system, this model extends our understanding of the
evolution and maintenance of haplotype diversity observed in a self recognition
system common in flowering plants.'
article_processing_charge: No
article_type: original
author:
- first_name: Katarina
full_name: Bodova, Katarina
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bodova
orcid: 0000-0002-7214-0171
- first_name: Tadeas
full_name: Priklopil, Tadeas
id: 3C869AA0-F248-11E8-B48F-1D18A9856A87
last_name: Priklopil
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
citation:
ama: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways
for the generation of new self-incompatibility haplotypes in a non-self recognition
system. Genetics. 2018;209(3):861-883. doi:10.1534/genetics.118.300748
apa: Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018).
Evolutionary pathways for the generation of new self-incompatibility haplotypes
in a non-self recognition system. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.118.300748
chicago: Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and
Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility
Haplotypes in a Non-Self Recognition System.” Genetics. Genetics Society
of America, 2018. https://doi.org/10.1534/genetics.118.300748.
ieee: K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary
pathways for the generation of new self-incompatibility haplotypes in a non-self
recognition system,” Genetics, vol. 209, no. 3. Genetics Society of America,
pp. 861–883, 2018.
ista: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways
for the generation of new self-incompatibility haplotypes in a non-self recognition
system. Genetics. 209(3), 861–883.
mla: Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility
Haplotypes in a Non-Self Recognition System.” Genetics, vol. 209, no. 3,
Genetics Society of America, 2018, pp. 861–83, doi:10.1534/genetics.118.300748.
short: K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018)
861–883.
date_created: 2018-12-11T11:45:47Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-09-11T13:57:43Z
day: '01'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1534/genetics.118.300748
ec_funded: 1
external_id:
isi:
- '000437171700017'
intvolume: ' 209'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/node/80098.abstract
month: '07'
oa: 1
oa_version: Preprint
page: 861-883
project:
- _id: 25B36484-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '329960'
name: Mating system and the evolutionary dynamics of hybrid zones
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Genetics
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/
record:
- id: '9813'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Evolutionary pathways for the generation of new self-incompatibility haplotypes
in a non-self recognition system
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 209
year: '2018'
...
---
_id: '9813'
abstract:
- lang: eng
text: 'File S1 contains figures that clarify the following features: (i) effect
of population size on the average number/frequency of SI classes, (ii) changes
in the minimal completeness deficit in time for a single class, and (iii) diversification
diagrams for all studied pathways, including the summary figure for k = 8. File
S2 contains the code required for a stochastic simulation of the SLF system with
an example. This file also includes the output in the form of figures and tables.'
article_processing_charge: No
author:
- first_name: Katarína
full_name: Bod'ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'ová
orcid: 0000-0002-7214-0171
- first_name: Tadeas
full_name: Priklopil, Tadeas
id: 3C869AA0-F248-11E8-B48F-1D18A9856A87
last_name: Priklopil
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
citation:
ama: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material
for Bodova et al., 2018. 2018. doi:10.25386/genetics.6148304.v1
apa: Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018).
Supplemental material for Bodova et al., 2018. Genetics Society of America. https://doi.org/10.25386/genetics.6148304.v1
chicago: Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and
Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society
of America, 2018. https://doi.org/10.25386/genetics.6148304.v1.
ieee: K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental
material for Bodova et al., 2018.” Genetics Society of America, 2018.
ista: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material
for Bodova et al., 2018, Genetics Society of America, 10.25386/genetics.6148304.v1.
mla: Bodova, Katarina, et al. Supplemental Material for Bodova et Al., 2018.
Genetics Society of America, 2018, doi:10.25386/genetics.6148304.v1.
short: K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).
date_created: 2021-08-06T13:04:32Z
date_published: 2018-04-30T00:00:00Z
date_updated: 2023-09-11T13:57:42Z
day: '30'
department:
- _id: NiBa
- _id: GaTk
doi: 10.25386/genetics.6148304.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.25386/genetics.6148304.v1
month: '04'
oa: 1
oa_version: Published Version
publisher: Genetics Society of America
related_material:
record:
- id: '316'
relation: used_in_publication
status: public
status: public
title: Supplemental material for Bodova et al., 2018
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '406'
abstract:
- lang: eng
text: 'Recent developments in automated tracking allow uninterrupted, high-resolution
recording of animal trajectories, sometimes coupled with the identification of
stereotyped changes of body pose or other behaviors of interest. Analysis and
interpretation of such data represents a challenge: the timing of animal behaviors
may be stochastic and modulated by kinematic variables, by the interaction with
the environment or with the conspecifics within the animal group, and dependent
on internal cognitive or behavioral state of the individual. Existing models for
collective motion typically fail to incorporate the discrete, stochastic, and
internal-state-dependent aspects of behavior, while models focusing on individual
animal behavior typically ignore the spatial aspects of the problem. Here we propose
a probabilistic modeling framework to address this gap. Each animal can switch
stochastically between different behavioral states, with each state resulting
in a possibly different law of motion through space. Switching rates for behavioral
transitions can depend in a very general way, which we seek to identify from data,
on the effects of the environment as well as the interaction between the animals.
We represent the switching dynamics as a Generalized Linear Model and show that:
(i) forward simulation of multiple interacting animals is possible using a variant
of the Gillespie’s Stochastic Simulation Algorithm; (ii) formulated properly,
the maximum likelihood inference of switching rate functions is tractably solvable
by gradient descent; (iii) model selection can be used to identify factors that
modulate behavioral state switching and to appropriately adjust model complexity
to data. To illustrate our framework, we apply it to two synthetic models of animal
motion and to real zebrafish tracking data. '
acknowledgement: This work was supported by the Human Frontier Science Program RGP0065/2012
(GT, ES).
article_processing_charge: Yes
author:
- first_name: Katarína
full_name: Bod’Ová, Katarína
last_name: Bod’Ová
- first_name: Gabriel
full_name: Mitchell, Gabriel
id: 315BCD80-F248-11E8-B48F-1D18A9856A87
last_name: Mitchell
- first_name: Roy
full_name: Harpaz, Roy
last_name: Harpaz
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models
of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049
apa: Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018).
Probabilistic models of individual and collective animal behavior. PLoS One.
Public Library of Science. https://doi.org/10.1371/journal.pone.0193049
chicago: Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper
Tkačik. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS
One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049.
ieee: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic
models of individual and collective animal behavior,” PLoS One, vol. 13,
no. 3. Public Library of Science, 2018.
ista: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Probabilistic
models of individual and collective animal behavior. PLoS One. 13(3).
mla: Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective
Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science,
2018, doi:10.1371/journal.pone.0193049.
short: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13
(2018).
date_created: 2018-12-11T11:46:18Z
date_published: 2018-03-07T00:00:00Z
date_updated: 2023-09-15T12:06:19Z
day: '07'
ddc:
- '530'
- '571'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0193049
external_id:
isi:
- '000426896800032'
file:
- access_level: open_access
checksum: 684229493db75b43e98a46cd922da497
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:43Z
date_updated: 2020-07-14T12:46:22Z
file_id: '5165'
file_name: IST-2018-995-v1+1_2018_Bodova_Probabilistic.pdf
file_size: 6887358
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
project:
- _id: 255008E4-B435-11E9-9278-68D0E5697425
grant_number: RGP0065/2012
name: Information processing and computation in fish groups
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '7423'
pubrep_id: '995'
quality_controlled: '1'
related_material:
record:
- id: '9831'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Probabilistic models of individual and collective animal behavior
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13
year: '2018'
...
---
_id: '457'
abstract:
- lang: eng
text: Temperate bacteriophages integrate in bacterial genomes as prophages and represent
an important source of genetic variation for bacterial evolution, frequently transmitting
fitness-augmenting genes such as toxins responsible for virulence of major pathogens.
However, only a fraction of bacteriophage infections are lysogenic and lead to
prophage acquisition, whereas the majority are lytic and kill the infected bacteria.
Unless able to discriminate lytic from lysogenic infections, mechanisms of immunity
to bacteriophages are expected to act as a double-edged sword and increase the
odds of survival at the cost of depriving bacteria of potentially beneficial prophages.
We show that although restriction-modification systems as mechanisms of innate
immunity prevent both lytic and lysogenic infections indiscriminately in individual
bacteria, they increase the number of prophage-acquiring individuals at the population
level. We find that this counterintuitive result is a consequence of phage-host
population dynamics, in which restriction-modification systems delay infection
onset until bacteria reach densities at which the probability of lysogeny increases.
These results underscore the importance of population-level dynamics as a key
factor modulating costs and benefits of immunity to temperate bacteriophages
article_processing_charge: No
author:
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Dominik
full_name: Refardt, Dominik
last_name: Refardt
- first_name: Bruce
full_name: Levin, Bruce
last_name: Levin
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Pleska M, Lang M, Refardt D, Levin B, Guet CC. Phage-host population dynamics
promotes prophage acquisition in bacteria with innate immunity. Nature Ecology
and Evolution. 2018;2(2):359-366. doi:10.1038/s41559-017-0424-z
apa: Pleska, M., Lang, M., Refardt, D., Levin, B., & Guet, C. C. (2018). Phage-host
population dynamics promotes prophage acquisition in bacteria with innate immunity.
Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0424-z
chicago: Pleska, Maros, Moritz Lang, Dominik Refardt, Bruce Levin, and Calin C Guet.
“Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with
Innate Immunity.” Nature Ecology and Evolution. Springer Nature, 2018.
https://doi.org/10.1038/s41559-017-0424-z.
ieee: M. Pleska, M. Lang, D. Refardt, B. Levin, and C. C. Guet, “Phage-host population
dynamics promotes prophage acquisition in bacteria with innate immunity,” Nature
Ecology and Evolution, vol. 2, no. 2. Springer Nature, pp. 359–366, 2018.
ista: Pleska M, Lang M, Refardt D, Levin B, Guet CC. 2018. Phage-host population
dynamics promotes prophage acquisition in bacteria with innate immunity. Nature
Ecology and Evolution. 2(2), 359–366.
mla: Pleska, Maros, et al. “Phage-Host Population Dynamics Promotes Prophage Acquisition
in Bacteria with Innate Immunity.” Nature Ecology and Evolution, vol. 2,
no. 2, Springer Nature, 2018, pp. 359–66, doi:10.1038/s41559-017-0424-z.
short: M. Pleska, M. Lang, D. Refardt, B. Levin, C.C. Guet, Nature Ecology and Evolution
2 (2018) 359–366.
date_created: 2018-12-11T11:46:35Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2023-09-15T12:04:57Z
day: '01'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1038/s41559-017-0424-z
ec_funded: 1
external_id:
isi:
- '000426516400027'
intvolume: ' 2'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 359 - 366
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 251BCBEC-B435-11E9-9278-68D0E5697425
grant_number: RGY0079/2011
name: Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification
Systems (HFSP Young investigators' grant)
- _id: 251D65D8-B435-11E9-9278-68D0E5697425
grant_number: '24210'
name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems
at the Single-Cell Level (DOC Fellowship)
publication: Nature Ecology and Evolution
publication_status: published
publisher: Springer Nature
publist_id: '7364'
quality_controlled: '1'
related_material:
record:
- id: '202'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Phage-host population dynamics promotes prophage acquisition in bacteria with
innate immunity
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2
year: '2018'
...
---
_id: '9831'
abstract:
- lang: eng
text: 'Implementation of the inference method in Matlab, including three applications
of the method: The first one for the model of ant motion, the second one for bacterial
chemotaxis, and the third one for the motion of fish.'
article_processing_charge: No
author:
- first_name: Katarína
full_name: Bod’Ová, Katarína
last_name: Bod’Ová
- first_name: Gabriel
full_name: Mitchell, Gabriel
id: 315BCD80-F248-11E8-B48F-1D18A9856A87
last_name: Mitchell
- first_name: Roy
full_name: Harpaz, Roy
last_name: Harpaz
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of
the inference method in Matlab. 2018. doi:10.1371/journal.pone.0193049.s001
apa: Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018).
Implementation of the inference method in Matlab. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049.s001
chicago: Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper
Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of
Science, 2018. https://doi.org/10.1371/journal.pone.0193049.s001.
ieee: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation
of the inference method in Matlab.” Public Library of Science, 2018.
ista: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Implementation
of the inference method in Matlab, Public Library of Science, 10.1371/journal.pone.0193049.s001.
mla: Bod’Ová, Katarína, et al. Implementation of the Inference Method in Matlab.
Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.s001.
short: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).
date_created: 2021-08-09T07:01:24Z
date_published: 2018-03-07T00:00:00Z
date_updated: 2023-09-15T12:06:18Z
day: '07'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0193049.s001
month: '03'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '406'
relation: used_in_publication
status: public
status: public
title: Implementation of the inference method in Matlab
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '31'
abstract:
- lang: eng
text: Correlations in sensory neural networks have both extrinsic and intrinsic
origins. Extrinsic or stimulus correlations arise from shared inputs to the network
and, thus, depend strongly on the stimulus ensemble. Intrinsic or noise correlations
reflect biophysical mechanisms of interactions between neurons, which are expected
to be robust to changes in the stimulus ensemble. Despite the importance of this
distinction for understanding how sensory networks encode information collectively,
no method exists to reliably separate intrinsic interactions from extrinsic correlations
in neural activity data, limiting our ability to build predictive models of the
network response. In this paper we introduce a general strategy to infer population
models of interacting neurons that collectively encode stimulus information. The
key to disentangling intrinsic from extrinsic correlations is to infer the couplings
between neurons separately from the encoding model and to combine the two using
corrections calculated in a mean-field approximation. We demonstrate the effectiveness
of this approach in retinal recordings. The same coupling network is inferred
from responses to radically different stimulus ensembles, showing that these couplings
indeed reflect stimulus-independent interactions between neurons. The inferred
model predicts accurately the collective response of retinal ganglion cell populations
as a function of the stimulus.
acknowledgement: This work was supported by ANR Trajectory, the French State program
Investissements d’Avenir managed by the Agence Nationale de la Recherche (LIFESENSES;
ANR-10-LABX-65), EC Grant No. H2020-785907 from the Human Brain Project, NIH Grant
No. U01NS090501, and an AVIESAN-UNADEV grant to O.M. M.C. was supported by the Agence
Nationale de la Recherche Jeune Chercheur/Jeune Chercheuse grant (ANR-17-CE37-0013).
article_number: '042410'
article_processing_charge: No
article_type: original
author:
- first_name: Ulisse
full_name: Ferrari, Ulisse
last_name: Ferrari
- first_name: Stephane
full_name: Deny, Stephane
last_name: Deny
- first_name: Matthew J
full_name: Chalk, Matthew J
last_name: Chalk
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Thierry
full_name: Mora, Thierry
last_name: Mora
citation:
ama: Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. Separating intrinsic
interactions from extrinsic correlations in a network of sensory neurons. Physical
Review E. 2018;98(4). doi:10.1103/PhysRevE.98.042410
apa: Ferrari, U., Deny, S., Chalk, M. J., Tkačik, G., Marre, O., & Mora, T.
(2018). Separating intrinsic interactions from extrinsic correlations in a network
of sensory neurons. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.042410
chicago: Ferrari, Ulisse, Stephane Deny, Matthew J Chalk, Gašper Tkačik, Olivier
Marre, and Thierry Mora. “Separating Intrinsic Interactions from Extrinsic Correlations
in a Network of Sensory Neurons.” Physical Review E. American Physical
Society, 2018. https://doi.org/10.1103/PhysRevE.98.042410.
ieee: U. Ferrari, S. Deny, M. J. Chalk, G. Tkačik, O. Marre, and T. Mora, “Separating
intrinsic interactions from extrinsic correlations in a network of sensory neurons,”
Physical Review E, vol. 98, no. 4. American Physical Society, 2018.
ista: Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. 2018. Separating intrinsic
interactions from extrinsic correlations in a network of sensory neurons. Physical
Review E. 98(4), 042410.
mla: Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations
in a Network of Sensory Neurons.” Physical Review E, vol. 98, no. 4, 042410,
American Physical Society, 2018, doi:10.1103/PhysRevE.98.042410.
short: U. Ferrari, S. Deny, M.J. Chalk, G. Tkačik, O. Marre, T. Mora, Physical Review
E 98 (2018).
date_created: 2018-12-11T11:44:15Z
date_published: 2018-10-17T00:00:00Z
date_updated: 2023-09-18T09:18:44Z
day: '17'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.98.042410
ec_funded: 1
external_id:
isi:
- '000447486100004'
intvolume: ' 98'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/243816v2.full
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 26436750-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '785907'
name: Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)
publication: Physical Review E
publication_identifier:
issn:
- '24700045'
publication_status: published
publisher: American Physical Society
publist_id: '8024'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Separating intrinsic interactions from extrinsic correlations in a network
of sensory neurons
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 98
year: '2018'
...
---
_id: '543'
abstract:
- lang: eng
text: A central goal in theoretical neuroscience is to predict the response properties
of sensory neurons from first principles. To this end, “efficient coding” posits
that sensory neurons encode maximal information about their inputs given internal
constraints. There exist, however, many variants of efficient coding (e.g., redundancy
reduction, different formulations of predictive coding, robust coding, sparse
coding, etc.), differing in their regimes of applicability, in the relevance of
signals to be encoded, and in the choice of constraints. It is unclear how these
types of efficient coding relate or what is expected when different coding objectives
are combined. Here we present a unified framework that encompasses previously
proposed efficient coding models and extends to unique regimes. We show that optimizing
neural responses to encode predictive information can lead them to either correlate
or decorrelate their inputs, depending on the stimulus statistics; in contrast,
at low noise, efficiently encoding the past always predicts decorrelation. Later,
we investigate coding of naturalistic movies and show that qualitatively different
types of visual motion tuning and levels of response sparsity are predicted, depending
on whether the objective is to recover the past or predict the future. Our approach
promises a way to explain the observed diversity of sensory neural responses,
as due to multiple functional goals and constraints fulfilled by different cell
types and/or circuits.
article_processing_charge: No
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive,
and sparse coding. PNAS. 2018;115(1):186-191. doi:10.1073/pnas.1711114115
apa: Chalk, M. J., Marre, O., & Tkačik, G. (2018). Toward a unified theory of
efficient, predictive, and sparse coding. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1711114115
chicago: Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory
of Efficient, Predictive, and Sparse Coding.” PNAS. National Academy of
Sciences, 2018. https://doi.org/10.1073/pnas.1711114115.
ieee: M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient,
predictive, and sparse coding,” PNAS, vol. 115, no. 1. National Academy
of Sciences, pp. 186–191, 2018.
ista: Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive,
and sparse coding. PNAS. 115(1), 186–191.
mla: Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive,
and Sparse Coding.” PNAS, vol. 115, no. 1, National Academy of Sciences,
2018, pp. 186–91, doi:10.1073/pnas.1711114115.
short: M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 186–191.
date_created: 2018-12-11T11:47:04Z
date_published: 2018-01-02T00:00:00Z
date_updated: 2023-09-19T10:16:35Z
day: '02'
department:
- _id: GaTk
doi: 10.1073/pnas.1711114115
external_id:
isi:
- '000419128700049'
intvolume: ' 115'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/152660 '
month: '01'
oa: 1
oa_version: Submitted Version
page: 186 - 191
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '7273'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Toward a unified theory of efficient, predictive, and sparse coding
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '607'
abstract:
- lang: eng
text: We study the Fokker-Planck equation derived in the large system limit of the
Markovian process describing the dynamics of quantitative traits. The Fokker-Planck
equation is posed on a bounded domain and its transport and diffusion coefficients
vanish on the domain's boundary. We first argue that, despite this degeneracy,
the standard no-flux boundary condition is valid. We derive the weak formulation
of the problem and prove the existence and uniqueness of its solutions by constructing
the corresponding contraction semigroup on a suitable function space. Then, we
prove that for the parameter regime with high enough mutation rate the problem
exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next,
we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt)
method for approximation of observables (moments) of the Fokker-Planck solution,
which can be interpreted as a nonlinear Galerkin approximation. The limited applicability
of the DynMaxEnt method inspires us to introduce its modified version that is
valid for the whole range of admissible parameters. Finally, we present several
numerical experiments to demonstrate the performance of both the original and
modified DynMaxEnt methods. We observe that in the parameter regimes where both
methods are valid, the modified one exhibits slightly better approximation properties
compared to the original one.
acknowledgement: "JH and PM are funded by KAUST baseline funds and grant no. 1000000193
.\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions.
\r\n\r\n"
article_processing_charge: No
author:
- first_name: Katarina
full_name: Bodova, Katarina
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bodova
orcid: 0000-0002-7214-0171
- first_name: Jan
full_name: Haskovec, Jan
last_name: Haskovec
- first_name: Peter
full_name: Markowich, Peter
last_name: Markowich
citation:
ama: 'Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation
for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena.
2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015'
apa: 'Bodova, K., Haskovec, J., & Markowich, P. (2018). Well posedness and maximum
entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear
Phenomena. Elsevier. https://doi.org/10.1016/j.physd.2017.10.015'
chicago: 'Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and
Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica
D: Nonlinear Phenomena. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015.'
ieee: 'K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy
approximation for the dynamics of quantitative traits,” Physica D: Nonlinear
Phenomena, vol. 376–377. Elsevier, pp. 108–120, 2018.'
ista: 'Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy
approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena.
376–377, 108–120.'
mla: 'Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation
for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena,
vol. 376–377, Elsevier, 2018, pp. 108–20, doi:10.1016/j.physd.2017.10.015.'
short: 'K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377
(2018) 108–120.'
date_created: 2018-12-11T11:47:28Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-19T10:38:34Z
day: '01'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1016/j.physd.2017.10.015
external_id:
arxiv:
- '1704.08757'
isi:
- '000437962900012'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.08757
month: '08'
oa: 1
oa_version: Submitted Version
page: 108-120
publication: 'Physica D: Nonlinear Phenomena'
publication_status: published
publisher: Elsevier
publist_id: '7198'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Well posedness and maximum entropy approximation for the dynamics of quantitative
traits
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 376-377
year: '2018'
...
---
_id: '19'
abstract:
- lang: eng
text: Bacteria regulate genes to survive antibiotic stress, but regulation can be
far from perfect. When regulation is not optimal, mutations that change gene expression
can contribute to antibiotic resistance. It is not systematically understood to
what extent natural gene regulation is or is not optimal for distinct antibiotics,
and how changes in expression of specific genes quantitatively affect antibiotic
resistance. Here we discover a simple quantitative relation between fitness, gene
expression, and antibiotic potency, which rationalizes our observation that a
multitude of genes and even innate antibiotic defense mechanisms have expression
that is critically nonoptimal under antibiotic treatment. First, we developed
a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression
and knockout libraries, finding that resistance to a range of 31 antibiotics could
result from changing expression of a large and functionally diverse set of genes,
in a primarily but not exclusively drug-specific manner. Second, by synthetically
controlling the expression of single-drug and multidrug resistance genes, we observed
that their fitness-expression functions changed dramatically under antibiotic
treatment in accordance with a log-sensitivity relation. Thus, because many genes
are nonoptimally expressed under antibiotic treatment, many regulatory mutations
can contribute to resistance by altering expression and by activating latent defenses.
article_processing_charge: No
article_type: original
author:
- first_name: Adam
full_name: Palmer, Adam
last_name: Palmer
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Roy
full_name: Kishony, Roy
last_name: Kishony
citation:
ama: Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential
for antibiotic resistance. Molecular Biology and Evolution. 2018;35(11):2669-2684.
doi:10.1093/molbev/msy163
apa: Palmer, A., Chait, R. P., & Kishony, R. (2018). Nonoptimal gene expression
creates latent potential for antibiotic resistance. Molecular Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/molbev/msy163
chicago: Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression
Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and
Evolution. Oxford University Press, 2018. https://doi.org/10.1093/molbev/msy163.
ieee: A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates
latent potential for antibiotic resistance,” Molecular Biology and Evolution,
vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.
ista: Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent
potential for antibiotic resistance. Molecular Biology and Evolution. 35(11),
2669–2684.
mla: Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for
Antibiotic Resistance.” Molecular Biology and Evolution, vol. 35, no. 11,
Oxford University Press, 2018, pp. 2669–84, doi:10.1093/molbev/msy163.
short: A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018)
2669–2684.
date_created: 2018-12-11T11:44:11Z
date_published: 2018-08-28T00:00:00Z
date_updated: 2023-10-17T11:51:06Z
day: '28'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1093/molbev/msy163
external_id:
isi:
- '000452567200006'
pmid:
- '30169679'
intvolume: ' 35'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30169679
month: '08'
oa: 1
oa_version: Submitted Version
page: 2669 - 2684
pmid: 1
publication: Molecular Biology and Evolution
publication_identifier:
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
publist_id: '8036'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nonoptimal gene expression creates latent potential for antibiotic resistance
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2018'
...
---
_id: '292'
abstract:
- lang: eng
text: 'Retina is a paradigmatic system for studying sensory encoding: the transformation
of light into spiking activity of ganglion cells. The inverse problem, where stimulus
is reconstructed from spikes, has received less attention, especially for complex
stimuli that should be reconstructed “pixel-by-pixel”. We recorded around a hundred
neurons from a dense patch in a rat retina and decoded movies of multiple small
randomly-moving discs. We constructed nonlinear (kernelized and neural network)
decoders that improved significantly over linear results. An important contribution
to this was the ability of nonlinear decoders to reliably separate between neural
responses driven by locally fluctuating light signals, and responses at locally
constant light driven by spontaneous-like activity. This improvement crucially
depended on the precise, non-Poisson temporal structure of individual spike trains,
which originated in the spike-history dependence of neural responses. We propose
a general principle by which downstream circuitry could discriminate between spontaneous
and stimulus-driven activity based solely on higher-order statistical structure
in the incoming spike trains.'
article_number: e1006057
article_processing_charge: Yes
article_type: original
author:
- first_name: Vicent
full_name: Botella Soler, Vicent
id: 421234E8-F248-11E8-B48F-1D18A9856A87
last_name: Botella Soler
orcid: 0000-0002-8790-1914
- first_name: Stephane
full_name: Deny, Stephane
last_name: Deny
- first_name: Georg S
full_name: Martius, Georg S
last_name: Martius
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. Nonlinear decoding
of a complex movie from the mammalian retina. PLoS Computational Biology.
2018;14(5). doi:10.1371/journal.pcbi.1006057
apa: Botella Soler, V., Deny, S., Martius, G. S., Marre, O., & Tkačik, G. (2018).
Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1006057
chicago: Botella Soler, Vicente, Stephane Deny, Georg S Martius, Olivier Marre,
and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.”
PLoS Computational Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pcbi.1006057.
ieee: V. Botella Soler, S. Deny, G. S. Martius, O. Marre, and G. Tkačik, “Nonlinear
decoding of a complex movie from the mammalian retina,” PLoS Computational
Biology, vol. 14, no. 5. Public Library of Science, 2018.
ista: Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. 2018. Nonlinear decoding
of a complex movie from the mammalian retina. PLoS Computational Biology. 14(5),
e1006057.
mla: Botella Soler, Vicente, et al. “Nonlinear Decoding of a Complex Movie from
the Mammalian Retina.” PLoS Computational Biology, vol. 14, no. 5, e1006057,
Public Library of Science, 2018, doi:10.1371/journal.pcbi.1006057.
short: V. Botella Soler, S. Deny, G.S. Martius, O. Marre, G. Tkačik, PLoS Computational
Biology 14 (2018).
date_created: 2018-12-11T11:45:39Z
date_published: 2018-05-10T00:00:00Z
date_updated: 2024-02-21T13:45:25Z
day: '10'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1006057
ec_funded: 1
external_id:
isi:
- '000434012100002'
file:
- access_level: open_access
checksum: 3026f94d235219e15514505fdbadf34e
content_type: application/pdf
creator: dernst
date_created: 2019-02-13T11:07:15Z
date_updated: 2020-07-14T12:45:53Z
file_id: '5974'
file_name: 2018_Plos_Botella_Soler.pdf
file_size: 3460786
relation: main_file
file_date_updated: 2020-07-14T12:45:53Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25CBA828-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '720270'
name: Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/video-of-moving-discs-reconstructed-from-rat-retinal-neuron-signals/
record:
- id: '5584'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Nonlinear decoding of a complex movie from the mammalian retina
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2018'
...
---
_id: '161'
abstract:
- lang: eng
text: 'Which properties of metabolic networks can be derived solely from stoichiometry?
Predictive results have been obtained by flux balance analysis (FBA), by postulating
that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization
of FBA to single-cell level using maximum entropy modeling, which we extend and
test experimentally. Specifically, we define for Escherichia coli metabolism a
flux distribution that yields the experimental growth rate: the model, containing
FBA as a limit, provides a better match to measured fluxes and it makes a wide
range of predictions: on flux variability, regulation, and correlations; on the
relative importance of stoichiometry vs. optimization; on scaling relations for
growth rate distributions. We validate the latter here with single-cell data at
different sub-inhibitory antibiotic concentrations. The model quantifies growth
optimization as emerging from the interplay of competitive dynamics in the population
and regulation of metabolism at the level of single cells.'
article_number: '2988'
article_processing_charge: No
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Andersson Anna
full_name: Mc, Andersson Anna
last_name: Mc
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics
for metabolic networks during steady state growth. Nature Communications.
2018;9(1). doi:10.1038/s41467-018-05417-9
apa: De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., & Tkačik, G. (2018).
Statistical mechanics for metabolic networks during steady state growth. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-018-05417-9
chicago: De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet,
and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady
State Growth.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-05417-9.
ieee: D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical
mechanics for metabolic networks during steady state growth,” Nature Communications,
vol. 9, no. 1. Springer Nature, 2018.
ista: De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics
for metabolic networks during steady state growth. Nature Communications. 9(1),
2988.
mla: De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during
Steady State Growth.” Nature Communications, vol. 9, no. 1, 2988, Springer
Nature, 2018, doi:10.1038/s41467-018-05417-9.
short: D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications
9 (2018).
date_created: 2018-12-11T11:44:57Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2024-02-21T13:45:39Z
day: '30'
ddc:
- '570'
department:
- _id: GaTk
- _id: CaGu
doi: 10.1038/s41467-018-05417-9
ec_funded: 1
external_id:
isi:
- '000440149300021'
file:
- access_level: open_access
checksum: 3ba7ab27b27723c7dcf633e8fc1f8f18
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:44:28Z
date_updated: 2020-07-14T12:45:06Z
file_id: '5728'
file_name: 2018_NatureComm_DeMartino.pdf
file_size: 1043205
relation: main_file
file_date_updated: 2020-07-14T12:45:06Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Nature Communications
publication_status: published
publisher: Springer Nature
publist_id: '7760'
quality_controlled: '1'
related_material:
record:
- id: '5587'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Statistical mechanics for metabolic networks during steady state growth
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 9
year: '2018'
...
---
_id: '67'
abstract:
- lang: eng
text: 'Gene regulatory networks evolve through rewiring of individual components—that
is, through changes in regulatory connections. However, the mechanistic basis
of regulatory rewiring is poorly understood. Using a canonical gene regulatory
system, we quantify the properties of transcription factors that determine the
evolutionary potential for rewiring of regulatory connections: robustness, tunability
and evolvability. In vivo repression measurements of two repressors at mutated
operator sites reveal their contrasting evolutionary potential: while robustness
and evolvability were positively correlated, both were in trade-off with tunability.
Epistatic interactions between adjacent operators alleviated this trade-off. A
thermodynamic model explains how the differences in robustness, tunability and
evolvability arise from biophysical characteristics of repressor–DNA binding.
The model also uncovers that the energy matrix, which describes how mutations
affect repressor–DNA binding, encodes crucial information about the evolutionary
potential of a repressor. The biophysical determinants of evolutionary potential
for regulatory rewiring constitute a mechanistic framework for understanding network
evolution.'
article_processing_charge: No
article_type: original
author:
- first_name: Claudia
full_name: Igler, Claudia
id: 46613666-F248-11E8-B48F-1D18A9856A87
last_name: Igler
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Evolutionary potential
of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution.
2018;2(10):1633-1643. doi:10.1038/s41559-018-0651-y
apa: Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018).
Evolutionary potential of transcription factors for gene regulatory rewiring.
Nature Ecology and Evolution. Nature Publishing Group. https://doi.org/10.1038/s41559-018-0651-y
chicago: Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin
C Guet. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.”
Nature Ecology and Evolution. Nature Publishing Group, 2018. https://doi.org/10.1038/s41559-018-0651-y.
ieee: C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Evolutionary
potential of transcription factors for gene regulatory rewiring,” Nature Ecology
and Evolution, vol. 2, no. 10. Nature Publishing Group, pp. 1633–1643, 2018.
ista: Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Evolutionary potential
of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution.
2(10), 1633–1643.
mla: Igler, Claudia, et al. “Evolutionary Potential of Transcription Factors for
Gene Regulatory Rewiring.” Nature Ecology and Evolution, vol. 2, no. 10,
Nature Publishing Group, 2018, pp. 1633–43, doi:10.1038/s41559-018-0651-y.
short: C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, Nature Ecology
and Evolution 2 (2018) 1633–1643.
date_created: 2018-12-11T11:44:27Z
date_published: 2018-09-10T00:00:00Z
date_updated: 2024-03-28T23:30:49Z
day: '10'
ddc:
- '570'
department:
- _id: CaGu
- _id: GaTk
- _id: JoBo
doi: 10.1038/s41559-018-0651-y
ec_funded: 1
external_id:
isi:
- '000447947600021'
file:
- access_level: open_access
checksum: 383a2e2c944a856e2e821ec8e7bf71b6
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T11:28:52Z
date_updated: 2020-07-14T12:47:37Z
file_id: '7830'
file_name: 2018_NatureEcology_Igler.pdf
file_size: 1135973
relation: main_file
file_date_updated: 2020-07-14T12:47:37Z
has_accepted_license: '1'
intvolume: ' 2'
isi: 1
issue: '10'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 1633 - 1643
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
- _id: 251EE76E-B435-11E9-9278-68D0E5697425
grant_number: '24573'
name: Design principles underlying genetic switch architecture (DOC Fellowship)
publication: Nature Ecology and Evolution
publication_status: published
publisher: Nature Publishing Group
publist_id: '7987'
quality_controlled: '1'
related_material:
record:
- id: '5585'
relation: popular_science
status: public
- id: '6371'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Evolutionary potential of transcription factors for gene regulatory rewiring
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2
year: '2018'
...
---
_id: '613'
abstract:
- lang: eng
text: 'Bacteria in groups vary individually, and interact with other bacteria and
the environment to produce population-level patterns of gene expression. Investigating
such behavior in detail requires measuring and controlling populations at the
single-cell level alongside precisely specified interactions and environmental
characteristics. Here we present an automated, programmable platform that combines
image-based gene expression and growth measurements with on-line optogenetic expression
control for hundreds of individual Escherichia coli cells over days, in a dynamically
adjustable environment. This integrated platform broadly enables experiments that
bridge individual and population behaviors. We demonstrate: (i) population structuring
by independent closed-loop control of gene expression in many individual cells,
(ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid
bio-digital circuits in single cells, and freely specifiable digital communication
between individual bacteria. These examples showcase the potential for real-time
integration of theoretical models with measurement and control of many individual
cells to investigate and engineer microbial population behavior.'
acknowledgement: We are grateful to M. Lang, H. Janovjak, M. Khammash, A. Milias-Argeitis,
M. Rullan, G. Batt, A. Bosma-Moody, Aryan, S. Leibler, and members of the Guet and
Tkačik groups for helpful discussion, comments, and suggestions. We thank A. Moglich,
T. Mathes, J. Tabor, and S. Schmidl for kind gifts of strains, and R. Hauschild,
B. Knep, M. Lang, T. Asenov, E. Papusheva, T. Menner, T. Adletzberger, and J. Merrin
for technical assistance. The research leading to these results has received funding
from the People Programme (Marie Curie Actions) of the European Union’s Seventh
Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. (to
R.C. and J.R.), Austrian Science Fund grant FWF P28844 (to G.T.), and internal IST
Austria Interdisciplinary Project Support. J.R. acknowledges support from the Agence
Nationale de la Recherche (ANR) under Grant Nos. ANR-16-CE33-0018 (MEMIP), ANR-16-CE12-0025
(COGEX) and ANR-10-BINF-06-01 (ICEBERG).
article_number: '1535'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. Shaping bacterial population
behavior through computer interfaced control of individual cells. Nature Communications.
2017;8(1). doi:10.1038/s41467-017-01683-1
apa: Chait, R. P., Ruess, J., Bergmiller, T., Tkačik, G., & Guet, C. C. (2017).
Shaping bacterial population behavior through computer interfaced control of individual
cells. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01683-1
chicago: Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, and Calin
C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control
of Individual Cells.” Nature Communications. Nature Publishing Group, 2017.
https://doi.org/10.1038/s41467-017-01683-1.
ieee: R. P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, and C. C. Guet, “Shaping
bacterial population behavior through computer interfaced control of individual
cells,” Nature Communications, vol. 8, no. 1. Nature Publishing Group,
2017.
ista: Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. 2017. Shaping bacterial
population behavior through computer interfaced control of individual cells. Nature
Communications. 8(1), 1535.
mla: Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer
Interfaced Control of Individual Cells.” Nature Communications, vol. 8,
no. 1, 1535, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01683-1.
short: R.P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, C.C. Guet, Nature Communications
8 (2017).
date_created: 2018-12-11T11:47:30Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:06:15Z
day: '01'
ddc:
- '576'
- '579'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1038/s41467-017-01683-1
ec_funded: 1
file:
- access_level: open_access
checksum: 44bb5d0229926c23a9955d9fe0f9723f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:05Z
date_updated: 2020-07-14T12:47:20Z
file_id: '5190'
file_name: IST-2017-911-v1+1_s41467-017-01683-1.pdf
file_size: 1951699
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7191'
pubrep_id: '911'
quality_controlled: '1'
scopus_import: 1
status: public
title: Shaping bacterial population behavior through computer interfaced control of
individual cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '652'
abstract:
- lang: eng
text: 'We present an approach that enables robots to self-organize their sensorimotor
behavior from scratch without providing specific information about neither the
robot nor its environment. This is achieved by a simple neural control law that
increases the consistency between external sensor dynamics and internal neural
dynamics of the utterly simple controller. In this way, the embodiment and the
agent-environment coupling are the only source of individual development. We show
how an anthropomorphic tendon driven arm-shoulder system develops different behaviors
depending on that coupling. For instance: Given a bottle half-filled with water,
the arm starts to shake it, driven by the physical response of the water. When
attaching a brush, the arm can be manipulated into wiping a table, and when connected
to a revolvable wheel it finds out how to rotate it. Thus, the robot may be said
to discover the affordances of the world. When allowing two (simulated) humanoid
robots to interact physically, they engage into a joint behavior development leading
to, for instance, spontaneous cooperation. More social effects are observed if
the robots can visually perceive each other. Although, as an observer, it is tempting
to attribute an apparent intentionality, there is nothing of the kind put in.
