---
_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
license: https://creativecommons.org/licenses/by/4.0/
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: '5584'
abstract:
- lang: eng
text: "This package contains data for the publication \"Nonlinear decoding of a
complex movie from the mammalian retina\" by Deny S. et al, PLOS Comput Biol (2018).
\r\n\r\nThe data consists of\r\n(i) 91 spike sorted, isolated rat retinal ganglion
cells that pass stability and quality criteria, recorded on the multi-electrode
array, in response to the presentation of the complex movie with many randomly
moving dark discs. The responses are represented as 648000 x 91 binary matrix,
where the first index indicates the timebin of duration 12.5 ms, and the second
index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike
in the particular time bin.\r\n(ii) README file and a graphical illustration of
the structure of the experiment, specifying how the 648000 timebins are split
into epochs where 1, 2, 4, or 10 discs were displayed, and which stimulus segments
are exact repeats or unique ball trajectories.\r\n(iii) a 648000 x 400 matrix
of luminance traces for each of the 20 x 20 positions (\"sites\") in the movie
frame, with time that is locked to the recorded raster. The luminance traces are
produced as described in the manuscript by filtering the raw disc movie with a
small gaussian spatial kernel. "
article_processing_charge: No
author:
- first_name: Stephane
full_name: Deny, Stephane
last_name: Deny
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Vicente
full_name: Botella-Soler, Vicente
last_name: Botella-Soler
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding
of a complex movie from the mammalian retina. 2018. doi:10.15479/AT:ISTA:98
apa: Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., & Tkačik, G. (2018).
Nonlinear decoding of a complex movie from the mammalian retina. Institute of
Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:98
chicago: Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius,
and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:98.
ieee: S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear
decoding of a complex movie from the mammalian retina.” Institute of Science and
Technology Austria, 2018.
ista: Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. 2018. Nonlinear decoding
of a complex movie from the mammalian retina, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:98.
mla: Deny, Stephane, et al. Nonlinear Decoding of a Complex Movie from the Mammalian
Retina. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:98.
short: S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).
datarep_id: '98'
date_created: 2018-12-12T12:31:39Z
date_published: 2018-03-29T00:00:00Z
date_updated: 2024-02-21T13:45:26Z
day: '29'
ddc:
- '570'
department:
- _id: ChLa
- _id: GaTk
doi: 10.15479/AT:ISTA:98
file:
- access_level: open_access
checksum: 6808748837b9afbbbabc2a356ca2b88a
content_type: application/octet-stream
creator: system
date_created: 2018-12-12T13:02:24Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5590'
file_name: IST-2018-98-v1+1_BBalls_area2_tile2_20x20.mat
file_size: 1142543971
relation: main_file
- access_level: open_access
checksum: d6d6cd07743038fe3a12352983fcf9dd
content_type: application/pdf
creator: system
date_created: 2018-12-12T13:02:25Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5591'
file_name: IST-2018-98-v1+2_ExperimentStructure.pdf
file_size: 702336
relation: main_file
- access_level: open_access
checksum: 0c9cfb4dab35bb3dc25a04395600b1c8
content_type: application/octet-stream
creator: system
date_created: 2018-12-12T13:02:26Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5592'
file_name: IST-2018-98-v1+3_GoodLocations_area2_20x20.mat
file_size: 432
relation: main_file
- access_level: open_access
checksum: 2a83b011012e21e934b4596285b1a183
content_type: text/plain
creator: system
date_created: 2018-12-12T13:02:26Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5593'
file_name: IST-2018-98-v1+4_README.txt
file_size: 986
relation: main_file
file_date_updated: 2020-07-14T12:47:07Z
has_accepted_license: '1'
keyword:
- retina
- decoding
- regression
- neural networks
- complex stimulus
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '292'
relation: used_in_publication
status: public
status: public
title: Nonlinear decoding of a complex movie from the mammalian retina
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: '2018'
...
---
_id: '5587'
abstract:
- lang: eng
text: "Supporting material to the article \r\nSTATISTICAL MECHANICS FOR METABOLIC
NETWORKS IN STEADY-STATE GROWTH\r\n\r\nboundscoli.dat\r\nFlux Bounds of the E.
