---
_id: '548'
abstract:
- lang: eng
text: In this work maximum entropy distributions in the space of steady states of
metabolic networks are considered upon constraining the first and second moments
of the growth rate. Coexistence of fast and slow phenotypes, with bimodal flux
distributions, emerges upon considering control on the average growth (optimization)
and its fluctuations (heterogeneity). This is applied to the carbon catabolic
core of Escherichia coli where it quantifies the metabolic activity of slow growing
phenotypes and it provides a quantitative map with metabolic fluxes, opening the
possibility to detect coexistence from flux data. A preliminary analysis on data
for E. coli cultures in standard conditions shows degeneracy for the inferred
parameters that extend in the coexistence region.
alternative_title:
- Rapid Communications
article_number: '060401'
article_processing_charge: No
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: De Martino D. Maximum entropy modeling of metabolic networks by constraining
growth-rate moments predicts coexistence of phenotypes. Physical Review E.
2017;96(6). doi:10.1103/PhysRevE.96.060401
apa: De Martino, D. (2017). Maximum entropy modeling of metabolic networks by constraining
growth-rate moments predicts coexistence of phenotypes. Physical Review E.
American Physical Society. https://doi.org/10.1103/PhysRevE.96.060401
chicago: De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by
Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” Physical
Review E. American Physical Society, 2017. https://doi.org/10.1103/PhysRevE.96.060401.
ieee: D. De Martino, “Maximum entropy modeling of metabolic networks by constraining
growth-rate moments predicts coexistence of phenotypes,” Physical Review E,
vol. 96, no. 6. American Physical Society, 2017.
ista: De Martino D. 2017. Maximum entropy modeling of metabolic networks by constraining
growth-rate moments predicts coexistence of phenotypes. Physical Review E. 96(6),
060401.
mla: De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining
Growth-Rate Moments Predicts Coexistence of Phenotypes.” Physical Review E,
vol. 96, no. 6, 060401, American Physical Society, 2017, doi:10.1103/PhysRevE.96.060401.
short: D. De Martino, Physical Review E 96 (2017).
date_created: 2018-12-11T11:47:06Z
date_published: 2017-12-21T00:00:00Z
date_updated: 2023-10-10T13:29:38Z
day: '21'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.96.060401
ec_funded: 1
intvolume: ' 96'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1707.00320
month: '12'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review E
publication_identifier:
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
publist_id: '7266'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Maximum entropy modeling of metabolic networks by constraining growth-rate
moments predicts coexistence of phenotypes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 96
year: '2017'
...
---
_id: '1007'
abstract:
- lang: eng
text: 'A nonlinear system possesses an invariance with respect to a set of transformations
if its output dynamics remain invariant when transforming the input, and adjusting
the initial condition accordingly. Most research has focused on invariances with
respect to time-independent pointwise transformations like translational-invariance
(u(t) -> u(t) + p, p in R) or scale-invariance (u(t) -> pu(t), p in R>0).
In this article, we introduce the concept of s0-invariances with respect to continuous
input transformations exponentially growing/decaying over time. We show that s0-invariant
systems not only encompass linear time-invariant (LTI) systems with transfer functions
having an irreducible zero at s0 in R, but also that the input/output relationship
of nonlinear s0-invariant systems possesses properties well known from their linear
counterparts. Furthermore, we extend the concept of s0-invariances to second-
and higher-order s0-invariances, corresponding to invariances with respect to
transformations of the time-derivatives of the input, and encompassing LTI systems
with zeros of multiplicity two or higher. Finally, we show that nth-order 0-invariant
systems realize – under mild conditions – nth-order nonlinear differential operators:
when excited by an input of a characteristic functional form, the system’s output
converges to a constant value only depending on the nth (nonlinear) derivative
of the input.'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Eduardo
full_name: Sontag, Eduardo
last_name: Sontag
citation:
ama: Lang M, Sontag E. Zeros of nonlinear systems with input invariances. Automatica.
2017;81C:46-55. doi:10.1016/j.automatica.2017.03.030
apa: Lang, M., & Sontag, E. (2017). Zeros of nonlinear systems with input invariances.
Automatica. International Federation of Automatic Control. https://doi.org/10.1016/j.automatica.2017.03.030
chicago: Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input
Invariances.” Automatica. International Federation of Automatic Control,
2017. https://doi.org/10.1016/j.automatica.2017.03.030.
ieee: M. Lang and E. Sontag, “Zeros of nonlinear systems with input invariances,”
Automatica, vol. 81C. International Federation of Automatic Control, pp.
46–55, 2017.
ista: Lang M, Sontag E. 2017. Zeros of nonlinear systems with input invariances.
Automatica. 81C, 46–55.
mla: Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input Invariances.”
Automatica, vol. 81C, International Federation of Automatic Control, 2017,
pp. 46–55, doi:10.1016/j.automatica.2017.03.030.
short: M. Lang, E. Sontag, Automatica 81C (2017) 46–55.
date_created: 2018-12-11T11:49:39Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-10-17T08:51:18Z
day: '01'
ddc:
- '000'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1016/j.automatica.2017.03.030
ec_funded: 1
external_id:
isi:
- '000403513900006'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:29Z
date_updated: 2018-12-12T10:11:29Z
file_id: '4884'
file_name: IST-2017-813-v1+1_ZerosOfNonlinearSystems.pdf
file_size: 1401954
relation: main_file
file_date_updated: 2018-12-12T10:11:29Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 46 - 55
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Automatica
publication_identifier:
issn:
- 0005-1098
publication_status: published
publisher: International Federation of Automatic Control
publist_id: '6391'
pubrep_id: '813'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Zeros of nonlinear systems with input invariances
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 81C
year: '2017'
...
---
_id: '5562'
abstract:
- lang: eng
text: "This data was collected as part of the study [1]. It consists of preprocessed
multi-electrode array recording from 160 salamander retinal ganglion cells responding
to 297 repeats of a 19 s natural movie. The data is available in two formats:
(1) a .mat file containing an array with dimensions “number of repeats” x “number
of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data
represented as an array with dimensions “number of neurons” x “number of samples”,
where the number of samples is equal to the product of the number of repeats and
timebins within a repeat. The time dimension is divided into 20 ms time windows,
and the array is binary indicating whether a given cell elicited at least one
spike in a given time window during a particular repeat. See the reference below
for details regarding collection and preprocessing:\r\n\r\n[1] Tkačik G, Marre
O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior
in a Large Network of Sensory Neurons. PLoS Comput Biol. 2014;10(1):e1003408."
article_processing_charge: No
author:
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Dario
full_name: Amodei, Dario
last_name: Amodei
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
citation:
ama: Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. Multi-electrode
array recording from salamander retinal ganglion cells. 2017. doi:10.15479/AT:ISTA:61
apa: Marre, O., Tkačik, G., Amodei, D., Schneidman, E., Bialek, W., & Berry,
M. (2017). Multi-electrode array recording from salamander retinal ganglion cells.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:61
chicago: Marre, Olivier, Gašper Tkačik, Dario Amodei, Elad Schneidman, William Bialek,
and Michael Berry. “Multi-Electrode Array Recording from Salamander Retinal Ganglion
Cells.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:61.
ieee: O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Multi-electrode
array recording from salamander retinal ganglion cells.” Institute of Science
and Technology Austria, 2017.
ista: Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. 2017. Multi-electrode
array recording from salamander retinal ganglion cells, Institute of Science and
Technology Austria, 10.15479/AT:ISTA:61.
mla: Marre, Olivier, et al. Multi-Electrode Array Recording from Salamander Retinal
Ganglion Cells. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:61.
short: O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, M. Berry, (2017).