As a conclusion, we argue that emergent behavior may be much less rooted in explicit
intentions, internal motivations, or specific reward systems than is commonly
believed.'
article_number: '7846789'
author:
- first_name: Ralf
full_name: Der, Ralf
last_name: Der
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
citation:
ama: 'Der R, Martius GS. Dynamical self consistency leads to behavioral development
and emergent social interactions in robots. In: IEEE; 2017. doi:10.1109/DEVLRN.2016.7846789'
apa: 'Der, R., & Martius, G. S. (2017). Dynamical self consistency leads to
behavioral development and emergent social interactions in robots. Presented at
the ICDL EpiRob: International Conference on Development and Learning and Epigenetic
Robotics , Cergy-Pontoise, France: IEEE. https://doi.org/10.1109/DEVLRN.2016.7846789'
chicago: Der, Ralf, and Georg S Martius. “Dynamical Self Consistency Leads to Behavioral
Development and Emergent Social Interactions in Robots.” IEEE, 2017. https://doi.org/10.1109/DEVLRN.2016.7846789.
ieee: 'R. Der and G. S. Martius, “Dynamical self consistency leads to behavioral
development and emergent social interactions in robots,” presented at the ICDL
EpiRob: International Conference on Development and Learning and Epigenetic Robotics
, Cergy-Pontoise, France, 2017.'
ista: 'Der R, Martius GS. 2017. Dynamical self consistency leads to behavioral development
and emergent social interactions in robots. ICDL EpiRob: International Conference
on Development and Learning and Epigenetic Robotics , 7846789.'
mla: Der, Ralf, and Georg S. Martius. Dynamical Self Consistency Leads to Behavioral
Development and Emergent Social Interactions in Robots. 7846789, IEEE, 2017,
doi:10.1109/DEVLRN.2016.7846789.
short: R. Der, G.S. Martius, in:, IEEE, 2017.
conference:
end_date: 2016-09-22
location: Cergy-Pontoise, France
name: 'ICDL EpiRob: International Conference on Development and Learning and Epigenetic
Robotics '
start_date: 2016-09-19
date_created: 2018-12-11T11:47:43Z
date_published: 2017-02-07T00:00:00Z
date_updated: 2021-01-12T08:07:51Z
day: '07'
department:
- _id: ChLa
- _id: GaTk
doi: 10.1109/DEVLRN.2016.7846789
language:
- iso: eng
month: '02'
oa_version: None
publication_identifier:
isbn:
- 978-150905069-7
publication_status: published
publisher: IEEE
publist_id: '7100'
quality_controlled: '1'
scopus_import: 1
status: public
title: Dynamical self consistency leads to behavioral development and emergent social
interactions in robots
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '658'
abstract:
- lang: eng
text: 'With the accelerated development of robot technologies, control becomes one
of the central themes of research. In traditional approaches, the controller,
by its internal functionality, finds appropriate actions on the basis of specific
objectives for the task at hand. While very successful in many applications, self-organized
control schemes seem to be favored in large complex systems with unknown dynamics
or which are difficult to model. Reasons are the expected scalability, robustness,
and resilience of self-organizing systems. The paper presents a self-learning
neurocontroller based on extrinsic differential plasticity introduced recently,
applying it to an anthropomorphic musculoskeletal robot arm with attached objects
of unknown physical dynamics. The central finding of the paper is the following
effect: by the mere feedback through the internal dynamics of the object, the
robot is learning to relate each of the objects with a very specific sensorimotor
pattern. Specifically, an attached pendulum pilots the arm into a circular motion,
a half-filled bottle produces axis oriented shaking behavior, a wheel is getting
rotated, and wiping patterns emerge automatically in a table-plus-brush setting.
By these object-specific dynamical patterns, the robot may be said to recognize
the object''s identity, or in other words, it discovers dynamical affordances
of objects. Furthermore, when including hand coordinates obtained from a camera,
a dedicated hand-eye coordination self-organizes spontaneously. These phenomena
are discussed from a specific dynamical system perspective. Central is the dedicated
working regime at the border to instability with its potentially infinite reservoir
of (limit cycle) attractors "waiting" to be excited. Besides converging
toward one of these attractors, variate behavior is also arising from a self-induced
attractor morphing driven by the learning rule. We claim that experimental investigations
with this anthropomorphic, self-learning robot not only generate interesting and
potentially useful behaviors, but may also help to better understand what subjective
human muscle feelings are, how they can be rooted in sensorimotor patterns, and
how these concepts may feed back on robotics.'
article_number: '00008'
article_processing_charge: Yes
author:
- first_name: Ralf
full_name: Der, Ralf
last_name: Der
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
citation:
ama: Der R, Martius GS. Self organized behavior generation for musculoskeletal robots.
Frontiers in Neurorobotics. 2017;11(MAR). doi:10.3389/fnbot.2017.00008
apa: Der, R., & Martius, G. S. (2017). Self organized behavior generation for
musculoskeletal robots. Frontiers in Neurorobotics. Frontiers Research
Foundation. https://doi.org/10.3389/fnbot.2017.00008
chicago: Der, Ralf, and Georg S Martius. “Self Organized Behavior Generation for
Musculoskeletal Robots.” Frontiers in Neurorobotics. Frontiers Research
Foundation, 2017. https://doi.org/10.3389/fnbot.2017.00008.
ieee: R. Der and G. S. Martius, “Self organized behavior generation for musculoskeletal
robots,” Frontiers in Neurorobotics, vol. 11, no. MAR. Frontiers Research
Foundation, 2017.
ista: Der R, Martius GS. 2017. Self organized behavior generation for musculoskeletal
robots. Frontiers in Neurorobotics. 11(MAR), 00008.
mla: Der, Ralf, and Georg S. Martius. “Self Organized Behavior Generation for Musculoskeletal
Robots.” Frontiers in Neurorobotics, vol. 11, no. MAR, 00008, Frontiers
Research Foundation, 2017, doi:10.3389/fnbot.2017.00008.
short: R. Der, G.S. Martius, Frontiers in Neurorobotics 11 (2017).
date_created: 2018-12-11T11:47:45Z
date_published: 2017-03-16T00:00:00Z
date_updated: 2021-01-12T08:08:04Z
day: '16'
ddc:
- '006'
department:
- _id: ChLa
- _id: GaTk
doi: 10.3389/fnbot.2017.00008
ec_funded: 1
file:
- access_level: open_access
checksum: b1bc43f96d1df3313c03032c2a46388d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:49Z
date_updated: 2020-07-14T12:47:33Z
file_id: '5371'
file_name: IST-2017-903-v1+1_fnbot-11-00008.pdf
file_size: 8439566
relation: main_file
file_date_updated: 2020-07-14T12:47:33Z
has_accepted_license: '1'
intvolume: ' 11'
issue: MAR
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Frontiers in Neurorobotics
publication_identifier:
issn:
- '16625218'
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '7078'
pubrep_id: '903'
quality_controlled: '1'
scopus_import: 1
status: public
title: Self organized behavior generation for musculoskeletal robots
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2017'
...
---
_id: '720'
abstract:
- lang: eng
text: 'Advances in multi-unit recordings pave the way for statistical modeling of
activity patterns in large neural populations. Recent studies have shown that
the summed activity of all neurons strongly shapes the population response. A
separate recent finding has been that neural populations also exhibit criticality,
an anomalously large dynamic range for the probabilities of different population
activity patterns. Motivated by these two observations, we introduce a class of
probabilistic models which takes into account the prior knowledge that the neural
population could be globally coupled and close to critical. These models consist
of an energy function which parametrizes interactions between small groups of
neurons, and an arbitrary positive, strictly increasing, and twice differentiable
function which maps the energy of a population pattern to its probability. We
show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an
accurate description of the activity of retinal ganglion cells which outperforms
previous models based on the summed activity of neurons; 2) prior knowledge that
the population is critical translates to prior expectations about the shape of
the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous
latent variable globally coupling the system whose distribution we can infer from
data. Our method is independent of the underlying system’s state space; hence,
it can be applied to other systems such as natural scenes or amino acid sequences
of proteins which are also known to exhibit criticality.'
article_number: e1005763
article_processing_charge: Yes
author:
- first_name: Jan
full_name: Humplik, Jan
id: 2E9627A8-F248-11E8-B48F-1D18A9856A87
last_name: Humplik
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Humplik J, Tkačik G. Probabilistic models for neural populations that naturally
capture global coupling and criticality. PLoS Computational Biology. 2017;13(9).
doi:10.1371/journal.pcbi.1005763
apa: Humplik, J., & Tkačik, G. (2017). Probabilistic models for neural populations
that naturally capture global coupling and criticality. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005763
chicago: Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations
That Naturally Capture Global Coupling and Criticality.” PLoS Computational
Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005763.
ieee: J. Humplik and G. Tkačik, “Probabilistic models for neural populations that
naturally capture global coupling and criticality,” PLoS Computational Biology,
vol. 13, no. 9. Public Library of Science, 2017.
ista: Humplik J, Tkačik G. 2017. Probabilistic models for neural populations that
naturally capture global coupling and criticality. PLoS Computational Biology.
13(9), e1005763.
mla: Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations
That Naturally Capture Global Coupling and Criticality.” PLoS Computational
Biology, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005763.
short: J. Humplik, G. Tkačik, PLoS Computational Biology 13 (2017).
date_created: 2018-12-11T11:48:08Z
date_published: 2017-09-19T00:00:00Z
date_updated: 2021-01-12T08:12:21Z
day: '19'
ddc:
- '530'
- '571'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1005763
file:
- access_level: open_access
checksum: 81107096c19771c36ddbe6f0282a3acb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:30Z
date_updated: 2020-07-14T12:47:53Z
file_id: '5352'
file_name: IST-2017-884-v1+1_journal.pcbi.1005763.pdf
file_size: 14167050
relation: main_file
file_date_updated: 2020-07-14T12:47:53Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 255008E4-B435-11E9-9278-68D0E5697425
grant_number: RGP0065/2012
name: Information processing and computation in fish groups
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: PLoS Computational Biology
publication_identifier:
issn:
- 1553734X
publication_status: published
publisher: Public Library of Science
publist_id: '6960'
pubrep_id: '884'
quality_controlled: '1'
scopus_import: 1
status: public
title: Probabilistic models for neural populations that naturally capture global coupling
and criticality
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '725'
abstract:
- lang: eng
text: Individual computations and social interactions underlying collective behavior
in groups of animals are of great ethological, behavioral, and theoretical interest.
While complex individual behaviors have successfully been parsed into small dictionaries
of stereotyped behavioral modes, studies of collective behavior largely ignored
these findings; instead, their focus was on inferring single, mode-independent
social interaction rules that reproduced macroscopic and often qualitative features
of group behavior. Here, we bring these two approaches together to predict individual
swimming patterns of adult zebrafish in a group. We show that fish alternate between
an “active” mode, in which they are sensitive to the swimming patterns of conspecifics,
and a “passive” mode, where they ignore them. Using a model that accounts for
these two modes explicitly, we predict behaviors of individual fish with high
accuracy, outperforming previous approaches that assumed a single continuous computation
by individuals and simple metric or topological weighing of neighbors’ behavior.
At the group level, switching between active and passive modes is uncorrelated
among fish, but correlated directional swimming behavior still emerges. Our quantitative
approach for studying complex, multi-modal individual behavior jointly with emergent
group behavior is readily extensible to additional behavioral modes and their
neural correlates as well as to other species.
author:
- first_name: Roy
full_name: Harpaz, Roy
last_name: Harpaz
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
citation:
ama: Harpaz R, Tkačik G, Schneidman E. Discrete modes of social information processing
predict individual behavior of fish in a group. PNAS. 2017;114(38):10149-10154.
doi:10.1073/pnas.1703817114
apa: Harpaz, R., Tkačik, G., & Schneidman, E. (2017). Discrete modes of social
information processing predict individual behavior of fish in a group. PNAS.
National Academy of Sciences. https://doi.org/10.1073/pnas.1703817114
chicago: Harpaz, Roy, Gašper Tkačik, and Elad Schneidman. “Discrete Modes of Social
Information Processing Predict Individual Behavior of Fish in a Group.” PNAS.
National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1703817114.
ieee: R. Harpaz, G. Tkačik, and E. Schneidman, “Discrete modes of social information
processing predict individual behavior of fish in a group,” PNAS, vol.
114, no. 38. National Academy of Sciences, pp. 10149–10154, 2017.
ista: Harpaz R, Tkačik G, Schneidman E. 2017. Discrete modes of social information
processing predict individual behavior of fish in a group. PNAS. 114(38), 10149–10154.
mla: Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict
Individual Behavior of Fish in a Group.” PNAS, vol. 114, no. 38, National
Academy of Sciences, 2017, pp. 10149–54, doi:10.1073/pnas.1703817114.
short: R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 10149–10154.
date_created: 2018-12-11T11:48:10Z
date_published: 2017-09-19T00:00:00Z
date_updated: 2021-01-12T08:12:36Z
day: '19'
department:
- _id: GaTk
doi: 10.1073/pnas.1703817114
external_id:
pmid:
- '28874581'
intvolume: ' 114'
issue: '38'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617265/
month: '09'
oa: 1
oa_version: Submitted Version
page: 10149 - 10154
pmid: 1
publication: PNAS
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
publist_id: '6953'
quality_controlled: '1'
scopus_import: 1
status: public
title: Discrete modes of social information processing predict individual behavior
of fish in a group
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '9709'
abstract:
- lang: eng
text: Across the nervous system, certain population spiking patterns are observed
far more frequently than others. A hypothesis about this structure is that these
collective activity patterns function as population codewords–collective modes–carrying
information distinct from that of any single cell. We investigate this phenomenon
in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop
a novel statistical model that decomposes the population response into modes;
it predicts the distribution of spiking activity in the ganglion cell population
with high accuracy. We found that the modes represent localized features of the
visual stimulus that are distinct from the features represented by single neurons.