coli catabolic core model iAF1260 in a glucose limited minimal medium. \r\n\r\npolcoli.dat\r\nMatrix
enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose
limited minimal medium, \r\nobtained from the soichiometric matrix by standard
linear algebra (reduced row echelon form).\r\n\r\nellis.dat\r\nApproximate Lowner-John
ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in
a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\npoint0.dat\r\nCenter
of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli
catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with
the Lovasz method.\r\n\r\nlovasz.cpp \r\nThis c++ code file receives in input
the polytope of the feasible steady states of a metabolic network, \r\n(matrix
and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding
the polytope\r\nwith the Lovasz method \r\nNB inputs are referred by defaults
to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we
refer to PLoS ONE 10.4 e0122670 (2015).\r\n\r\nsampleHRnew.cpp \r\nThis c++
code file receives in input the polytope of the feasible steady states of a metabolic
network, \r\n(matrix and bounds), the ellipsoid rounding the polytope, a point
inside and \r\nit gives in output a max entropy sampling at fixed average growth
rate \r\nof the steady states by performing an Hit-and-Run Monte Carlo Markov
chain.\r\nNB inputs are referred by defaults to the catabolic core of the E.Coli
network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015)."
article_processing_charge: No
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC
NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:10.15479/AT:ISTA:62
apa: De Martino, D., & Tkačik, G. (2018). Supporting materials “STATISTICAL
MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:62
chicago: De Martino, Daniele, and Gašper Tkačik. “Supporting Materials ‘STATISTICAL
MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science
and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:62.
ieee: D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS
FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology
Austria, 2018.
ista: De Martino D, Tkačik G. 2018. Supporting materials ‘STATISTICAL MECHANICS
FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:62.
mla: De Martino, Daniele, and Gašper Tkačik. Supporting Materials “STATISTICAL
MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science
and Technology Austria, 2018, doi:10.15479/AT:ISTA:62.
short: D. De Martino, G. Tkačik, (2018).
datarep_id: '111'
date_created: 2018-12-12T12:31:41Z
date_published: 2018-09-21T00:00:00Z
date_updated: 2024-02-21T13:45:39Z
day: '21'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.15479/AT:ISTA:62
ec_funded: 1
file:
- access_level: open_access
checksum: 97992e3e8cf8544ec985a48971708726
content_type: application/zip
creator: system
date_created: 2018-12-12T13:05:13Z
date_updated: 2020-07-14T12:47:08Z
file_id: '5641'
file_name: IST-2018-111-v1+1_CODES.zip
file_size: 14376
relation: main_file
file_date_updated: 2020-07-14T12:47:08Z
has_accepted_license: '1'
keyword:
- metabolic networks
- e.coli core
- maximum entropy
- monte carlo markov chain sampling
- ellipsoidal rounding
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '161'
relation: research_paper
status: public
status: public
title: Supporting materials "STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE
GROWTH"
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: '2018'
...
---
_id: '5585'
abstract:
- lang: eng
text: Mean repression values and standard error of the mean are given for all operator
mutant libraries.
article_processing_charge: No
author:
- first_name: Claudia
full_name: Igler, Claudia
id: 46613666-F248-11E8-B48F-1D18A9856A87
last_name: Igler
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary
potential of transcription factors for gene regulatory rewiring. 2018. doi:10.15479/AT:ISTA:108
apa: Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018).
Data for the paper Evolutionary potential of transcription factors for gene regulatory
rewiring. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:108
chicago: Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin
C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for
Gene Regulatory Rewiring.” Institute of Science and Technology Austria, 2018.
https://doi.org/10.15479/AT:ISTA:108.
ieee: C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Data for
the paper Evolutionary potential of transcription factors for gene regulatory
rewiring.” Institute of Science and Technology Austria, 2018.
ista: Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Data for the paper
Evolutionary potential of transcription factors for gene regulatory rewiring,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:108.
mla: Igler, Claudia, et al. Data for the Paper Evolutionary Potential of Transcription
Factors for Gene Regulatory Rewiring. Institute of Science and Technology
Austria, 2018, doi:10.15479/AT:ISTA:108.
short: C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).
datarep_id: '108'
date_created: 2018-12-12T12:31:40Z
date_published: 2018-07-20T00:00:00Z
date_updated: 2024-03-28T23:30:49Z
day: '20'
ddc:
- '576'
department:
- _id: CaGu
- _id: GaTk
doi: 10.15479/AT:ISTA:108
ec_funded: 1
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file_name: IST-2018-108-v1+1_data_figures.xlsx
file_size: 16507
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month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
- _id: 251EE76E-B435-11E9-9278-68D0E5697425
grant_number: '24573'
name: Design principles underlying genetic switch architecture (DOC Fellowship)
publisher: Institute of Science and Technology Austria
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relation: research_paper
status: public
status: public
title: Data for the paper Evolutionary potential of transcription factors for gene
regulatory rewiring
tmp:
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year: '2018'
...
---
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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:
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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
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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
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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'
...