datarep_id: '61'
date_created: 2018-12-12T12:31:33Z
date_published: 2017-02-27T00:00:00Z
date_updated: 2024-02-21T13:46:14Z
day: '27'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.15479/AT:ISTA:61
file:
- access_level: open_access
checksum: e620eff260646f57b479a69492c8b765
content_type: application/octet-stream
creator: system
date_created: 2018-12-12T13:03:04Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5622'
file_name: IST-2017-61-v1+1_bint_fishmovie32_100.mat
file_size: 1336936
relation: main_file
- access_level: open_access
checksum: de83f9b81ea0aae3cddfc3ed982e0759
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:05Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5623'
file_name: IST-2017-61-v1+2_bint_fishmovie32_100.zip
file_size: 1897543
relation: main_file
file_date_updated: 2020-07-14T12:47:03Z
has_accepted_license: '1'
keyword:
- multi-electrode recording
- retinal ganglion cells
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '2257'
relation: research_paper
status: public
status: public
title: Multi-electrode array recording from salamander retinal ganglion cells
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '5560'
abstract:
- lang: eng
text: "This repository contains the data collected for the manuscript \"Biased partitioning
of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity\".\r\nThe
data is compressed into a single archive. Within the archive, different folders
correspond to figures of the main text and the SI of the related publication.\r\nData
is saved as plain text, with each folder containing a separate readme file describing
the format. Typically, the data is from fluorescence microscopy measurements of
single cells growing in a microfluidic \"mother machine\" device, and consists
of relevant values (primarily arbitrary unit or normalized fluorescence measurements,
and division times / growth rates) after raw microscopy images have been processed,
segmented, and their features extracted, as described in the methods section of
the related publication."
article_processing_charge: No
author:
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Anna M
full_name: Andersson, Anna M
id: 2B8A40DA-F248-11E8-B48F-1D18A9856A87
last_name: Andersson
orcid: 0000-0003-2912-6769
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
- first_name: Enrique
full_name: Balleza, Enrique
last_name: Balleza
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multi-drug
efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. 2017. doi:10.15479/AT:ISTA:53
apa: Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild,
R., … Guet, C. C. (2017). Biased partitioning of the multi-drug efflux pump AcrAB-TolC
underlies long-lived phenotypic heterogeneity. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:53
chicago: Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza,
Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning
of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity.”
Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:53.
ieee: T. Bergmiller et al., “Biased partitioning of the multi-drug efflux
pump AcrAB-TolC underlies long-lived phenotypic heterogeneity.” Institute of Science
and Technology Austria, 2017.
ista: Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik
G, Guet CC. 2017. Biased partitioning of the multi-drug efflux pump AcrAB-TolC
underlies long-lived phenotypic heterogeneity, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:53.
mla: Bergmiller, Tobias, et al. Biased Partitioning of the Multi-Drug Efflux
Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity. Institute of
Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:53.
short: T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild,
G. Tkačik, C.C. Guet, (2017).
datarep_id: '53'
date_created: 2018-12-12T12:31:32Z
date_published: 2017-03-10T00:00:00Z
date_updated: 2024-02-21T13:49:00Z
day: '10'
ddc:
- '571'
department:
- _id: CaGu
- _id: GaTk
- _id: Bio
doi: 10.15479/AT:ISTA:53
file:
- access_level: open_access
checksum: d77859af757ac8025c50c7b12b52eaf3
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:38Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5603'
file_name: IST-2017-53-v1+1_Data_MDE.zip
file_size: 6773204
relation: main_file
file_date_updated: 2020-07-14T12:47:03Z
has_accepted_license: '1'
keyword:
- single cell microscopy
- mother machine microfluidic device
- AcrAB-TolC pump
- multi-drug efflux
- Escherichia coli
month: '03'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '665'
relation: research_paper
status: public
status: public
title: Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived
phenotypic heterogeneity
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '665'
abstract:
- lang: eng
text: The molecular mechanisms underlying phenotypic variation in isogenic bacterial
populations remain poorly understood.We report that AcrAB-TolC, the main multidrug
efflux pump of Escherichia coli, exhibits a strong partitioning bias for old cell
poles by a segregation mechanism that is mediated by ternary AcrAB-TolC complex
formation. Mother cells inheriting old poles are phenotypically distinct and display
increased drug efflux activity relative to daughters. Consequently, we find systematic
and long-lived growth differences between mother and daughter cells in the presence
of subinhibitory drug concentrations. A simple model for biased partitioning predicts
a population structure of long-lived and highly heterogeneous phenotypes. This
straightforward mechanism of generating sustained growth rate differences at subinhibitory
antibiotic concentrations has implications for understanding the emergence of
multidrug resistance in bacteria.
article_processing_charge: No
article_type: original
author:
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Anna M
full_name: Andersson, Anna M
id: 2B8A40DA-F248-11E8-B48F-1D18A9856A87
last_name: Andersson
orcid: 0000-0003-2912-6769
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
- first_name: Enrique
full_name: Balleza, Enrique
last_name: Balleza
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multidrug
efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science.
2017;356(6335):311-315. doi:10.1126/science.aaf4762
apa: Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild,
R., … Guet, C. C. (2017). Biased partitioning of the multidrug efflux pump AcrAB
TolC underlies long lived phenotypic heterogeneity. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.aaf4762
chicago: Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza,
Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning
of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.”
Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aaf4762.
ieee: T. Bergmiller et al., “Biased partitioning of the multidrug efflux
pump AcrAB TolC underlies long lived phenotypic heterogeneity,” Science,
vol. 356, no. 6335. American Association for the Advancement of Science, pp. 311–315,
2017.
ista: Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik
G, Guet CC. 2017. Biased partitioning of the multidrug efflux pump AcrAB TolC
underlies long lived phenotypic heterogeneity. Science. 356(6335), 311–315.
mla: Bergmiller, Tobias, et al. “Biased Partitioning of the Multidrug Efflux Pump
AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science, vol.
356, no. 6335, American Association for the Advancement of Science, 2017, pp.
311–15, doi:10.1126/science.aaf4762.
short: T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild,
G. Tkačik, C.C. Guet, Science 356 (2017) 311–315.
date_created: 2018-12-11T11:47:48Z
date_published: 2017-04-21T00:00:00Z
date_updated: 2024-02-21T13:49:00Z
day: '21'
department:
- _id: CaGu
- _id: GaTk
- _id: Bio
doi: 10.1126/science.aaf4762
intvolume: ' 356'
issue: '6335'
language:
- iso: eng
month: '04'
oa_version: None
page: 311 - 315
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Science
publication_identifier:
issn:
- '00368075'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7064'
quality_controlled: '1'
related_material:
record:
- id: '5560'
relation: popular_science
status: public
scopus_import: 1
status: public
title: Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long
lived phenotypic heterogeneity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 356
year: '2017'
...
---
_id: '735'
abstract:
- lang: eng
text: Cell-cell contact formation constitutes an essential step in evolution, leading
to the differentiation of specialized cell types. However, remarkably little is
known about whether and how the interplay between contact formation and fate specification
affects development. Here, we identify a positive feedback loop between cell-cell
contact duration, morphogen signaling, and mesendoderm cell-fate specification
during zebrafish gastrulation. We show that long-lasting cell-cell contacts enhance
the competence of prechordal plate (ppl) progenitor cells to respond to Nodal
signaling, required for ppl cell-fate specification. We further show that Nodal
signaling promotes ppl cell-cell contact duration, generating a positive feedback
loop between ppl cell-cell contact duration and cell-fate specification. Finally,
by combining mathematical modeling and experimentation, we show that this feedback
determines whether anterior axial mesendoderm cells become ppl or, instead, turn
into endoderm. Thus, the interdependent activities of cell-cell signaling and
contact formation control fate diversification within the developing embryo.
article_processing_charge: No
author:
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Saurabh
full_name: Pradhan, Saurabh
last_name: Pradhan
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
- first_name: Keisuke
full_name: Sako, Keisuke
id: 3BED66BE-F248-11E8-B48F-1D18A9856A87
last_name: Sako
orcid: 0000-0002-6453-8075
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Barone V, Lang M, Krens G, et al. An effective feedback loop between cell-cell
contact duration and morphogen signaling determines cell fate. Developmental
Cell. 2017;43(2):198-211. doi:10.1016/j.devcel.2017.09.014
apa: Barone, V., Lang, M., Krens, G., Pradhan, S., Shamipour, S., Sako, K., … Heisenberg,
C.-P. J. (2017). An effective feedback loop between cell-cell contact duration
and morphogen signaling determines cell fate. Developmental Cell. Cell
Press. https://doi.org/10.1016/j.devcel.2017.09.014
chicago: Barone, Vanessa, Moritz Lang, Gabriel Krens, Saurabh Pradhan, Shayan Shamipour,
Keisuke Sako, Mateusz K Sikora, Calin C Guet, and Carl-Philipp J Heisenberg. “An
Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling
Determines Cell Fate.” Developmental Cell. Cell Press, 2017. https://doi.org/10.1016/j.devcel.2017.09.014.