Modes form clusters of activity states that are readily discriminated from one
another. When we repeated the same visual stimulus, we found that the same mode
was robustly elicited. These results suggest that retinal ganglion cells’ collective
signaling is endowed with a form of error-correcting code–a principle that may
hold in brain areas beyond retina.
article_processing_charge: No
author:
- first_name: Jason
full_name: Prentice, Jason
last_name: Prentice
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Mark
full_name: Ioffe, Mark
last_name: Ioffe
- first_name: Adrianna
full_name: Loback, Adrianna
last_name: Loback
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
citation:
ama: 'Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust
modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc'
apa: 'Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M.
(2017). Data from: Error-robust modes of the retinal population code. Dryad. https://doi.org/10.5061/dryad.1f1rc'
chicago: 'Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik,
and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.”
Dryad, 2017. https://doi.org/10.5061/dryad.1f1rc.'
ieee: 'J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data
from: Error-robust modes of the retinal population code.” Dryad, 2017.'
ista: 'Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from:
Error-robust modes of the retinal population code, Dryad, 10.5061/dryad.1f1rc.'
mla: 'Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population
Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.'
short: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).
date_created: 2021-07-23T11:34:34Z
date_published: 2017-10-18T00:00:00Z
date_updated: 2023-02-21T16:34:41Z
day: '18'
department:
- _id: GaTk
doi: 10.5061/dryad.1f1rc
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.1f1rc
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1197'
relation: used_in_publication
status: public
status: public
title: 'Data from: Error-robust modes of the retinal population code'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '680'
abstract:
- lang: eng
text: In order to respond reliably to specific features of their environment, sensory
neurons need to integrate multiple incoming noisy signals. Crucially, they also
need to compete for the interpretation of those signals with other neurons representing
similar features. The form that this competition should take depends critically
on the noise corrupting these signals. In this study we show that for the type
of noise commonly observed in sensory systems, whose variance scales with the
mean signal, sensory neurons should selectively divide their input signals by
their predictions, suppressing ambiguous cues while amplifying others. Any change
in the stimulus context alters which inputs are suppressed, leading to a deep
dynamic reshaping of neural receptive fields going far beyond simple surround
suppression. Paradoxically, these highly variable receptive fields go alongside
and are in fact required for an invariant representation of external sensory features.
In addition to offering a normative account of context-dependent changes in sensory
responses, perceptual inference in the presence of signal-dependent noise accounts
for ubiquitous features of sensory neurons such as divisive normalization, gain
control and contrast dependent temporal dynamics.
article_number: e1005582
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Paul
full_name: Masset, Paul
last_name: Masset
- first_name: Boris
full_name: Gutkin, Boris
last_name: Gutkin
- first_name: Sophie
full_name: Denève, Sophie
last_name: Denève
citation:
ama: Chalk MJ, Masset P, Gutkin B, Denève S. Sensory noise predicts divisive reshaping
of receptive fields. PLoS Computational Biology. 2017;13(6). doi:10.1371/journal.pcbi.1005582
apa: Chalk, M. J., Masset, P., Gutkin, B., & Denève, S. (2017). Sensory noise
predicts divisive reshaping of receptive fields. PLoS Computational Biology.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005582
chicago: Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Sensory
Noise Predicts Divisive Reshaping of Receptive Fields.” PLoS Computational
Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005582.
ieee: M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Sensory noise predicts
divisive reshaping of receptive fields,” PLoS Computational Biology, vol.
13, no. 6. Public Library of Science, 2017.
ista: Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Sensory noise predicts divisive
reshaping of receptive fields. PLoS Computational Biology. 13(6), e1005582.
mla: Chalk, Matthew J., et al. “Sensory Noise Predicts Divisive Reshaping of Receptive
Fields.” PLoS Computational Biology, vol. 13, no. 6, e1005582, Public Library
of Science, 2017, doi:10.1371/journal.pcbi.1005582.
short: M.J. Chalk, P. Masset, B. Gutkin, S. Denève, PLoS Computational Biology 13
(2017).
date_created: 2018-12-11T11:47:53Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-02-23T14:10:54Z
day: '01'
ddc:
- '571'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1005582
file:
- access_level: open_access
checksum: 796a1026076af6f4405a47d985bc7b68
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:47Z
date_updated: 2020-07-14T12:47:40Z
file_id: '4645'
file_name: IST-2017-898-v1+1_journal.pcbi.1005582.pdf
file_size: 14555676
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_identifier:
issn:
- 1553734X
publication_status: published
publisher: Public Library of Science
publist_id: '7035'
pubrep_id: '898'
quality_controlled: '1'
related_material:
record:
- id: '9855'
relation: research_data
status: public
scopus_import: 1
status: public
title: Sensory noise predicts divisive reshaping of receptive fields
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '9855'
abstract:
- lang: eng
text: Includes derivation of optimal estimation algorithm, generalisation to non-poisson
noise statistics, correlated input noise, and implementation of in a multi-layer
neural network.
article_processing_charge: No
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Paul
full_name: Masset, Paul
last_name: Masset
- first_name: Boris
full_name: Gutkin, Boris
last_name: Gutkin
- first_name: Sophie
full_name: Denève, Sophie
last_name: Denève
citation:
ama: Chalk MJ, Masset P, Gutkin B, Denève S. Supplementary appendix. 2017. doi:10.1371/journal.pcbi.1005582.s001
apa: Chalk, M. J., Masset, P., Gutkin, B., & Denève, S. (2017). Supplementary
appendix. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005582.s001
chicago: Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Supplementary
Appendix.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005582.s001.
ieee: M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Supplementary appendix.”
Public Library of Science, 2017.
ista: Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Supplementary appendix, Public
Library of Science, 10.1371/journal.pcbi.1005582.s001.
mla: Chalk, Matthew J., et al. Supplementary Appendix. Public Library of
Science, 2017, doi:10.1371/journal.pcbi.1005582.s001.
short: M.J. Chalk, P. Masset, B. Gutkin, S. Denève, (2017).
date_created: 2021-08-10T07:05:10Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-02-23T12:52:17Z
day: '01'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1005582.s001
month: '06'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '680'
relation: used_in_publication
status: public
status: public
title: Supplementary appendix
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '666'
abstract:
- lang: eng
text: Antibiotics elicit drastic changes in microbial gene expression, including
the induction of stress response genes. While certain stress responses are known
to “cross-protect” bacteria from other stressors, it is unclear whether cellular
responses to antibiotics have a similar protective role. By measuring the genome-wide
transcriptional response dynamics of Escherichia coli to four antibiotics, we
found that trimethoprim induces a rapid acid stress response that protects bacteria
from subsequent exposure to acid. Combining microfluidics with time-lapse imaging
to monitor survival and acid stress response in single cells revealed that the
noisy expression of the acid resistance operon gadBC correlates with single-cell
survival. Cells with higher gadBC expression following trimethoprim maintain higher
intracellular pH and survive the acid stress longer. The seemingly random single-cell
survival under acid stress can therefore be predicted from gadBC expression and
rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap
for identifying the molecular mechanisms of single-cell cross-protection between
antibiotics and other stressors.
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
- first_name: Georg
full_name: Rieckh, Georg
id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87
last_name: Rieckh
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Mitosch K, Rieckh G, Bollenbach MT. Noisy response to antibiotic stress predicts
subsequent single cell survival in an acidic environment. Cell Systems.
2017;4(4):393-403. doi:10.1016/j.cels.2017.03.001
apa: Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2017). Noisy response to
antibiotic stress predicts subsequent single cell survival in an acidic environment.
Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2017.03.001
chicago: Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response
to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.”
Cell Systems. Cell Press, 2017. https://doi.org/10.1016/j.cels.2017.03.001.
ieee: K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic
stress predicts subsequent single cell survival in an acidic environment,” Cell
Systems, vol. 4, no. 4. Cell Press, pp. 393–403, 2017.
ista: Mitosch K, Rieckh G, Bollenbach MT. 2017. Noisy response to antibiotic stress
predicts subsequent single cell survival in an acidic environment. Cell Systems.
4(4), 393–403.
mla: Mitosch, Karin, et al. “Noisy Response to Antibiotic Stress Predicts Subsequent
Single Cell Survival in an Acidic Environment.” Cell Systems, vol. 4, no.
4, Cell Press, 2017, pp. 393–403, doi:10.1016/j.cels.2017.03.001.
short: K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403.
date_created: 2018-12-11T11:47:48Z
date_published: 2017-04-26T00:00:00Z
date_updated: 2023-09-07T12:00:25Z
day: '26'
ddc:
- '576'
- '610'
department:
- _id: ToBo
- _id: GaTk
doi: 10.1016/j.cels.2017.03.001
ec_funded: 1
file:
- access_level: open_access
checksum: 04ff20011c3d9a601c514aa999a5fe1a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:54Z
date_updated: 2020-07-14T12:47:35Z
file_id: '5041'
file_name: IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf
file_size: 2438660
relation: main_file
file_date_updated: 2020-07-14T12:47:35Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 393 - 403
project:
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
publication: Cell Systems
publication_identifier:
issn:
- '24054712'
publication_status: published
publisher: Cell Press
publist_id: '7061'
pubrep_id: '901'
quality_controlled: '1'
related_material:
record:
- id: '818'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Noisy response to antibiotic stress predicts subsequent single cell survival
in an acidic environment
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2017'
...
---
_id: '2016'
abstract:
- lang: eng
text: The Ising model is one of the simplest and most famous models of interacting
systems. It was originally proposed to model ferromagnetic interactions in statistical
physics and is now widely used to model spatial processes in many areas such as
ecology, sociology, and genetics, usually without testing its goodness-of-fit.
Here, we propose an exact goodness-of-fit test for the finite-lattice Ising model.
The theory of Markov bases has been developed in algebraic statistics for exact
goodness-of-fit testing using a Monte Carlo approach. However, this beautiful
theory has fallen short of its promise for applications, because finding a Markov
basis is usually computationally intractable. We develop a Monte Carlo method
for exact goodness-of-fit testing for the Ising model which avoids computing a
Markov basis and also leads to a better connectivity of the Markov chain and hence
to a faster convergence. We show how this method can be applied to analyze the
spatial organization of receptors on the cell membrane.
article_processing_charge: No
author:
- first_name: Abraham
full_name: Martin Del Campo Sanchez, Abraham
last_name: Martin Del Campo Sanchez
- first_name: Sarah A
full_name: Cepeda Humerez, Sarah A
id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87
last_name: Cepeda Humerez
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. Exact goodness-of-fit
testing for the Ising model. Scandinavian Journal of Statistics. 2017;44(2):285-306.
doi:10.1111/sjos.12251
apa: Martin Del Campo Sanchez, A., Cepeda Humerez, S. A., & Uhler, C. (2017).
Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of
Statistics. Wiley-Blackwell. https://doi.org/10.1111/sjos.12251
chicago: Martin Del Campo Sanchez, Abraham, Sarah A Cepeda Humerez, and Caroline
Uhler. “Exact Goodness-of-Fit Testing for the Ising Model.” Scandinavian Journal
of Statistics. Wiley-Blackwell, 2017. https://doi.org/10.1111/sjos.12251.
ieee: A. Martin Del Campo Sanchez, S. A. Cepeda Humerez, and C. Uhler, “Exact goodness-of-fit
testing for the Ising model,” Scandinavian Journal of Statistics, vol.
44, no. 2. Wiley-Blackwell, pp. 285–306, 2017.
ista: Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. 2017. Exact goodness-of-fit
testing for the Ising model. Scandinavian Journal of Statistics. 44(2), 285–306.
mla: Martin Del Campo Sanchez, Abraham, et al. “Exact Goodness-of-Fit Testing for
the Ising Model.” Scandinavian Journal of Statistics, vol. 44, no. 2, Wiley-Blackwell,
2017, pp. 285–306, doi:10.1111/sjos.12251.
short: A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian
Journal of Statistics 44 (2017) 285–306.
date_created: 2018-12-11T11:55:13Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-19T15:13:27Z
day: '01'
department:
- _id: GaTk
doi: 10.1111/sjos.12251
external_id:
arxiv:
- '1410.1242'
isi:
- '000400985000001'
intvolume: ' 44'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1410.1242
month: '06'
oa: 1
oa_version: Preprint
page: 285 - 306
publication: Scandinavian Journal of Statistics
publication_identifier:
issn:
- '03036898'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5060'
quality_controlled: '1'
related_material:
record:
- id: '6473'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Exact goodness-of-fit testing for the Ising model
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 44
year: '2017'
...
