---
_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
license: https://creativecommons.org/licenses/by/4.0/
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
relation: main_file
success: 1
file_date_updated: 2021-08-09T09:44:03Z
has_accepted_license: '1'
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:
- id: '7673'
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
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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:
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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'
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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
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oa_version: Published Version
page: 171-190
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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:
- access_level: open_access
content_type: application/pdf
creator: rgrah
date_created: 2020-07-27T12:00:07Z
date_updated: 2020-07-27T12:00:07Z
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date_created: 2020-07-27T12:02:23Z
date_updated: 2020-07-30T13:04:55Z
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file_size: 347459978
relation: main_file
file_date_updated: 2020-07-30T13:04:55Z
has_accepted_license: '1'
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:
- id: '7675'
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'
- '570'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pcbi.1007642
external_id:
isi:
- '000526725200019'
file:
- access_level: open_access
checksum: 5239dd134dc6e1c71fe7b3ce2953da37
content_type: application/pdf
creator: dernst
date_created: 2020-03-09T15:12:21Z
date_updated: 2020-07-14T12:48:00Z
file_id: '7579'
file_name: 2020_PlosCompBio_Grah.pdf
file_size: 2209325
relation: main_file
file_date_updated: 2020-07-14T12:48:00Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: PLOS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '9716'
relation: research_data
status: deleted
- id: '9776'
relation: research_data
status: public
- id: '9779'
relation: used_in_publication
status: public
- id: '8155'
relation: dissertation_contains
status: public
- id: '9777'
relation: research_data
status: public
scopus_import: '1'
status: public
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)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 16
year: '2020'
...
---
_id: '9777'
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. 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
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pcbi.1007642.s002
month: '02'
oa: 1
oa_version: None
publisher: Public Library of Science
related_material:
record:
- id: '7569'
relation: used_in_publication
status: public
status: public
title: Maximizing crosstalk
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8097'
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.'
acknowledged_ssus:
- _id: LifeSc
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. Analysis scripts and research data for the paper “Mechanisms of drug
interactions between translation-inhibiting antibiotics.” 2020. doi:10.15479/AT:ISTA:8097
apa: Kavcic, B. (2020). Analysis scripts and research data for the paper “Mechanisms
of drug interactions between translation-inhibiting antibiotics.” Institute of
Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8097
chicago: Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Mechanisms
of Drug Interactions between Translation-Inhibiting Antibiotics.’” Institute of
Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8097.
ieee: B. Kavcic, “Analysis scripts and research data for the paper ‘Mechanisms of
drug interactions between translation-inhibiting antibiotics.’” Institute of Science
and Technology Austria, 2020.
ista: Kavcic B. 2020. Analysis scripts and research data for the paper ‘Mechanisms
of drug interactions between translation-inhibiting antibiotics’, Institute of
Science and Technology Austria, 10.15479/AT:ISTA:8097.
mla: Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Mechanisms
of Drug Interactions between Translation-Inhibiting Antibiotics.” Institute
of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8097.
short: B. Kavcic, (2020).
contributor:
- contributor_type: research_group
first_name: Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- contributor_type: research_group
first_name: Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
date_created: 2020-07-06T20:40:19Z
date_published: 2020-07-15T00:00:00Z
date_updated: 2024-02-21T12:40:51Z
day: '15'
department:
- _id: GaTk
doi: 10.15479/AT:ISTA:8097
file:
- access_level: open_access
checksum: 5c321dbbb6d4b3c85da786fd3ebbdc98
content_type: application/zip
creator: bkavcic
date_created: 2020-07-06T20:38:27Z
date_updated: 2020-07-14T12:48:09Z
file_id: '8098'
file_name: natComm_2020_scripts.zip
file_size: 255770756
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
keyword:
- Escherichia coli
- antibiotic combinations
- translation
- growth laws
- drug interactions
- bacterial physiology
- translation inhibitors
month: '07'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
status: public
title: Analysis scripts and research data for the paper "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: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8930'
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.