ieee: V. Barone et al., “An effective feedback loop between cell-cell contact
duration and morphogen signaling determines cell fate,” Developmental Cell,
vol. 43, no. 2. Cell Press, pp. 198–211, 2017.
ista: Barone V, Lang M, Krens G, Pradhan S, Shamipour S, Sako K, Sikora MK, Guet
CC, Heisenberg C-PJ. 2017. An effective feedback loop between cell-cell contact
duration and morphogen signaling determines cell fate. Developmental Cell. 43(2),
198–211.
mla: Barone, Vanessa, et al. “An Effective Feedback Loop between Cell-Cell Contact
Duration and Morphogen Signaling Determines Cell Fate.” Developmental Cell,
vol. 43, no. 2, Cell Press, 2017, pp. 198–211, doi:10.1016/j.devcel.2017.09.014.
short: V. Barone, M. Lang, G. Krens, S. Pradhan, S. Shamipour, K. Sako, M.K. Sikora,
C.C. Guet, C.-P.J. Heisenberg, Developmental Cell 43 (2017) 198–211.
date_created: 2018-12-11T11:48:13Z
date_published: 2017-10-23T00:00:00Z
date_updated: 2024-03-28T23:30:39Z
day: '23'
department:
- _id: CaHe
- _id: CaGu
- _id: GaTk
doi: 10.1016/j.devcel.2017.09.014
ec_funded: 1
external_id:
isi:
- '000413443700011'
intvolume: ' 43'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa_version: None
page: 198 - 211
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 252DD2A6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I2058
name: 'Cell segregation in gastrulation: the role of cell fate specification'
publication: Developmental Cell
publication_identifier:
issn:
- '15345807'
publication_status: published
publisher: Cell Press
publist_id: '6934'
quality_controlled: '1'
related_material:
record:
- id: '961'
relation: dissertation_contains
status: public
- id: '8350'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: An effective feedback loop between cell-cell contact duration and morphogen
signaling determines cell fate
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 43
year: '2017'
...
---
_id: '1082'
abstract:
- lang: eng
text: In many applications, it is desirable to extract only the relevant aspects
of data. A principled way to do this is the information bottleneck (IB) method,
where one seeks a code that maximises information about a relevance variable,
Y, while constraining the information encoded about the original data, X. Unfortunately
however, the IB method is computationally demanding when data are high-dimensional
and/or non-gaussian. Here we propose an approximate variational scheme for maximising
a lower bound on the IB objective, analogous to variational EM. Using this method,
we derive an IB algorithm to recover features that are both relevant and sparse.
Finally, we demonstrate how kernelised versions of the algorithm can be used to
address a broad range of problems with non-linear relation between X and Y.
alternative_title:
- Advances in Neural Information Processing Systems
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: 'Chalk MJ, Marre O, Tkačik G. Relevant sparse codes with variational information
bottleneck. In: Vol 29. Neural Information Processing Systems; 2016:1965-1973.'
apa: 'Chalk, M. J., Marre, O., & Tkačik, G. (2016). Relevant sparse codes with
variational information bottleneck (Vol. 29, pp. 1965–1973). Presented at the
NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information
Processing Systems.'
chicago: Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Relevant Sparse Codes
with Variational Information Bottleneck,” 29:1965–73. Neural Information Processing
Systems, 2016.
ieee: 'M. J. Chalk, O. Marre, and G. Tkačik, “Relevant sparse codes with variational
information bottleneck,” presented at the NIPS: Neural Information Processing
Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.'
ista: 'Chalk MJ, Marre O, Tkačik G. 2016. Relevant sparse codes with variational
information bottleneck. NIPS: Neural Information Processing Systems, Advances
in Neural Information Processing Systems, vol. 29, 1965–1973.'
mla: Chalk, Matthew J., et al. Relevant Sparse Codes with Variational Information
Bottleneck. Vol. 29, Neural Information Processing Systems, 2016, pp. 1965–73.
short: M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems,
2016, pp. 1965–1973.
conference:
end_date: 2016-12-10
location: Barcelona, Spain
name: 'NIPS: Neural Information Processing Systems'
start_date: 2016-12-05
date_created: 2018-12-11T11:50:03Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:48:09Z
day: '01'
department:
- _id: GaTk
intvolume: ' 29'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1605.07332
month: '12'
oa: 1
oa_version: Preprint
page: 1965-1973
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '6298'
quality_controlled: '1'
related_material:
link:
- relation: other
url: https://papers.nips.cc/paper/6101-relevant-sparse-codes-with-variational-information-bottleneck
scopus_import: 1
status: public
title: Relevant sparse codes with variational information bottleneck
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2016'
...
---
_id: '1105'
abstract:
- lang: eng
text: Jointly characterizing neural responses in terms of several external variables
promises novel insights into circuit function, but remains computationally prohibitive
in practice. Here we use gaussian process (GP) priors and exploit recent advances
in fast GP inference and learning based on Kronecker methods, to efficiently estimate
multidimensional nonlinear tuning functions. Our estimator require considerably
less data than traditional methods and further provides principled uncertainty
estimates. We apply these tools to hippocampal recordings during open field exploration
and use them to characterize the joint dependence of CA1 responses on the position
of the animal and several other variables, including the animal\'s speed, direction
of motion, and network oscillations.Our results provide an unprecedentedly detailed
quantification of the tuning of hippocampal neurons. The model\'s generality suggests
that our approach can be used to estimate neural response properties in other
brain regions.
acknowledgement: "We thank Jozsef Csicsvari for kindly sharing the CA1 data.\r\nThis
work was supported by the People Programme (Marie Curie Actions) of the European
Union’s Seventh Framework Programme(FP7/2007-2013) under REA grant agreement no.
291734."
alternative_title:
- Advances in Neural Information Processing Systems
author:
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: 'Savin C, Tkačik G. Estimating nonlinear neural response functions using GP
priors and Kronecker methods. In: Vol 29. Neural Information Processing Systems;
2016:3610-3618.'
apa: 'Savin, C., & Tkačik, G. (2016). Estimating nonlinear neural response functions
using GP priors and Kronecker methods (Vol. 29, pp. 3610–3618). Presented at the
NIPS: Neural Information Processing Systems, Barcelona; Spain: Neural Information
Processing Systems.'
chicago: Savin, Cristina, and Gašper Tkačik. “Estimating Nonlinear Neural Response
Functions Using GP Priors and Kronecker Methods,” 29:3610–18. Neural Information
Processing Systems, 2016.
ieee: 'C. Savin and G. Tkačik, “Estimating nonlinear neural response functions using
GP priors and Kronecker methods,” presented at the NIPS: Neural Information Processing
Systems, Barcelona; Spain, 2016, vol. 29, pp. 3610–3618.'
ista: 'Savin C, Tkačik G. 2016. Estimating nonlinear neural response functions using
GP priors and Kronecker methods. NIPS: Neural Information Processing Systems,
Advances in Neural Information Processing Systems, vol. 29, 3610–3618.'
mla: Savin, Cristina, and Gašper Tkačik. Estimating Nonlinear Neural Response
Functions Using GP Priors and Kronecker Methods. Vol. 29, Neural Information
Processing Systems, 2016, pp. 3610–18.
short: C. Savin, G. Tkačik, in:, Neural Information Processing Systems, 2016, pp.
3610–3618.
conference:
end_date: 2016-12-10
location: Barcelona; Spain
name: 'NIPS: Neural Information Processing Systems'
start_date: 2016-12-05
date_created: 2018-12-11T11:50:10Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:48:19Z
day: '01'
department:
- _id: GaTk
ec_funded: 1
intvolume: ' 29'
language:
- iso: eng
main_file_link:
- url: http://papers.nips.cc/paper/6153-estimating-nonlinear-neural-response-functions-using-gp-priors-and-kronecker-methods
month: '12'
oa_version: None
page: 3610-3618
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '6265'
quality_controlled: '1'
scopus_import: 1
status: public
title: Estimating nonlinear neural response functions using GP priors and Kronecker
methods
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2016'
...
---
_id: '1170'
abstract:
- lang: eng
text: The increasing complexity of dynamic models in systems and synthetic biology
poses computational challenges especially for the identification of model parameters.
While modularization of the corresponding optimization problems could help reduce
the “curse of dimensionality,” abundant feedback and crosstalk mechanisms prohibit
a simple decomposition of most biomolecular networks into subnetworks, or modules.