---
_id: '1104'
abstract:
- lang: eng
text: In the early visual system, cells of the same type perform the same computation
in different places of the visual field. How these cells code together a complex
visual scene is unclear. A common assumption is that cells of a single-type extract
a single-stimulus feature to form a feature map, but this has rarely been observed
directly. Using large-scale recordings in the rat retina, we show that a homogeneous
population of fast OFF ganglion cells simultaneously encodes two radically different
features of a visual scene. Cells close to a moving object code quasilinearly
for its position, while distant cells remain largely invariant to the object's
position and, instead, respond nonlinearly to changes in the object's speed. We
develop a quantitative model that accounts for this effect and identify a disinhibitory
circuit that mediates it. Ganglion cells of a single type thus do not code for
one, but two features simultaneously. This richer, flexible neural map might also
be present in other sensory systems.
article_number: '1964'
article_processing_charge: No
author:
- first_name: Stephane
full_name: Deny, Stephane
last_name: Deny
- first_name: Ulisse
full_name: Ferrari, Ulisse
last_name: Ferrari
- first_name: Emilie
full_name: Mace, Emilie
last_name: Mace
- first_name: Pierre
full_name: Yger, Pierre
last_name: Yger
- first_name: Romain
full_name: Caplette, Romain
last_name: Caplette
- first_name: Serge
full_name: Picaud, Serge
last_name: Picaud
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
citation:
ama: Deny S, Ferrari U, Mace E, et al. Multiplexed computations in retinal ganglion
cells of a single type. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-02159-y
apa: Deny, S., Ferrari, U., Mace, E., Yger, P., Caplette, R., Picaud, S., … Marre,
O. (2017). Multiplexed computations in retinal ganglion cells of a single type.
Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-02159-y
chicago: Deny, Stephane, Ulisse Ferrari, Emilie Mace, Pierre Yger, Romain Caplette,
Serge Picaud, Gašper Tkačik, and Olivier Marre. “Multiplexed Computations in Retinal
Ganglion Cells of a Single Type.” Nature Communications. Nature Publishing
Group, 2017. https://doi.org/10.1038/s41467-017-02159-y.
ieee: S. Deny et al., “Multiplexed computations in retinal ganglion cells
of a single type,” Nature Communications, vol. 8, no. 1. Nature Publishing
Group, 2017.
ista: Deny S, Ferrari U, Mace E, Yger P, Caplette R, Picaud S, Tkačik G, Marre O.
2017. Multiplexed computations in retinal ganglion cells of a single type. Nature
Communications. 8(1), 1964.
mla: Deny, Stephane, et al. “Multiplexed Computations in Retinal Ganglion Cells
of a Single Type.” Nature Communications, vol. 8, no. 1, 1964, Nature Publishing
Group, 2017, doi:10.1038/s41467-017-02159-y.
short: S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkačik,
O. Marre, Nature Communications 8 (2017).
date_created: 2018-12-11T11:50:10Z
date_published: 2017-12-06T00:00:00Z
date_updated: 2023-09-20T11:41:19Z
day: '06'
ddc:
- '571'
department:
- _id: GaTk
doi: 10.1038/s41467-017-02159-y
ec_funded: 1
external_id:
isi:
- '000417241200004'
file:
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content_type: application/pdf
creator: system
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isi: 1
issue: '1'
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- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25CD3DD2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '604102'
name: Localization of ion channels and receptors by two and three-dimensional immunoelectron
microscopic approaches
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6266'
pubrep_id: '921'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multiplexed computations in retinal ganglion cells of a single type
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2017'
...
---
_id: '993'
abstract:
- lang: eng
text: In real-world applications, observations are often constrained to a small
fraction of a system. Such spatial subsampling can be caused by the inaccessibility
or the sheer size of the system, and cannot be overcome by longer sampling. Spatial
subsampling can strongly bias inferences about a system’s aggregated properties.
To overcome the bias, we derive analytically a subsampling scaling framework that
is applicable to different observables, including distributions of neuronal avalanches,
of number of people infected during an epidemic outbreak, and of node degrees.
We demonstrate how to infer the correct distributions of the underlying full system,
how to apply it to distinguish critical from subcritical systems, and how to disentangle
subsampling and finite size effects. Lastly, we apply subsampling scaling to neuronal
avalanche models and to recordings from developing neural networks. We show that
only mature, but not young networks follow power-law scaling, indicating self-organization
to criticality during development.
article_number: '15140'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Anna
full_name: Levina (Martius), Anna
id: 35AF8020-F248-11E8-B48F-1D18A9856A87
last_name: Levina (Martius)
- first_name: Viola
full_name: Priesemann, Viola
last_name: Priesemann
citation:
ama: Levina (Martius) A, Priesemann V. Subsampling scaling. Nature Communications.
2017;8. doi:10.1038/ncomms15140
apa: Levina (Martius), A., & Priesemann, V. (2017). Subsampling scaling. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms15140
chicago: Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature
Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15140.
ieee: A. Levina (Martius) and V. Priesemann, “Subsampling scaling,” Nature Communications,
vol. 8. Nature Publishing Group, 2017.
ista: Levina (Martius) A, Priesemann V. 2017. Subsampling scaling. Nature Communications.
8, 15140.
mla: Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature
Communications, vol. 8, 15140, Nature Publishing Group, 2017, doi:10.1038/ncomms15140.
short: A. Levina (Martius), V. Priesemann, Nature Communications 8 (2017).
date_created: 2018-12-11T11:49:35Z
date_published: 2017-05-04T00:00:00Z
date_updated: 2023-09-22T09:54:07Z
day: '04'
ddc:
- '005'
- '571'
department:
- _id: GaTk
- _id: JoCs
doi: 10.1038/ncomms15140
ec_funded: 1
external_id:
isi:
- '000400560700001'
file:
- access_level: open_access
checksum: 9880212f8c4c53404c7c6fbf9023c53a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:05Z
date_updated: 2020-07-14T12:48:19Z
file_id: '5122'
file_name: IST-2017-819-v1+1_2017_Levina_SubsamplingScaling.pdf
file_size: 746224
relation: main_file
file_date_updated: 2020-07-14T12:48:19Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6406'
pubrep_id: '819'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Subsampling scaling
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2017'
...
---
_id: '955'
abstract:
- lang: eng
text: 'Gene expression is controlled by networks of regulatory proteins that interact
specifically with external signals and DNA regulatory sequences. These interactions
force the network components to co-evolve so as to continually maintain function.
Yet, existing models of evolution mostly focus on isolated genetic elements. In
contrast, we study the essential process by which regulatory networks grow: the
duplication and subsequent specialization of network components. We synthesize
a biophysical model of molecular interactions with the evolutionary framework
to find the conditions and pathways by which new regulatory functions emerge.
We show that specialization of new network components is usually slow, but can
be drastically accelerated in the presence of regulatory crosstalk and mutations
that promote promiscuous interactions between network components.'
article_number: '216'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions
on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1).
doi:10.1038/s41467-017-00238-8
apa: Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution
of new regulatory functions on biophysically realistic fitness landscapes. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8
chicago: Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik.
“Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.”
Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8.
ieee: T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new
regulatory functions on biophysically realistic fitness landscapes,” Nature
Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
ista: Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory
functions on biophysically realistic fitness landscapes. Nature Communications.
8(1), 216.
mla: Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically
Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216,
Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.
short: T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications
8 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-08-09T00:00:00Z
date_updated: 2023-09-22T10:00:49Z
day: '09'
ddc:
- '539'
- '576'
department:
- _id: GaTk
- _id: NiBa
doi: 10.1038/s41467-017-00238-8
ec_funded: 1
external_id:
isi:
- '000407198800005'
file:
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checksum: 29a1b5db458048d3bd5c67e0e2a56818
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creator: system
date_created: 2018-12-12T10:14:14Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5064'
file_name: IST-2017-864-v1+1_s41467-017-00238-8.pdf
file_size: 998157
relation: main_file
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content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:15Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5065'
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file_size: 9715993
relation: main_file
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has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6459'
pubrep_id: '864'
quality_controlled: '1'
related_material:
record:
- id: '6071'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Evolution of new regulatory functions on biophysically realistic fitness landscapes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2017'
...
---
_id: '959'
abstract:
- lang: eng
text: In this work it is shown that scale-free tails in metabolic flux distributions
inferred in stationary models are an artifact due to reactions involved in thermodynamically
unfeasible cycles, unbounded by physical constraints and in principle able to
perform work without expenditure of free energy. After implementing thermodynamic
constraints by removing such loops, metabolic flux distributions scale meaningfully
with the physical limiting factors, acquiring in turn a richer multimodal structure
potentially leading to symmetry breaking while optimizing for objective functions.
article_processing_charge: No
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: De Martino D. Scales and multimodal flux distributions in stationary metabolic
network models via thermodynamics. Physical Review E Statistical Nonlinear
and Soft Matter Physics . 2017;95(6):062419. doi:10.1103/PhysRevE.95.062419
apa: De Martino, D. (2017). Scales and multimodal flux distributions in stationary
metabolic network models via thermodynamics. Physical Review E Statistical
Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.95.062419
chicago: De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary
Metabolic Network Models via Thermodynamics.” Physical Review E Statistical
Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.95.062419.
ieee: D. De Martino, “Scales and multimodal flux distributions in stationary metabolic
network models via thermodynamics,” Physical Review E Statistical Nonlinear
and Soft Matter Physics , vol. 95, no. 6. American Institute of Physics, p.
062419, 2017.
ista: De Martino D. 2017. Scales and multimodal flux distributions in stationary
metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear
and Soft Matter Physics . 95(6), 062419.
mla: De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary
Metabolic Network Models via Thermodynamics.” Physical Review E Statistical
Nonlinear and Soft Matter Physics , vol. 95, no. 6, American Institute of
Physics, 2017, p. 062419, doi:10.1103/PhysRevE.95.062419.
short: D. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 95
(2017) 062419.
date_created: 2018-12-11T11:49:25Z
date_published: 2017-06-28T00:00:00Z
date_updated: 2023-09-22T09:59:01Z
day: '28'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.95.062419
ec_funded: 1
external_id:
isi:
- '000404546400004'
intvolume: ' 95'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/pdf/1703.00853.pdf
month: '06'
oa: 1
oa_version: Submitted Version
page: '062419'
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Physical Review E Statistical Nonlinear and Soft Matter Physics '
publication_identifier:
issn:
- '24700045'
publication_status: published
publisher: American Institute of Physics
publist_id: '6446'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scales and multimodal flux distributions in stationary metabolic network models
via thermodynamics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 95
year: '2017'
...
---
_id: '947'
abstract:
- lang: eng
text: Viewing the ways a living cell can organize its metabolism as the phase space
of a physical system, regulation can be seen as the ability to reduce the entropy
of that space by selecting specific cellular configurations that are, in some
sense, optimal. Here we quantify the amount of regulation required to control
a cell's growth rate by a maximum-entropy approach to the space of underlying
metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern
as described by genome-scale models. We link the mean growth rate achieved by
a population of cells to the minimal amount of metabolic regulation needed to
achieve it through a phase diagram that highlights how growth suppression can
be as costly (in regulatory terms) as growth enhancement. Moreover, we provide
an interpretation of the inverse temperature β controlling maximum-entropy distributions
based on the underlying growth dynamics. Specifically, we show that the asymptotic
value of β for a cell population can be expected to depend on (i) the carrying
capacity of the environment, (ii) the initial size of the colony, and (iii) the
probability distribution from which the inoculum was sampled. Results obtained
for E. coli and human cells are found to be remarkably consistent with empirical
evidence.
article_number: '010401'
article_processing_charge: No
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Fabrizio
full_name: Capuani, Fabrizio
last_name: Capuani
- first_name: Andrea
full_name: De Martino, Andrea
last_name: De Martino
citation:
ama: De Martino D, Capuani F, De Martino A. Quantifying the entropic cost of cellular
growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics
. 2017;96(1). doi:10.1103/PhysRevE.96.010401
apa: De Martino, D., Capuani, F., & De Martino, A. (2017). Quantifying the entropic
cost of cellular growth control. Physical Review E Statistical Nonlinear and
Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.96.010401
chicago: De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Quantifying
the Entropic Cost of Cellular Growth Control.” Physical Review E Statistical
Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.96.010401.
ieee: D. De Martino, F. Capuani, and A. De Martino, “Quantifying the entropic cost
of cellular growth control,” Physical Review E Statistical Nonlinear and Soft
Matter Physics , vol. 96, no. 1. American Institute of Physics, 2017.
ista: De Martino D, Capuani F, De Martino A. 2017. Quantifying the entropic cost
of cellular growth control. Physical Review E Statistical Nonlinear and Soft
Matter Physics . 96(1), 010401.
mla: De Martino, Daniele, et al. “Quantifying the Entropic Cost of Cellular Growth
Control.” Physical Review E Statistical Nonlinear and Soft Matter Physics
, vol. 96, no. 1, 010401, American Institute of Physics, 2017, doi:10.1103/PhysRevE.96.010401.
short: D. De Martino, F. Capuani, A. De Martino, Physical Review E Statistical
Nonlinear and Soft Matter Physics 96 (2017).
date_created: 2018-12-11T11:49:21Z
date_published: 2017-07-10T00:00:00Z
date_updated: 2023-09-22T10:03:50Z
day: '10'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.96.010401
ec_funded: 1
external_id:
isi:
- '000405194200002'
intvolume: ' 96'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.00219
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Physical Review E Statistical Nonlinear and Soft Matter Physics '
publication_identifier:
issn:
- '24700045'
publication_status: published
publisher: American Institute of Physics
publist_id: '6470'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantifying the entropic cost of cellular growth control
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 96
year: '2017'
...
---
_id: '943'
abstract:
- lang: eng
text: Like many developing tissues, the vertebrate neural tube is patterned by antiparallel
morphogen gradients. To understand how these inputs are interpreted, we measured
morphogen signaling and target gene expression in mouse embryos and chick ex vivo
assays. From these data, we derived and validated a characteristic decoding map
that relates morphogen input to the positional identity of neural progenitors.