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. Analysis scripts and research data for the paper “Minimal biophysical
model of combined antibiotic action.” 2020. doi:10.15479/AT:ISTA:8930
apa: Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal
biophysical model of combined antibiotic action.” Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:8930
chicago: Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal
Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology
Austria, 2020. https://doi.org/10.15479/AT:ISTA:8930.
ieee: B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical
model of combined antibiotic action.’” Institute of Science and Technology Austria,
2020.
ista: Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal
biophysical model of combined antibiotic action’, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:8930.
mla: Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Minimal Biophysical
Model of Combined Antibiotic Action.” Institute of Science and Technology
Austria, 2020, doi:10.15479/AT:ISTA:8930.
short: B. Kavcic, (2020).
contributor:
- contributor_type: supervisor
first_name: Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- contributor_type: supervisor
first_name: Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
date_created: 2020-12-09T15:04:02Z
date_published: 2020-12-10T00:00:00Z
date_updated: 2024-02-21T12:41:42Z
day: '10'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.15479/AT:ISTA:8930
file:
- access_level: open_access
checksum: 60a818edeffaa7da1ebf5f8fbea9ba18
content_type: application/zip
creator: bkavcic
date_created: 2020-12-09T15:00:19Z
date_updated: 2020-12-09T15:00:19Z
file_id: '8932'
file_name: PLoSCompBiol2020_datarep.zip
file_size: 315494370
relation: main_file
success: 1
file_date_updated: 2020-12-09T15:00:19Z
has_accepted_license: '1'
keyword:
- Escherichia coli
- antibiotic combinations
- translation
- growth laws
- drug interactions
- bacterial physiology
- translation inhibitors
month: '12'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8997'
relation: used_in_publication
status: public
status: public
title: Analysis scripts and research data for the paper "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: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7383'
abstract:
- lang: eng
text: Organisms cope with change by employing transcriptional regulators. However,
when faced with rare environments, the evolution of transcriptional regulators
and their promoters may be too slow. We ask whether the intrinsic instability
of gene duplication and amplification provides a generic alternative to canonical
gene regulation. By real-time monitoring of gene copy number mutations in E. coli,
we show that gene duplications and amplifications enable adaptation to fluctuating
environments by rapidly generating copy number, and hence expression level, polymorphism.
This ‘amplification-mediated gene expression tuning’ occurs on timescales similar
to canonical gene regulation and can deal with rapid environmental changes. Mathematical
modeling shows that amplifications also tune gene expression in stochastic environments
where 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 expression of any gene, without
leaving any genomic signature.
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. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level
Gene Expression regulation. 2020. doi:10.15479/AT:ISTA:7383'
apa: 'Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form
of Population-Level Gene Expression regulation. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:7383'
chicago: 'Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form
of Population-Level Gene Expression Regulation.” Institute of Science and Technology
Austria, 2020. https://doi.org/10.15479/AT:ISTA:7383.'
ieee: 'R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level
Gene Expression regulation.” Institute of Science and Technology Austria, 2020.'
ista: 'Grah R. 2020. Matlab scripts for the Paper: Gene Amplification as a Form
of Population-Level Gene Expression regulation, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:7383.'
mla: 'Grah, Rok. Matlab Scripts for the Paper: Gene Amplification as a Form of
Population-Level Gene Expression Regulation. Institute of Science and Technology
Austria, 2020, doi:10.15479/AT:ISTA:7383.'
short: R. Grah, (2020).
contributor:
- contributor_type: project_leader
first_name: Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
date_created: 2020-01-28T10:41:49Z
date_published: 2020-01-28T00:00:00Z
date_updated: 2024-02-21T12:42:31Z
day: '28'
department:
- _id: CaGu
- _id: GaTk
doi: 10.15479/AT:ISTA:7383
file:
- access_level: open_access
checksum: 9d292cf5207b3829225f44c044cdb3fd
content_type: application/zip
creator: rgrah
date_created: 2020-01-28T10:39:40Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7384'
file_name: Scripts.zip
file_size: 73363365
relation: main_file
- access_level: open_access
checksum: 4076ceab32ef588cc233802bab24c1ab
content_type: text/plain
creator: rgrah
date_created: 2020-01-28T10:39:30Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7385'
file_name: READ_ME_MAIN.txt
file_size: 962
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
keyword:
- Matlab scripts
- analysis of microfluidics
- mathematical model
month: '01'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7652'
relation: used_in_publication
status: public
status: public
title: 'Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level
Gene Expression regulation'
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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'
ddc:
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- '530'
- '570'
degree_awarded: PhD
department:
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doi: 10.15479/AT:ISTA:8657
file:
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date_updated: 2021-10-07T22:30:03Z
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language:
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month: '10'
oa: 1
oa_version: Published Version
page: '271'
publication_identifier:
isbn:
- 978-3-99078-011-4
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7673'
relation: part_of_dissertation
status: public
- id: '8250'
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
- 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'
...