Drawing on ideas from network modularization and multiple-shooting optimization,
we present here a modular parameter identification approach that explicitly allows
for such interdependencies. Interfaces between our modules are given by the experimentally
measured molecular species. This definition allows deriving good (initial) estimates
for the inter-module communication directly from the experimental data. Given
these estimates, the states and parameter sensitivities of different modules can
be integrated independently. To achieve consistency between modules, we iteratively
adjust the estimates for inter-module communication while optimizing the parameters.
After convergence to an optimal parameter set---but not during earlier iterations---the
intermodule communication as well as the individual modules\' state dynamics agree
with the dynamics of the nonmodularized network. Our modular parameter identification
approach allows for easy parallelization; it can reduce the computational complexity
for larger networks and decrease the probability to converge to suboptimal local
minima. We demonstrate the algorithm\'s performance in parameter estimation for
two biomolecular networks, a synthetic genetic oscillator and a mammalian signaling
pathway.
author:
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Jörg
full_name: Stelling, Jörg
last_name: Stelling
citation:
ama: Lang M, Stelling J. Modular parameter identification of biomolecular networks.
SIAM Journal on Scientific Computing. 2016;38(6):B988-B1008. doi:10.1137/15M103306X
apa: Lang, M., & Stelling, J. (2016). Modular parameter identification of biomolecular
networks. SIAM Journal on Scientific Computing. Society for Industrial
and Applied Mathematics . https://doi.org/10.1137/15M103306X
chicago: Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular
Networks.” SIAM Journal on Scientific Computing. Society for Industrial
and Applied Mathematics , 2016. https://doi.org/10.1137/15M103306X.
ieee: M. Lang and J. Stelling, “Modular parameter identification of biomolecular
networks,” SIAM Journal on Scientific Computing, vol. 38, no. 6. Society
for Industrial and Applied Mathematics , pp. B988–B1008, 2016.
ista: Lang M, Stelling J. 2016. Modular parameter identification of biomolecular
networks. SIAM Journal on Scientific Computing. 38(6), B988–B1008.
mla: Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular
Networks.” SIAM Journal on Scientific Computing, vol. 38, no. 6, Society
for Industrial and Applied Mathematics , 2016, pp. B988–1008, doi:10.1137/15M103306X.
short: M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) B988–B1008.
date_created: 2018-12-11T11:50:31Z
date_published: 2016-11-15T00:00:00Z
date_updated: 2021-01-12T06:48:49Z
day: '15'
ddc:
- '003'
- '518'
- '570'
- '621'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1137/15M103306X
file:
- access_level: local
checksum: 781bc3ffd30b2dd65b7727c5a285fc78
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:41Z
date_updated: 2020-07-14T12:44:37Z
file_id: '5095'
file_name: IST-2017-811-v1+1_modular_parameter_identification.pdf
file_size: 871964
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 38'
issue: '6'
language:
- iso: eng
month: '11'
oa_version: Submitted Version
page: B988 - B1008
publication: SIAM Journal on Scientific Computing
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '6186'
pubrep_id: '811'
quality_controlled: '1'
scopus_import: 1
status: public
title: Modular parameter identification of biomolecular networks
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2016'
...
---
_id: '1171'
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: 'Tkačik G. Understanding regulatory networks requires more than computing a
multitude of graph statistics: Comment on "Drivers of structural features
in gene regulatory networks: From biophysical constraints to biological function"
by O. C. Martin et al. Physics of Life Reviews. 2016;17:166-167. doi:10.1016/j.plrev.2016.06.005'
apa: 'Tkačik, G. (2016). Understanding regulatory networks requires more than computing
a multitude of graph statistics: Comment on "Drivers of structural features
in gene regulatory networks: From biophysical constraints to biological function"
by O. C. Martin et al. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.005'
chicago: 'Tkačik, Gašper. “Understanding Regulatory Networks Requires More than
Computing a Multitude of Graph Statistics: Comment on "Drivers of Structural
Features in Gene Regulatory Networks: From Biophysical Constraints to Biological
Function" by O. C. Martin et Al.” Physics of Life Reviews. Elsevier,
2016. https://doi.org/10.1016/j.plrev.2016.06.005.'
ieee: 'G. Tkačik, “Understanding regulatory networks requires more than computing
a multitude of graph statistics: Comment on "Drivers of structural features
in gene regulatory networks: From biophysical constraints to biological function"
by O. C. Martin et al.,” Physics of Life Reviews, vol. 17. Elsevier, pp.
166–167, 2016.'
ista: 'Tkačik G. 2016. Understanding regulatory networks requires more than computing
a multitude of graph statistics: Comment on "Drivers of structural features
in gene regulatory networks: From biophysical constraints to biological function"
by O. C. Martin et al. Physics of Life Reviews. 17, 166–167.'
mla: 'Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing
a Multitude of Graph Statistics: Comment on "Drivers of Structural Features
in Gene Regulatory Networks: From Biophysical Constraints to Biological Function"
by O. C. Martin et Al.” Physics of Life Reviews, vol. 17, Elsevier, 2016,
pp. 166–67, doi:10.1016/j.plrev.2016.06.005.'
short: G. Tkačik, Physics of Life Reviews 17 (2016) 166–167.
date_created: 2018-12-11T11:50:32Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:48:50Z
day: '01'
department:
- _id: GaTk
doi: 10.1016/j.plrev.2016.06.005
intvolume: ' 17'
language:
- iso: eng
month: '07'
oa_version: None
page: 166 - 167
publication: Physics of Life Reviews
publication_status: published
publisher: Elsevier
publist_id: '6185'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Understanding regulatory networks requires more than computing a multitude
of graph statistics: Comment on "Drivers of structural features in gene regulatory
networks: From biophysical constraints to biological function" by O. C. Martin
et al.'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2016'
...
---
_id: '1188'
abstract:
- lang: eng
text: "We consider a population dynamics model coupling cell growth to a diffusion
in the space of metabolic phenotypes as it can be obtained from realistic constraints-based
modelling. \r\nIn the asymptotic regime of slow\r\ndiffusion, that coincides with
the relevant experimental range, the resulting\r\nnon-linear Fokker–Planck equation
is solved for the steady state in the WKB\r\napproximation that maps it into the
ground state of a quantum particle in an\r\nAiry potential plus a centrifugal
term. We retrieve scaling laws for growth rate\r\nfluctuations and time response
with respect to the distance from the maximum\r\ngrowth rate suggesting that suboptimal
populations can have a faster response\r\nto perturbations."
acknowledgement: D De Martino is supported by the People Programme (Marie Curie Actions)
of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant
agreement no. [291734]. D Masoero is supported by the FCT scholarship, number SFRH/BPD/75908/2011.
D De Martino thanks the Grupo de Física Matemática of the Universidade de Lisboa
for the kind hospitality. We also wish to thank Matteo Osella, Vincenzo Vitagliano
and Vera Luz Masoero for useful discussions, also late at night.
article_number: '123502'
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Davide
full_name: Masoero, Davide
last_name: Masoero
citation:
ama: 'De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization,
applied to metabolism & growth. Journal of Statistical Mechanics:
Theory and Experiment. 2016;2016(12). doi:10.1088/1742-5468/aa4e8f'
apa: 'De Martino, D., & Masoero, D. (2016). Asymptotic analysis of noisy fitness
maximization, applied to metabolism & growth. Journal of Statistical
Mechanics: Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa4e8f'
chicago: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy
Fitness Maximization, Applied to Metabolism & Growth.” Journal of
Statistical Mechanics: Theory and Experiment. IOPscience, 2016. https://doi.org/10.1088/1742-5468/aa4e8f.'
ieee: 'D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization,
applied to metabolism & growth,” Journal of Statistical Mechanics:
Theory and Experiment, vol. 2016, no. 12. IOPscience, 2016.'
ista: 'De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization,
applied to metabolism & growth. Journal of Statistical Mechanics: Theory
and Experiment. 2016(12), 123502.'
mla: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness
Maximization, Applied to Metabolism & Growth.” Journal of Statistical
Mechanics: Theory and Experiment, vol. 2016, no. 12, 123502, IOPscience, 2016,
doi:10.1088/1742-5468/aa4e8f.'
short: 'D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and
Experiment 2016 (2016).'
date_created: 2018-12-11T11:50:37Z
date_published: 2016-12-30T00:00:00Z
date_updated: 2021-01-12T06:48:57Z
day: '30'
department:
- _id: GaTk
doi: 10.1088/1742-5468/aa4e8f
ec_funded: 1
intvolume: ' 2016'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1606.09048
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Journal of Statistical Mechanics: Theory and Experiment'
publication_status: published
publisher: IOPscience
publist_id: '6165'
quality_controlled: '1'
scopus_import: 1
status: public
title: Asymptotic analysis of noisy fitness maximization, applied to metabolism &
growth
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2016
year: '2016'
...