Analysis of the observed responses indicates that the underlying interpretation
strategy minimizes patterning errors in response to the joint input of noisy opposing
gradients. We reverse-engineered a transcriptional network that provides a mechanistic
basis for the observed cell fate decisions and accounts for the precision and
dynamics of pattern formation. Together, our data link opposing gradient dynamics
in a growing tissue to precise pattern formation.
article_processing_charge: No
author:
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Yoji
full_name: Tabata, Yoji
last_name: Tabata
- first_name: Nathalie
full_name: Brandenberg, Nathalie
last_name: Brandenberg
- first_name: Matthias
full_name: Lutolf, Matthias
last_name: Lutolf
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Tobias
full_name: Bollenbach, Tobias
last_name: Bollenbach
- first_name: James
full_name: Briscoe, James
last_name: Briscoe
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: Zagórski MP, Tabata Y, Brandenberg N, et al. Decoding of position in the developing
neural tube from antiparallel morphogen gradients. Science. 2017;356(6345):1379-1383.
doi:10.1126/science.aam5887
apa: Zagórski, M. P., Tabata, Y., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach,
T., … Kicheva, A. (2017). Decoding of position in the developing neural tube from
antiparallel morphogen gradients. Science. American Association for the
Advancement of Science. https://doi.org/10.1126/science.aam5887
chicago: Zagórski, Marcin P, Yoji Tabata, Nathalie Brandenberg, Matthias Lutolf,
Gašper Tkačik, Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Decoding of
Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.”
Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aam5887.
ieee: M. P. Zagórski et al., “Decoding of position in the developing neural
tube from antiparallel morphogen gradients,” Science, vol. 356, no. 6345.
American Association for the Advancement of Science, pp. 1379–1383, 2017.
ista: Zagórski MP, Tabata Y, Brandenberg N, Lutolf M, Tkačik G, Bollenbach T, Briscoe
J, Kicheva A. 2017. Decoding of position in the developing neural tube from antiparallel
morphogen gradients. Science. 356(6345), 1379–1383.
mla: Zagórski, Marcin P., et al. “Decoding of Position in the Developing Neural
Tube from Antiparallel Morphogen Gradients.” Science, vol. 356, no. 6345,
American Association for the Advancement of Science, 2017, pp. 1379–83, doi:10.1126/science.aam5887.
short: M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach,
J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383.
date_created: 2018-12-11T11:49:20Z
date_published: 2017-06-30T00:00:00Z
date_updated: 2023-09-26T15:38:05Z
day: '30'
department:
- _id: AnKi
- _id: GaTk
doi: 10.1126/science.aam5887
ec_funded: 1
external_id:
isi:
- '000404351500036'
pmid:
- '28663499'
intvolume: ' 356'
isi: 1
issue: '6345'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568706/
month: '06'
oa: 1
oa_version: Submitted Version
page: 1379 - 1383
pmid: 1
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2524F500-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '201439'
name: Developing High-Throughput Bioassays for Human Cancers in Zebrafish
publication: Science
publication_identifier:
issn:
- '00368075'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6474'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Decoding of position in the developing neural tube from antiparallel morphogen
gradients
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 356
year: '2017'
...
---
_id: '823'
abstract:
- lang: eng
text: The resolution of a linear system with positive integer variables is a basic
yet difficult computational problem with many applications. We consider sparse
uncorrelated random systems parametrised by the density c and the ratio α=N/M
between number of variables N and number of constraints M. By means of ensemble
calculations we show that the space of feasible solutions endows a Van-Der-Waals
phase diagram in the plane (c, α). We give numerical evidence that the associated
computational problems become more difficult across the critical point and in
particular in the coexistence region.
article_number: '093404'
article_processing_charge: No
author:
- first_name: Simona
full_name: Colabrese, Simona
last_name: Colabrese
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Luca
full_name: Leuzzi, Luca
last_name: Leuzzi
- first_name: Enzo
full_name: Marinari, Enzo
last_name: Marinari
citation:
ama: 'Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer
linear problems. Journal of Statistical Mechanics: Theory and Experiment.
2017;2017(9). doi:10.1088/1742-5468/aa85c3'
apa: 'Colabrese, S., De Martino, D., Leuzzi, L., & Marinari, E. (2017). Phase
transitions in integer linear problems. Journal of Statistical Mechanics:
Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa85c3'
chicago: 'Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari.
“Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics:
Theory and Experiment. IOPscience, 2017. https://doi.org/10.1088/1742-5468/aa85c3.'
ieee: 'S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions
in integer linear problems,” Journal of Statistical Mechanics: Theory and
Experiment, vol. 2017, no. 9. IOPscience, 2017.'
ista: 'Colabrese S, De Martino D, Leuzzi L, Marinari E. 2017. Phase transitions
in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment.
2017(9), 093404.'
mla: 'Colabrese, Simona, et al. “Phase Transitions in Integer Linear Problems.”
Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no.
9, 093404, IOPscience, 2017, doi:10.1088/1742-5468/aa85c3.'
short: 'S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari, Journal of Statistical
Mechanics: Theory and Experiment 2017 (2017).'
date_created: 2018-12-11T11:48:41Z
date_published: 2017-09-26T00:00:00Z
date_updated: 2023-09-26T16:18:12Z
day: '26'
department:
- _id: GaTk
doi: 10.1088/1742-5468/aa85c3
ec_funded: 1
external_id:
isi:
- '000411842900001'
intvolume: ' 2017'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.06303
month: '09'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Journal of Statistical Mechanics: Theory and Experiment'
publication_identifier:
issn:
- '17425468'
publication_status: published
publisher: IOPscience
publist_id: '6826'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phase transitions in integer linear problems
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '730'
abstract:
- lang: eng
text: Neural responses are highly structured, with population activity restricted
to a small subset of the astronomical range of possible activity patterns. Characterizing
these statistical regularities is important for understanding circuit computation,
but challenging in practice. Here we review recent approaches based on the maximum
entropy principle used for quantifying collective behavior in neural activity.
We highlight recent models that capture population-level statistics of neural
data, yielding insights into the organization of the neural code and its biological
substrate. Furthermore, the MaxEnt framework provides a general recipe for constructing
surrogate ensembles that preserve aspects of the data, but are otherwise maximally
unstructured. This idea can be used to generate a hierarchy of controls against
which rigorous statistical tests are possible.
article_processing_charge: No
author:
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Savin C, Tkačik G. Maximum entropy models as a tool for building precise neural
controls. Current Opinion in Neurobiology. 2017;46:120-126. doi:10.1016/j.conb.2017.08.001
apa: Savin, C., & Tkačik, G. (2017). Maximum entropy models as a tool for building
precise neural controls. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2017.08.001
chicago: Savin, Cristina, and Gašper Tkačik. “Maximum Entropy Models as a Tool for
Building Precise Neural Controls.” Current Opinion in Neurobiology. Elsevier,
2017. https://doi.org/10.1016/j.conb.2017.08.001.
ieee: C. Savin and G. Tkačik, “Maximum entropy models as a tool for building precise
neural controls,” Current Opinion in Neurobiology, vol. 46. Elsevier, pp.
120–126, 2017.
ista: Savin C, Tkačik G. 2017. Maximum entropy models as a tool for building precise
neural controls. Current Opinion in Neurobiology. 46, 120–126.
mla: Savin, Cristina, and Gašper Tkačik. “Maximum Entropy Models as a Tool for Building
Precise Neural Controls.” Current Opinion in Neurobiology, vol. 46, Elsevier,
2017, pp. 120–26, doi:10.1016/j.conb.2017.08.001.
short: C. Savin, G. Tkačik, Current Opinion in Neurobiology 46 (2017) 120–126.
date_created: 2018-12-11T11:48:11Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2023-09-28T11:32:22Z
day: '01'
department:
- _id: GaTk
doi: 10.1016/j.conb.2017.08.001
ec_funded: 1
external_id:
isi:
- '000416196400016'
intvolume: ' 46'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 120 - 126
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Current Opinion in Neurobiology
publication_identifier:
issn:
- '09594388'
publication_status: published
publisher: Elsevier
publist_id: '6943'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Maximum entropy models as a tool for building precise neural controls
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 46
year: '2017'
...
---
_id: '548'
abstract:
- lang: eng
text: In this work maximum entropy distributions in the space of steady states of
metabolic networks are considered upon constraining the first and second moments
of the growth rate. Coexistence of fast and slow phenotypes, with bimodal flux
distributions, emerges upon considering control on the average growth (optimization)
and its fluctuations (heterogeneity). This is applied to the carbon catabolic
core of Escherichia coli where it quantifies the metabolic activity of slow growing
phenotypes and it provides a quantitative map with metabolic fluxes, opening the
possibility to detect coexistence from flux data. A preliminary analysis on data
for E. coli cultures in standard conditions shows degeneracy for the inferred
parameters that extend in the coexistence region.
alternative_title:
- Rapid Communications
article_number: '060401'
article_processing_charge: No
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: De Martino D. Maximum entropy modeling of metabolic networks by constraining
growth-rate moments predicts coexistence of phenotypes. Physical Review E.
2017;96(6). doi:10.1103/PhysRevE.96.060401
apa: De Martino, D. (2017). Maximum entropy modeling of metabolic networks by constraining
growth-rate moments predicts coexistence of phenotypes. Physical Review E.
American Physical Society. https://doi.org/10.1103/PhysRevE.96.060401
chicago: De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by
Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” Physical
Review E. American Physical Society, 2017. https://doi.org/10.1103/PhysRevE.96.060401.
ieee: D. De Martino, “Maximum entropy modeling of metabolic networks by constraining
growth-rate moments predicts coexistence of phenotypes,” Physical Review E,
vol. 96, no. 6. American Physical Society, 2017.
ista: De Martino D. 2017. Maximum entropy modeling of metabolic networks by constraining
growth-rate moments predicts coexistence of phenotypes. Physical Review E. 96(6),
060401.
mla: De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining
Growth-Rate Moments Predicts Coexistence of Phenotypes.” Physical Review E,
vol. 96, no. 6, 060401, American Physical Society, 2017, doi:10.1103/PhysRevE.96.060401.
short: D. De Martino, Physical Review E 96 (2017).
date_created: 2018-12-11T11:47:06Z
date_published: 2017-12-21T00:00:00Z
date_updated: 2023-10-10T13:29:38Z
day: '21'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.96.060401
ec_funded: 1
intvolume: ' 96'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1707.00320
month: '12'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review E
publication_identifier:
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
publist_id: '7266'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Maximum entropy modeling of metabolic networks by constraining growth-rate
moments predicts coexistence of phenotypes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 96
year: '2017'
...
---
_id: '1007'
abstract:
- lang: eng
text: 'A nonlinear system possesses an invariance with respect to a set of transformations
if its output dynamics remain invariant when transforming the input, and adjusting
the initial condition accordingly. Most research has focused on invariances with
respect to time-independent pointwise transformations like translational-invariance
(u(t) -> u(t) + p, p in R) or scale-invariance (u(t) -> pu(t), p in R>0).
In this article, we introduce the concept of s0-invariances with respect to continuous
input transformations exponentially growing/decaying over time. We show that s0-invariant
systems not only encompass linear time-invariant (LTI) systems with transfer functions
having an irreducible zero at s0 in R, but also that the input/output relationship
of nonlinear s0-invariant systems possesses properties well known from their linear
counterparts. Furthermore, we extend the concept of s0-invariances to second-
and higher-order s0-invariances, corresponding to invariances with respect to
transformations of the time-derivatives of the input, and encompassing LTI systems
with zeros of multiplicity two or higher. Finally, we show that nth-order 0-invariant
systems realize – under mild conditions – nth-order nonlinear differential operators:
when excited by an input of a characteristic functional form, the system’s output
converges to a constant value only depending on the nth (nonlinear) derivative
of the input.'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Eduardo
full_name: Sontag, Eduardo
last_name: Sontag
citation:
ama: Lang M, Sontag E. Zeros of nonlinear systems with input invariances. Automatica.
2017;81C:46-55. doi:10.1016/j.automatica.2017.03.030
apa: Lang, M., & Sontag, E. (2017). Zeros of nonlinear systems with input invariances.
Automatica. International Federation of Automatic Control. https://doi.org/10.1016/j.automatica.2017.03.030
chicago: Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input
Invariances.” Automatica. International Federation of Automatic Control,
2017. https://doi.org/10.1016/j.automatica.2017.03.030.
ieee: M. Lang and E. Sontag, “Zeros of nonlinear systems with input invariances,”
Automatica, vol. 81C. International Federation of Automatic Control, pp.
46–55, 2017.
ista: Lang M, Sontag E. 2017. Zeros of nonlinear systems with input invariances.
Automatica. 81C, 46–55.
mla: Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input Invariances.”
Automatica, vol. 81C, International Federation of Automatic Control, 2017,
pp. 46–55, doi:10.1016/j.automatica.2017.03.030.
short: M. Lang, E. Sontag, Automatica 81C (2017) 46–55.
date_created: 2018-12-11T11:49:39Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-10-17T08:51:18Z
day: '01'
ddc:
- '000'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1016/j.automatica.2017.03.030
ec_funded: 1
external_id:
isi:
- '000403513900006'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:29Z
date_updated: 2018-12-12T10:11:29Z
file_id: '4884'
file_name: IST-2017-813-v1+1_ZerosOfNonlinearSystems.pdf
file_size: 1401954
relation: main_file
file_date_updated: 2018-12-12T10:11:29Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 46 - 55
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Automatica
publication_identifier:
issn:
- 0005-1098
publication_status: published
publisher: International Federation of Automatic Control
publist_id: '6391'
pubrep_id: '813'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Zeros of nonlinear systems with input invariances
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 81C
year: '2017'
...