---
_id: '1203'
abstract:
- lang: eng
text: Haemophilus haemolyticus has been recently discovered to have the potential
to cause invasive disease. It is closely related to nontypeable Haemophilus influenzae
(NT H. influenzae). NT H. influenzae and H. haemolyticus are often misidentified
because none of the existing tests targeting the known phenotypes of H. haemolyticus
are able to specifically identify H. haemolyticus. Through comparative genomic
analysis of H. haemolyticus and NT H. influenzae, we identified genes unique to
H. haemolyticus that can be used as targets for the identification of H. haemolyticus.
A real-time PCR targeting purT (encoding phosphoribosylglycinamide formyltransferase
2 in the purine synthesis pathway) was developed and evaluated. The lower limit
of detection was 40 genomes/PCR; the sensitivity and specificity in detecting
H. haemolyticus were 98.9% and 97%, respectively. To improve the discrimination
of H. haemolyticus and NT H. influenzae, a testing scheme combining two targets
(H. haemolyticus purT and H. influenzae hpd, encoding protein D lipoprotein) was
also evaluated and showed 96.7% sensitivity and 98.2% specificity for the identification
of H. haemolyticus and 92.8% sensitivity and 100% specificity for the identification
of H. influenzae, respectively. The dual-target testing scheme can be used for
the diagnosis and surveillance of infection and disease caused by H. haemolyticus
and NT H. influenzae.
acknowledgement: We are grateful to ABCs for providing strains and the Bacterial Meningitis
Laboratory for technical support.
author:
- first_name: Fang
full_name: Hu, Fang
last_name: Hu
- first_name: Lavanya
full_name: Rishishwar, Lavanya
last_name: Rishishwar
- first_name: Ambily
full_name: Sivadas, Ambily
last_name: Sivadas
- first_name: Gabriel
full_name: Mitchell, Gabriel
id: 315BCD80-F248-11E8-B48F-1D18A9856A87
last_name: Mitchell
- first_name: Jordan
full_name: King, Jordan
last_name: King
- first_name: Timothy
full_name: Murphy, Timothy
last_name: Murphy
- first_name: Janet
full_name: Gilsdorf, Janet
last_name: Gilsdorf
- first_name: Leonard
full_name: Mayer, Leonard
last_name: Mayer
- first_name: Xin
full_name: Wang, Xin
last_name: Wang
citation:
ama: Hu F, Rishishwar L, Sivadas A, et al. Comparative genomic analysis of Haemophilus
haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for
their discrimination. Journal of Clinical Microbiology. 2016;54(12):3010-3017.
doi:10.1128/JCM.01511-16
apa: Hu, F., Rishishwar, L., Sivadas, A., Mitchell, G., King, J., Murphy, T., …
Wang, X. (2016). Comparative genomic analysis of Haemophilus haemolyticus and
nontypeable Haemophilus influenzae and a new testing scheme for their discrimination.
Journal of Clinical Microbiology. American Society for Microbiology. https://doi.org/10.1128/JCM.01511-16
chicago: Hu, Fang, Lavanya Rishishwar, Ambily Sivadas, Gabriel Mitchell, Jordan
King, Timothy Murphy, Janet Gilsdorf, Leonard Mayer, and Xin Wang. “Comparative
Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae
and a New Testing Scheme for Their Discrimination.” Journal of Clinical Microbiology.
American Society for Microbiology, 2016. https://doi.org/10.1128/JCM.01511-16.
ieee: F. Hu et al., “Comparative genomic analysis of Haemophilus haemolyticus
and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination,”
Journal of Clinical Microbiology, vol. 54, no. 12. American Society for
Microbiology, pp. 3010–3017, 2016.
ista: Hu F, Rishishwar L, Sivadas A, Mitchell G, King J, Murphy T, Gilsdorf J, Mayer
L, Wang X. 2016. Comparative genomic analysis of Haemophilus haemolyticus and
nontypeable Haemophilus influenzae and a new testing scheme for their discrimination.
Journal of Clinical Microbiology. 54(12), 3010–3017.
mla: Hu, Fang, et al. “Comparative Genomic Analysis of Haemophilus Haemolyticus
and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.”
Journal of Clinical Microbiology, vol. 54, no. 12, American Society for
Microbiology, 2016, pp. 3010–17, doi:10.1128/JCM.01511-16.
short: F. Hu, L. Rishishwar, A. Sivadas, G. Mitchell, J. King, T. Murphy, J. Gilsdorf,
L. Mayer, X. Wang, Journal of Clinical Microbiology 54 (2016) 3010–3017.
date_created: 2018-12-11T11:50:41Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:49:04Z
day: '01'
department:
- _id: GaTk
doi: 10.1128/JCM.01511-16
intvolume: ' 54'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5121393/
month: '12'
oa: 1
oa_version: Submitted Version
page: 3010 - 3017
publication: Journal of Clinical Microbiology
publication_status: published
publisher: American Society for Microbiology
publist_id: '6146'
quality_controlled: '1'
scopus_import: 1
status: public
title: Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus
influenzae and a new testing scheme for their discrimination
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2016'
...
---
_id: '1214'
abstract:
- lang: eng
text: 'With the accelerated development of robot technologies, optimal control becomes
one of the central themes of research. In traditional approaches, the controller,
by its internal functionality, finds appropriate actions on the basis of the history
of sensor values, guided by the goals, intentions, objectives, learning schemes,
and so forth. While very successful with classical robots, these methods run into
severe difficulties when applied to soft robots, a new field of robotics with
large interest for human-robot interaction. We claim that a novel controller paradigm
opens new perspective for this field. This paper applies a recently developed
neuro controller with differential extrinsic synaptic plasticity to a muscle-tendon
driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we
observe a vast variety of self-organized behavior patterns: when left alone, the
arm realizes pseudo-random sequences of different poses. By applying physical
forces, the system can be entrained into definite motion patterns like wiping
a table. Most interestingly, after attaching an object, the controller gets in
a functional resonance with the object''s internal dynamics, starting to shake
spontaneously bottles half-filled with water or sensitively driving an attached
pendulum into a circular mode. When attached to the crank of a wheel the neural
system independently develops to rotate it. In this way, the robot discovers affordances
of objects its body is interacting with.'
acknowledgement: RD thanks for the hospitality at the Max-Planck-Institute and for
helpful discussions with Nihat Ay and Keyan Zahedi.
article_number: '7759138'
author:
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
- first_name: Raphael
full_name: Hostettler, Raphael
last_name: Hostettler
- first_name: Alois
full_name: Knoll, Alois
last_name: Knoll
- first_name: Ralf
full_name: Der, Ralf
last_name: Der
citation:
ama: 'Martius GS, Hostettler R, Knoll A, Der R. Compliant control for soft robots:
Emergent behavior of a tendon driven anthropomorphic arm. In: Vol 2016-November.
IEEE; 2016. doi:10.1109/IROS.2016.7759138'
apa: 'Martius, G. S., Hostettler, R., Knoll, A., & Der, R. (2016). Compliant
control for soft robots: Emergent behavior of a tendon driven anthropomorphic
arm (Vol. 2016–November). Presented at the IEEE RSJ International Conference on
Intelligent Robots and Systems IROS , Daejeon, Korea: IEEE. https://doi.org/10.1109/IROS.2016.7759138'
chicago: 'Martius, Georg S, Raphael Hostettler, Alois Knoll, and Ralf Der. “Compliant
Control for Soft Robots: Emergent Behavior of a Tendon Driven Anthropomorphic
Arm,” Vol. 2016–November. IEEE, 2016. https://doi.org/10.1109/IROS.2016.7759138.'
ieee: 'G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Compliant control for
soft robots: Emergent behavior of a tendon driven anthropomorphic arm,” presented
at the IEEE RSJ International Conference on Intelligent Robots and Systems IROS
, Daejeon, Korea, 2016, vol. 2016–November.'
ista: 'Martius GS, Hostettler R, Knoll A, Der R. 2016. Compliant control for soft
robots: Emergent behavior of a tendon driven anthropomorphic arm. IEEE RSJ International
Conference on Intelligent Robots and Systems IROS vol. 2016–November, 7759138.'
mla: 'Martius, Georg S., et al. Compliant Control for Soft Robots: Emergent Behavior
of a Tendon Driven Anthropomorphic Arm. Vol. 2016–November, 7759138, IEEE,
2016, doi:10.1109/IROS.2016.7759138.'
short: G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, IEEE, 2016.
conference:
end_date: 2016-09-14
location: Daejeon, Korea
name: 'IEEE RSJ International Conference on Intelligent Robots and Systems IROS '
start_date: 2016-09-09
date_created: 2018-12-11T11:50:45Z
date_published: 2016-11-28T00:00:00Z
date_updated: 2021-01-12T06:49:08Z
day: '28'
department:
- _id: ChLa
- _id: GaTk
doi: 10.1109/IROS.2016.7759138
language:
- iso: eng
month: '11'
oa_version: None
publication_status: published
publisher: IEEE
publist_id: '6121'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic
arm'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2016-November
year: '2016'
...
---
_id: '1220'
abstract:
- lang: eng
text: Theoretical and numerical aspects of aerodynamic efficiency of propulsion
systems coupled to the boundary layer of a fuselage are studied. We discuss the
effects of local flow fields, which are affected both by conservative flow acceleration
as well as total pressure losses, on the efficiency of boundary layer immersed
propulsion devices. We introduce the concept of a boundary layer retardation turbine
that helps reduce skin friction over the fuselage. We numerically investigate
efficiency gains offered by boundary layer and wake interacting devices. We discuss
the results in terms of a total energy consumption framework and show that efficiency
gains of any device depend on all the other elements of the propulsion system.
author:
- first_name: Gregor
full_name: Mikić, Gregor
last_name: Mikić
- first_name: Alex
full_name: Stoll, Alex
last_name: Stoll
- first_name: Joe
full_name: Bevirt, Joe
last_name: Bevirt
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: Mark
full_name: Moore, Mark
last_name: Moore
citation:
ama: 'Mikić G, Stoll A, Bevirt J, Grah R, Moore M. Fuselage boundary layer ingestion
propulsion applied to a thin haul commuter aircraft for optimal efficiency. In:
AIAA; 2016:1-19. doi:10.2514/6.2016-3764'
apa: 'Mikić, G., Stoll, A., Bevirt, J., Grah, R., & Moore, M. (2016). Fuselage
boundary layer ingestion propulsion applied to a thin haul commuter aircraft for
optimal efficiency (pp. 1–19). Presented at the AIAA: Aviation Technology, Integration,
and Operations Conference, Washington, D.C., USA: AIAA. https://doi.org/10.2514/6.2016-3764'
chicago: Mikić, Gregor, Alex Stoll, Joe Bevirt, Rok Grah, and Mark Moore. “Fuselage
Boundary Layer Ingestion Propulsion Applied to a Thin Haul Commuter Aircraft for
Optimal Efficiency,” 1–19. AIAA, 2016. https://doi.org/10.2514/6.2016-3764.
ieee: 'G. Mikić, A. Stoll, J. Bevirt, R. Grah, and M. Moore, “Fuselage boundary
layer ingestion propulsion applied to a thin haul commuter aircraft for optimal
efficiency,” presented at the AIAA: Aviation Technology, Integration, and Operations
Conference, Washington, D.C., USA, 2016, pp. 1–19.'
ista: 'Mikić G, Stoll A, Bevirt J, Grah R, Moore M. 2016. Fuselage boundary layer
ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency.
AIAA: Aviation Technology, Integration, and Operations Conference, 1–19.'
mla: Mikić, Gregor, et al. Fuselage Boundary Layer Ingestion Propulsion Applied
to a Thin Haul Commuter Aircraft for Optimal Efficiency. AIAA, 2016, pp. 1–19,
doi:10.2514/6.2016-3764.
short: G. Mikić, A. Stoll, J. Bevirt, R. Grah, M. Moore, in:, AIAA, 2016, pp. 1–19.
conference:
end_date: 2016-06-17
location: Washington, D.C., USA
name: 'AIAA: Aviation Technology, Integration, and Operations Conference'
start_date: 2016-06-13
date_created: 2018-12-11T11:50:47Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2023-02-21T10:17:50Z
day: '01'
department:
- _id: CaGu
- _id: GaTk
doi: 10.2514/6.2016-3764
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://ntrs.nasa.gov/search.jsp?R=20160010167&hterms=Fuselage+boundary+layer+ingestion+propulsion+applied+thin+haul+commuter+aircraft+optimal+efficiency&qs=N%3D0%26Ntk%3DAll%26Ntt%3DFuselage%2520boundary%2520layer%2520ingestion%2520propulsion%2520applied%2520to%2520a%2520thin%2520haul%2520commuter%2520aircraft%2520for%2520optimal%2520efficiency%26Ntx%3Dmode%2520matchallpartial%26Nm%3D123%7CCollection%7CNASA%2520STI%7C%7C17%7CCollection%7CNACA
month: '06'
oa: 1
oa_version: Preprint
page: 1 - 19
publication_status: published
publisher: AIAA
publist_id: '6114'
quality_controlled: '1'
scopus_import: 1
status: public
title: Fuselage boundary layer ingestion propulsion applied to a thin haul commuter
aircraft for optimal efficiency
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1242'
abstract:
- lang: eng
text: A crucial step in the regulation of gene expression is binding of transcription
factor (TF) proteins to regulatory sites along the DNA. But transcription factors
act at nanomolar concentrations, and noise due to random arrival of these molecules
at their binding sites can severely limit the precision of regulation. Recent
work on the optimization of information flow through regulatory networks indicates
that the lower end of the dynamic range of concentrations is simply inaccessible,
overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain
proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest
a scheme in which transcription factors also act as indirect translational regulators,
binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule
acts as an independent sensor of the input concentration, and averaging over these
multiple sensors reduces the noise. We analyze information flow through this scheme
and identify conditions under which it outperforms direct transcriptional regulation.
Our results suggest that the dual role of homeodomain proteins is not just a historical
accident, but a solution to a crucial physics problem in the regulation of gene
expression.
acknowledgement: "We thank T. Gregor, A. Prochaintz, and others for\r\nhelpful discussions.
This work was supported in part by\r\nGrants No. PHY-1305525 and No. CCF-0939370
from the\r\nUS National Science Foundation and by the W.M. Keck\r\nFoundation. A.M.W.
acknowledges the support by European\r\nResearch Council (ERC) Grant No. MCCIG PCIG10–GA-\r\n2011–303561.
G.T. and T.R.S. were supported by Austrian\r\nScience Fund (FWF) Grant No. P28844S."
article_number: '022404'
author:
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Aleksandra
full_name: Walczak, Aleksandra
last_name: Walczak
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Sokolowski TR, Walczak A, Bialek W, Tkačik G. Extending the dynamic range of
transcription factor action by translational regulation. Physical Review E
Statistical Nonlinear and Soft Matter Physics. 2016;93(2). doi:10.1103/PhysRevE.93.022404
apa: Sokolowski, T. R., Walczak, A., Bialek, W., & Tkačik, G. (2016). Extending
the dynamic range of transcription factor action by translational regulation.
Physical Review E Statistical Nonlinear and Soft Matter Physics. American
Institute of Physics. https://doi.org/10.1103/PhysRevE.93.022404
chicago: Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gašper Tkačik.
“Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.”
Physical Review E Statistical Nonlinear and Soft Matter Physics. American
Institute of Physics, 2016. https://doi.org/10.1103/PhysRevE.93.022404.
ieee: T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic
range of transcription factor action by translational regulation,” Physical
Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2. American
Institute of Physics, 2016.
ista: Sokolowski TR, Walczak A, Bialek W, Tkačik G. 2016. Extending the dynamic
range of transcription factor action by translational regulation. Physical Review
E Statistical Nonlinear and Soft Matter Physics. 93(2), 022404.
mla: Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription
Factor Action by Translational Regulation.” Physical Review E Statistical Nonlinear
and Soft Matter Physics, vol. 93, no. 2, 022404, American Institute of Physics,
2016, doi:10.1103/PhysRevE.93.022404.
short: T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E Statistical
Nonlinear and Soft Matter Physics 93 (2016).
date_created: 2018-12-11T11:50:54Z
date_published: 2016-02-04T00:00:00Z
date_updated: 2021-01-12T06:49:20Z
day: '04'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.93.022404
intvolume: ' 93'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1507.02562
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '6088'
quality_controlled: '1'
scopus_import: 1
status: public
title: Extending the dynamic range of transcription factor action by translational
regulation
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2016'
...