---
_id: '665'
abstract:
- lang: eng
text: The molecular mechanisms underlying phenotypic variation in isogenic bacterial
populations remain poorly understood.We report that AcrAB-TolC, the main multidrug
efflux pump of Escherichia coli, exhibits a strong partitioning bias for old cell
poles by a segregation mechanism that is mediated by ternary AcrAB-TolC complex
formation. Mother cells inheriting old poles are phenotypically distinct and display
increased drug efflux activity relative to daughters. Consequently, we find systematic
and long-lived growth differences between mother and daughter cells in the presence
of subinhibitory drug concentrations. A simple model for biased partitioning predicts
a population structure of long-lived and highly heterogeneous phenotypes. This
straightforward mechanism of generating sustained growth rate differences at subinhibitory
antibiotic concentrations has implications for understanding the emergence of
multidrug resistance in bacteria.
article_processing_charge: No
article_type: original
author:
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Anna M
full_name: Andersson, Anna M
id: 2B8A40DA-F248-11E8-B48F-1D18A9856A87
last_name: Andersson
orcid: 0000-0003-2912-6769
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
- first_name: Enrique
full_name: Balleza, Enrique
last_name: Balleza
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multidrug
efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science.
2017;356(6335):311-315. doi:10.1126/science.aaf4762
apa: Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild,
R., … Guet, C. C. (2017). Biased partitioning of the multidrug efflux pump AcrAB
TolC underlies long lived phenotypic heterogeneity. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.aaf4762
chicago: Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza,
Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning
of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.”
Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aaf4762.
ieee: T. Bergmiller et al., “Biased partitioning of the multidrug efflux
pump AcrAB TolC underlies long lived phenotypic heterogeneity,” Science,
vol. 356, no. 6335. American Association for the Advancement of Science, pp. 311–315,
2017.
ista: Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik
G, Guet CC. 2017. Biased partitioning of the multidrug efflux pump AcrAB TolC
underlies long lived phenotypic heterogeneity. Science. 356(6335), 311–315.
mla: Bergmiller, Tobias, et al. “Biased Partitioning of the Multidrug Efflux Pump
AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science, vol.
356, no. 6335, American Association for the Advancement of Science, 2017, pp.
311–15, doi:10.1126/science.aaf4762.
short: T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild,
G. Tkačik, C.C. Guet, Science 356 (2017) 311–315.
date_created: 2018-12-11T11:47:48Z
date_published: 2017-04-21T00:00:00Z
date_updated: 2024-02-21T13:49:00Z
day: '21'
department:
- _id: CaGu
- _id: GaTk
- _id: Bio
doi: 10.1126/science.aaf4762
intvolume: ' 356'
issue: '6335'
language:
- iso: eng
month: '04'
oa_version: None
page: 311 - 315
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Science
publication_identifier:
issn:
- '00368075'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7064'
quality_controlled: '1'
related_material:
record:
- id: '5560'
relation: popular_science
status: public
scopus_import: 1
status: public
title: Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long
lived phenotypic heterogeneity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 356
year: '2017'
...
---
_id: '735'
abstract:
- lang: eng
text: Cell-cell contact formation constitutes an essential step in evolution, leading
to the differentiation of specialized cell types. However, remarkably little is
known about whether and how the interplay between contact formation and fate specification
affects development. Here, we identify a positive feedback loop between cell-cell
contact duration, morphogen signaling, and mesendoderm cell-fate specification
during zebrafish gastrulation. We show that long-lasting cell-cell contacts enhance
the competence of prechordal plate (ppl) progenitor cells to respond to Nodal
signaling, required for ppl cell-fate specification. We further show that Nodal
signaling promotes ppl cell-cell contact duration, generating a positive feedback
loop between ppl cell-cell contact duration and cell-fate specification. Finally,
by combining mathematical modeling and experimentation, we show that this feedback
determines whether anterior axial mesendoderm cells become ppl or, instead, turn
into endoderm. Thus, the interdependent activities of cell-cell signaling and
contact formation control fate diversification within the developing embryo.
article_processing_charge: No
author:
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Saurabh
full_name: Pradhan, Saurabh
last_name: Pradhan
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
- first_name: Keisuke
full_name: Sako, Keisuke
id: 3BED66BE-F248-11E8-B48F-1D18A9856A87
last_name: Sako
orcid: 0000-0002-6453-8075
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Barone V, Lang M, Krens G, et al. An effective feedback loop between cell-cell
contact duration and morphogen signaling determines cell fate. Developmental
Cell. 2017;43(2):198-211. doi:10.1016/j.devcel.2017.09.014
apa: Barone, V., Lang, M., Krens, G., Pradhan, S., Shamipour, S., Sako, K., … Heisenberg,
C.-P. J. (2017). An effective feedback loop between cell-cell contact duration
and morphogen signaling determines cell fate. Developmental Cell. Cell
Press. https://doi.org/10.1016/j.devcel.2017.09.014
chicago: Barone, Vanessa, Moritz Lang, Gabriel Krens, Saurabh Pradhan, Shayan Shamipour,
Keisuke Sako, Mateusz K Sikora, Calin C Guet, and Carl-Philipp J Heisenberg. “An
Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling
Determines Cell Fate.” Developmental Cell. Cell Press, 2017. https://doi.org/10.1016/j.devcel.2017.09.014.
ieee: V. Barone et al., “An effective feedback loop between cell-cell contact
duration and morphogen signaling determines cell fate,” Developmental Cell,
vol. 43, no. 2. Cell Press, pp. 198–211, 2017.
ista: Barone V, Lang M, Krens G, Pradhan S, Shamipour S, Sako K, Sikora MK, Guet
CC, Heisenberg C-PJ. 2017. An effective feedback loop between cell-cell contact
duration and morphogen signaling determines cell fate. Developmental Cell. 43(2),
198–211.
mla: Barone, Vanessa, et al. “An Effective Feedback Loop between Cell-Cell Contact
Duration and Morphogen Signaling Determines Cell Fate.” Developmental Cell,
vol. 43, no. 2, Cell Press, 2017, pp. 198–211, doi:10.1016/j.devcel.2017.09.014.
short: V. Barone, M. Lang, G. Krens, S. Pradhan, S. Shamipour, K. Sako, M.K. Sikora,
C.C. Guet, C.-P.J. Heisenberg, Developmental Cell 43 (2017) 198–211.
date_created: 2018-12-11T11:48:13Z
date_published: 2017-10-23T00:00:00Z
date_updated: 2024-03-28T23:30:39Z
day: '23'
department:
- _id: CaHe
- _id: CaGu
- _id: GaTk
doi: 10.1016/j.devcel.2017.09.014
ec_funded: 1
external_id:
isi:
- '000413443700011'
intvolume: ' 43'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa_version: None
page: 198 - 211
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 252DD2A6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I2058
name: 'Cell segregation in gastrulation: the role of cell fate specification'
publication: Developmental Cell
publication_identifier:
issn:
- '15345807'
publication_status: published
publisher: Cell Press
publist_id: '6934'
quality_controlled: '1'
related_material:
record:
- id: '961'
relation: dissertation_contains
status: public
- id: '8350'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: An effective feedback loop between cell-cell contact duration and morphogen
signaling determines cell fate
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 43
year: '2017'
...
---
_id: '1082'
abstract:
- lang: eng
text: In many applications, it is desirable to extract only the relevant aspects
of data. A principled way to do this is the information bottleneck (IB) method,
where one seeks a code that maximises information about a relevance variable,
Y, while constraining the information encoded about the original data, X. Unfortunately
however, the IB method is computationally demanding when data are high-dimensional
and/or non-gaussian. Here we propose an approximate variational scheme for maximising
a lower bound on the IB objective, analogous to variational EM. Using this method,
we derive an IB algorithm to recover features that are both relevant and sparse.
Finally, we demonstrate how kernelised versions of the algorithm can be used to
address a broad range of problems with non-linear relation between X and Y.
alternative_title:
- Advances in Neural Information Processing Systems
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: 'Chalk MJ, Marre O, Tkačik G. Relevant sparse codes with variational information
bottleneck. In: Vol 29. Neural Information Processing Systems; 2016:1965-1973.'
apa: 'Chalk, M. J., Marre, O., & Tkačik, G. (2016). Relevant sparse codes with
variational information bottleneck (Vol. 29, pp. 1965–1973). Presented at the
NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information
Processing Systems.'
chicago: Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Relevant Sparse Codes
with Variational Information Bottleneck,” 29:1965–73. Neural Information Processing
Systems, 2016.
ieee: 'M. J. Chalk, O. Marre, and G. Tkačik, “Relevant sparse codes with variational
information bottleneck,” presented at the NIPS: Neural Information Processing
Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.'
ista: 'Chalk MJ, Marre O, Tkačik G. 2016. Relevant sparse codes with variational
information bottleneck. NIPS: Neural Information Processing Systems, Advances
in Neural Information Processing Systems, vol. 29, 1965–1973.'
mla: Chalk, Matthew J., et al. Relevant Sparse Codes with Variational Information
Bottleneck. Vol. 29, Neural Information Processing Systems, 2016, pp. 1965–73.
short: M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems,
2016, pp. 1965–1973.
conference:
end_date: 2016-12-10
location: Barcelona, Spain
name: 'NIPS: Neural Information Processing Systems'
start_date: 2016-12-05
date_created: 2018-12-11T11:50:03Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:48:09Z
day: '01'
department:
- _id: GaTk
intvolume: ' 29'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1605.07332
month: '12'
oa: 1
oa_version: Preprint
page: 1965-1973
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '6298'
quality_controlled: '1'
related_material:
link:
- relation: other
url: https://papers.nips.cc/paper/6101-relevant-sparse-codes-with-variational-information-bottleneck
scopus_import: 1
status: public
title: Relevant sparse codes with variational information bottleneck
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2016'
...
---
_id: '1105'
abstract:
- lang: eng
text: Jointly characterizing neural responses in terms of several external variables
promises novel insights into circuit function, but remains computationally prohibitive
in practice. Here we use gaussian process (GP) priors and exploit recent advances
in fast GP inference and learning based on Kronecker methods, to efficiently estimate
multidimensional nonlinear tuning functions. Our estimator require considerably
less data than traditional methods and further provides principled uncertainty
estimates. We apply these tools to hippocampal recordings during open field exploration
and use them to characterize the joint dependence of CA1 responses on the position
of the animal and several other variables, including the animal\'s speed, direction
of motion, and network oscillations.Our results provide an unprecedentedly detailed
quantification of the tuning of hippocampal neurons. The model\'s generality suggests
that our approach can be used to estimate neural response properties in other
brain regions.
acknowledgement: "We thank Jozsef Csicsvari for kindly sharing the CA1 data.\r\nThis
work was supported by the People Programme (Marie Curie Actions) of the European
Union’s Seventh Framework Programme(FP7/2007-2013) under REA grant agreement no.
291734."
alternative_title:
- Advances in Neural Information Processing Systems
author:
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: 'Savin C, Tkačik G. Estimating nonlinear neural response functions using GP
priors and Kronecker methods. In: Vol 29. Neural Information Processing Systems;
2016:3610-3618.'
apa: 'Savin, C., & Tkačik, G. (2016). Estimating nonlinear neural response functions
using GP priors and Kronecker methods (Vol. 29, pp. 3610–3618). Presented at the
NIPS: Neural Information Processing Systems, Barcelona; Spain: Neural Information
Processing Systems.'
chicago: Savin, Cristina, and Gašper Tkačik. “Estimating Nonlinear Neural Response
Functions Using GP Priors and Kronecker Methods,” 29:3610–18. Neural Information
Processing Systems, 2016.
ieee: 'C. Savin and G. Tkačik, “Estimating nonlinear neural response functions using
GP priors and Kronecker methods,” presented at the NIPS: Neural Information Processing
Systems, Barcelona; Spain, 2016, vol. 29, pp. 3610–3618.'
ista: 'Savin C, Tkačik G. 2016. Estimating nonlinear neural response functions using
GP priors and Kronecker methods. NIPS: Neural Information Processing Systems,
Advances in Neural Information Processing Systems, vol. 29, 3610–3618.'
mla: Savin, Cristina, and Gašper Tkačik. Estimating Nonlinear Neural Response
Functions Using GP Priors and Kronecker Methods. Vol. 29, Neural Information
Processing Systems, 2016, pp. 3610–18.
short: C. Savin, G. Tkačik, in:, Neural Information Processing Systems, 2016, pp.
3610–3618.
conference:
end_date: 2016-12-10
location: Barcelona; Spain
name: 'NIPS: Neural Information Processing Systems'
start_date: 2016-12-05
date_created: 2018-12-11T11:50:10Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:48:19Z
day: '01'
department:
- _id: GaTk
ec_funded: 1
intvolume: ' 29'
language:
- iso: eng
main_file_link:
- url: http://papers.nips.cc/paper/6153-estimating-nonlinear-neural-response-functions-using-gp-priors-and-kronecker-methods
month: '12'
oa_version: None
page: 3610-3618
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '6265'
quality_controlled: '1'
scopus_import: 1
status: public
title: Estimating nonlinear neural response functions using GP priors and Kronecker
methods
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2016'
...