---
_id: '1244'
abstract:
- lang: eng
text: Cell polarity refers to a functional spatial organization of proteins that
is crucial for the control of essential cellular processes such as growth and
division. To establish polarity, cells rely on elaborate regulation networks that
control the distribution of proteins at the cell membrane. In fission yeast cells,
a microtubule-dependent network has been identified that polarizes the distribution
of signaling proteins that restricts growth to cell ends and targets the cytokinetic
machinery to the middle of the cell. Although many molecular components have been
shown to play a role in this network, it remains unknown which molecular functionalities
are minimally required to establish a polarized protein distribution in this system.
Here we show that a membrane-binding protein fragment, which distributes homogeneously
in wild-type fission yeast cells, can be made to concentrate at cell ends by attaching
it to a cytoplasmic microtubule end-binding protein. This concentration results
in a polarized pattern of chimera proteins with a spatial extension that is very
reminiscent of natural polarity patterns in fission yeast. However, chimera levels
fluctuate in response to microtubule dynamics, and disruption of microtubules
leads to disappearance of the pattern. Numerical simulations confirm that the
combined functionality of membrane anchoring and microtubule tip affinity is in
principle sufficient to create polarized patterns. Our chimera protein may thus
represent a simple molecular functionality that is able to polarize the membrane,
onto which additional layers of molecular complexity may be built to provide the
temporal robustness that is typical of natural polarity patterns.
acknowledgement: "We thank Sophie Martin, Ken Sawin, Stephen Huisman,\r\nand Damian
Brunner for strains; Julianne\r\nTeapal, Marcel Janson, Sergio Rincon,\r\nand Phong
Tran for technical assistance; Andrew Mugler and Bela Mulder for\r\ndiscussions;
and Sander Tans, Phong Tran,\r\nand Anne Paoletti for critical reading\r\nof the
manuscript. This work is part of the research program of the\r\n“\r\nStichting\r\nvoor
Fundamenteel Onderzoek de Materie,\r\n”\r\nwhich is financially supported by\r\nthe\r\n“\r\nNederlandse
organisatie voor Wete\r\nnschappelijk Onderzoek (NWO).\r\n”"
author:
- first_name: Pierre
full_name: Recouvreux, Pierre
last_name: Recouvreux
- 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: Aristea
full_name: Grammoustianou, Aristea
last_name: Grammoustianou
- first_name: Pieter
full_name: Tenwolde, Pieter
last_name: Tenwolde
- first_name: Marileen
full_name: Dogterom, Marileen
last_name: Dogterom
citation:
ama: Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. Chimera
proteins with affinity for membranes and microtubule tips polarize in the membrane
of fission yeast cells. PNAS. 2016;113(7):1811-1816. doi:10.1073/pnas.1419248113
apa: Recouvreux, P., Sokolowski, T. R., Grammoustianou, A., Tenwolde, P., &
Dogterom, M. (2016). Chimera proteins with affinity for membranes and microtubule
tips polarize in the membrane of fission yeast cells. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.1419248113
chicago: Recouvreux, Pierre, Thomas R Sokolowski, Aristea Grammoustianou, Pieter
Tenwolde, and Marileen Dogterom. “Chimera Proteins with Affinity for Membranes
and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” PNAS.
National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1419248113.
ieee: P. Recouvreux, T. R. Sokolowski, A. Grammoustianou, P. Tenwolde, and M. Dogterom,
“Chimera proteins with affinity for membranes and microtubule tips polarize in
the membrane of fission yeast cells,” PNAS, vol. 113, no. 7. National Academy
of Sciences, pp. 1811–1816, 2016.
ista: Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. 2016.
Chimera proteins with affinity for membranes and microtubule tips polarize in
the membrane of fission yeast cells. PNAS. 113(7), 1811–1816.
mla: Recouvreux, Pierre, et al. “Chimera Proteins with Affinity for Membranes and
Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” PNAS,
vol. 113, no. 7, National Academy of Sciences, 2016, pp. 1811–16, doi:10.1073/pnas.1419248113.
short: P. Recouvreux, T.R. Sokolowski, A. Grammoustianou, P. Tenwolde, M. Dogterom,
PNAS 113 (2016) 1811–1816.
date_created: 2018-12-11T11:50:55Z
date_published: 2016-02-16T00:00:00Z
date_updated: 2021-01-12T06:49:21Z
day: '16'
department:
- _id: GaTk
doi: 10.1073/pnas.1419248113
intvolume: ' 113'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763754/
month: '02'
oa: 1
oa_version: Submitted Version
page: 1811 - 1816
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6085'
quality_controlled: '1'
scopus_import: 1
status: public
title: Chimera proteins with affinity for membranes and microtubule tips polarize
in the membrane of fission yeast cells
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '1248'
abstract:
- lang: eng
text: Life depends as much on the flow of information as on the flow of energy.
Here we review the many efforts to make this intuition precise. Starting with
the building blocks of information theory, we explore examples where it has been
possible to measure, directly, the flow of information in biological networks,
or more generally where information-theoretic ideas have been used to guide the
analysis of experiments. Systems of interest range from single molecules (the
sequence diversity in families of proteins) to groups of organisms (the distribution
of velocities in flocks of birds), and all scales in between. Many of these analyses
are motivated by the idea that biological systems may have evolved to optimize
the gathering and representation of information, and we review the experimental
evidence for this optimization, again across a wide range of scales.
acknowledgement: "Our work was supported in part by the US\r\nNational Science Foundation
(PHY–1305525 and CCF–\r\n0939370), by the Austrian Science Foundation (FWF\r\nP25651),
by the Human Frontiers Science Program, and\r\nby the Simons and Swartz Foundations."
author:
- 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
citation:
ama: Tkačik G, Bialek W. Information processing in living systems. Annual Review
of Condensed Matter Physics. 2016;7:89-117. doi:10.1146/annurev-conmatphys-031214-014803
apa: Tkačik, G., & Bialek, W. (2016). Information processing in living systems.
Annual Review of Condensed Matter Physics. Annual Reviews. https://doi.org/10.1146/annurev-conmatphys-031214-014803
chicago: Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.”
Annual Review of Condensed Matter Physics. Annual Reviews, 2016. https://doi.org/10.1146/annurev-conmatphys-031214-014803.
ieee: G. Tkačik and W. Bialek, “Information processing in living systems,” Annual
Review of Condensed Matter Physics, vol. 7. Annual Reviews, pp. 89–117, 2016.
ista: Tkačik G, Bialek W. 2016. Information processing in living systems. Annual
Review of Condensed Matter Physics. 7, 89–117.
mla: Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.”
Annual Review of Condensed Matter Physics, vol. 7, Annual Reviews, 2016,
pp. 89–117, doi:10.1146/annurev-conmatphys-031214-014803.
short: G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016)
89–117.
date_created: 2018-12-11T11:50:56Z
date_published: 2016-03-10T00:00:00Z
date_updated: 2021-01-12T06:49:23Z
day: '10'
department:
- _id: GaTk
doi: 10.1146/annurev-conmatphys-031214-014803
intvolume: ' 7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1412.8752
month: '03'
oa: 1
oa_version: Preprint
page: 89 - 117
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: Annual Review of Condensed Matter Physics
publication_status: published
publisher: Annual Reviews
publist_id: '6080'
quality_controlled: '1'
scopus_import: 1
status: public
title: Information processing in living systems
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2016'
...
---
_id: '1260'
abstract:
- lang: eng
text: In this work, the Gardner problem of inferring interactions and fields for
an Ising neural network from given patterns under a local stability hypothesis
is addressed under a dual perspective. By means of duality arguments, an integer
linear system is defined whose solution space is the dual of the Gardner space
and whose solutions represent mutually unstable patterns. We propose and discuss
Monte Carlo methods in order to find and remove unstable patterns and uniformly
sample the space of interactions thereafter. We illustrate the problem on a set
of real data and perform ensemble calculation that shows how the emergence of
phase dominated by unstable patterns can be triggered in a nonlinear discontinuous
way.
article_number: '1650067'
article_processing_charge: No
article_type: original
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. The dual of the space of interactions in neural network models.
International Journal of Modern Physics C. 2016;27(6). doi:10.1142/S0129183116500674
apa: De Martino, D. (2016). The dual of the space of interactions in neural network
models. International Journal of Modern Physics C. World Scientific Publishing.
https://doi.org/10.1142/S0129183116500674
chicago: De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network
Models.” International Journal of Modern Physics C. World Scientific Publishing,
2016. https://doi.org/10.1142/S0129183116500674.
ieee: D. De Martino, “The dual of the space of interactions in neural network models,”
International Journal of Modern Physics C, vol. 27, no. 6. World Scientific
Publishing, 2016.
ista: De Martino D. 2016. The dual of the space of interactions in neural network
models. International Journal of Modern Physics C. 27(6), 1650067.
mla: De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network
Models.” International Journal of Modern Physics C, vol. 27, no. 6, 1650067,
World Scientific Publishing, 2016, doi:10.1142/S0129183116500674.
short: D. De Martino, International Journal of Modern Physics C 27 (2016).
date_created: 2018-12-11T11:51:00Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2021-01-12T06:49:28Z
day: '01'
department:
- _id: GaTk
doi: 10.1142/S0129183116500674
external_id:
arxiv:
- '1505.02963'
intvolume: ' 27'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1505.02963
month: '06'
oa: 1
oa_version: Preprint
publication: International Journal of Modern Physics C
publication_status: published
publisher: World Scientific Publishing
publist_id: '6065'
quality_controlled: '1'
scopus_import: 1
status: public
title: The dual of the space of interactions in neural network models
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2016'
...
---
_id: '1266'
abstract:
- lang: eng
text: 'Cortical networks exhibit ‘global oscillations’, in which neural spike times
are entrained to an underlying oscillatory rhythm, but where individual neurons
fire irregularly, on only a fraction of cycles. While the network dynamics underlying
global oscillations have been well characterised, their function is debated. Here,
we show that such global oscillations are a direct consequence of optimal efficient
coding in spiking networks with synaptic delays and noise. To avoid firing unnecessary
spikes, neurons need to share information about the network state. Ideally, membrane
potentials should be strongly correlated and reflect a ‘prediction error’ while
the spikes themselves are uncorrelated and occur rarely. We show that the most
efficient representation is when: (i) spike times are entrained to a global Gamma
rhythm (implying a consistent representation of the error); but (ii) few neurons
fire on each cycle (implying high efficiency), while (iii) excitation and inhibition
are tightly balanced. This suggests that cortical networks exhibiting such dynamics
are tuned to achieve a maximally efficient population code.'
acknowledgement: Boris Gutkin acknowledges funding by the Russian Academic Excellence
Project '5-100’.
article_number: e13824
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: Boris
full_name: Gutkin, Boris
last_name: Gutkin
- first_name: Sophie
full_name: Denève, Sophie
last_name: Denève
citation:
ama: Chalk MJ, Gutkin B, Denève S. Neural oscillations as a signature of efficient
coding in the presence of synaptic delays. eLife. 2016;5(2016JULY). doi:10.7554/eLife.13824
apa: Chalk, M. J., Gutkin, B., & Denève, S. (2016). Neural oscillations as a
signature of efficient coding in the presence of synaptic delays. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.13824
chicago: Chalk, Matthew J, Boris Gutkin, and Sophie Denève. “Neural Oscillations
as a Signature of Efficient Coding in the Presence of Synaptic Delays.” ELife.
eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.13824.
ieee: M. J. Chalk, B. Gutkin, and S. Denève, “Neural oscillations as a signature
of efficient coding in the presence of synaptic delays,” eLife, vol. 5,
no. 2016JULY. eLife Sciences Publications, 2016.
ista: Chalk MJ, Gutkin B, Denève S. 2016. Neural oscillations as a signature of
efficient coding in the presence of synaptic delays. eLife. 5(2016JULY), e13824.
mla: Chalk, Matthew J., et al. “Neural Oscillations as a Signature of Efficient
Coding in the Presence of Synaptic Delays.” ELife, vol. 5, no. 2016JULY,
e13824, eLife Sciences Publications, 2016, doi:10.7554/eLife.13824.
short: M.J. Chalk, B. Gutkin, S. Denève, ELife 5 (2016).
date_created: 2018-12-11T11:51:02Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:49:30Z
day: '01'
ddc:
- '571'
department:
- _id: GaTk
doi: 10.7554/eLife.13824
file:
- access_level: open_access
checksum: dc52d967dc76174477bb258d84be2899
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:20Z
date_updated: 2020-07-14T12:44:42Z
file_id: '4874'
file_name: IST-2016-700-v1+1_e13824-download.pdf
file_size: 2819055
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 5'
issue: 2016JULY
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6056'
pubrep_id: '700'
quality_controlled: '1'
scopus_import: 1
status: public
title: Neural oscillations as a signature of efficient coding in the presence of synaptic
delays
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2016'
...
---
_id: '1290'
abstract:
- lang: eng
text: We developed a competition-based screening strategy to identify compounds
that invert the selective advantage of antibiotic resistance. Using our assay,
we screened over 19,000 compounds for the ability to select against the TetA tetracycline-resistance
efflux pump in Escherichia coli and identified two hits, β-thujaplicin and disulfiram.
Treating a tetracycline-resistant population with β-thujaplicin selects for loss
of the resistance gene, enabling an effective second-phase treatment with doxycycline.
acknowledgement: "This work was supported in part by National Institute of Allergy
and Infectious Diseases grant U54 AI057159, US National Institutes of Health grants
R01 GM081617 (to R.K.) and GM086258 (to J.C.), European Research Council FP7 ERC
grant 281891 (to R.K.) and a National Science Foundation Graduate Fellowship (to
L.K.S.).\r\n"
author:
- first_name: Laura
full_name: Stone, Laura
last_name: Stone
- first_name: Michael
full_name: Baym, Michael
last_name: Baym
- first_name: Tami
full_name: Lieberman, Tami
last_name: Lieberman
- 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: Jon
full_name: Clardy, Jon
last_name: Clardy
- first_name: Roy
full_name: Kishony, Roy
last_name: Kishony
citation:
ama: Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. Compounds that
select against the tetracycline-resistance efflux pump. Nature Chemical Biology.
2016;12(11):902-904. doi:10.1038/nchembio.2176
apa: Stone, L., Baym, M., Lieberman, T., Chait, R. P., Clardy, J., & Kishony,
R. (2016). Compounds that select against the tetracycline-resistance efflux pump.
Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.2176
chicago: Stone, Laura, Michael Baym, Tami Lieberman, Remy P Chait, Jon Clardy, and
Roy Kishony. “Compounds That Select against the Tetracycline-Resistance Efflux
Pump.” Nature Chemical Biology. Nature Publishing Group, 2016. https://doi.org/10.1038/nchembio.2176.
ieee: L. Stone, M. Baym, T. Lieberman, R. P. Chait, J. Clardy, and R. Kishony, “Compounds
that select against the tetracycline-resistance efflux pump,” Nature Chemical
Biology, vol. 12, no. 11. Nature Publishing Group, pp. 902–904, 2016.
ista: Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. 2016. Compounds
that select against the tetracycline-resistance efflux pump. Nature Chemical Biology.
12(11), 902–904.
mla: Stone, Laura, et al. “Compounds That Select against the Tetracycline-Resistance
Efflux Pump.” Nature Chemical Biology, vol. 12, no. 11, Nature Publishing
Group, 2016, pp. 902–04, doi:10.1038/nchembio.2176.
short: L. Stone, M. Baym, T. Lieberman, R.P. Chait, J. Clardy, R. Kishony, Nature
Chemical Biology 12 (2016) 902–904.
date_created: 2018-12-11T11:51:10Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2021-01-12T06:49:39Z
day: '01'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1038/nchembio.2176
intvolume: ' 12'
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069154/
month: '11'
oa: 1
oa_version: Preprint
page: 902 - 904
publication: Nature Chemical Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '6026'
quality_controlled: '1'
scopus_import: 1
status: public
title: Compounds that select against the tetracycline-resistance efflux pump
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2016'
...