---
_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:<a href="https://doi.org/10.15479/AT:ISTA:8097">10.15479/AT:ISTA:8097</a>
  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. <a href="https://doi.org/10.15479/AT:ISTA:8097">https://doi.org/10.15479/AT:ISTA:8097</a>
  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. <a href="https://doi.org/10.15479/AT:ISTA:8097">https://doi.org/10.15479/AT:ISTA:8097</a>.
  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, <a href="https://doi.org/10.15479/AT:ISTA:8097">10.15479/AT:ISTA:8097</a>.
  mla: Kavcic, Bor. <i>Analysis Scripts and Research Data for the Paper “Mechanisms
    of Drug Interactions between Translation-Inhibiting Antibiotics.”</i> Institute
    of Science and Technology Austria, 2020, doi:<a href="https://doi.org/10.15479/AT:ISTA:8097">10.15479/AT:ISTA:8097</a>.
  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: '8653'
abstract:
- lang: eng
  text: "Mutations are the raw material of evolution and come in many different flavors.
    Point mutations change a single letter in the DNA sequence, while copy number
    mutations like duplications or deletions add or remove many letters of the DNA
    sequence simultaneously.  Each type of mutation exhibits specific properties like
    its rate of formation and reversal. \r\nGene expression is a fundamental phenotype
    that can be altered by both, point and copy number mutations. The following thesis
    is concerned with the dynamics of gene expression evolution and how it is affected
    by the properties exhibited by point and copy number mutations. Specifically,
    we are considering i) copy number mutations during adaptation to fluctuating environments
    and ii) the interaction of copy number and point mutations during adaptation to
    constant environments.  "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Isabella
  full_name: Tomanek, Isabella
  id: 3981F020-F248-11E8-B48F-1D18A9856A87
  last_name: Tomanek
  orcid: 0000-0001-6197-363X
citation:
  ama: Tomanek I. The evolution of gene expression by copy number and point mutations.
    2020. doi:<a href="https://doi.org/10.15479/AT:ISTA:8653">10.15479/AT:ISTA:8653</a>
  apa: Tomanek, I. (2020). <i>The evolution of gene expression by copy number and
    point mutations</i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:8653">https://doi.org/10.15479/AT:ISTA:8653</a>
  chicago: Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and
    Point Mutations.” Institute of Science and Technology Austria, 2020. <a href="https://doi.org/10.15479/AT:ISTA:8653">https://doi.org/10.15479/AT:ISTA:8653</a>.
  ieee: I. Tomanek, “The evolution of gene expression by copy number and point mutations,”
    Institute of Science and Technology Austria, 2020.
  ista: Tomanek I. 2020. The evolution of gene expression by copy number and point
    mutations. Institute of Science and Technology Austria.
  mla: Tomanek, Isabella. <i>The Evolution of Gene Expression by Copy Number and Point
    Mutations</i>. Institute of Science and Technology Austria, 2020, doi:<a href="https://doi.org/10.15479/AT:ISTA:8653">10.15479/AT:ISTA:8653</a>.
  short: I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations,
    Institute of Science and Technology Austria, 2020.
date_created: 2020-10-13T13:02:33Z
date_published: 2020-10-13T00:00:00Z
date_updated: 2023-09-07T13:22:42Z
day: '13'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:8653
file:
- access_level: closed
  checksum: c01d9f59794b4b70528f37637c17ad02
  content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
  creator: itomanek
  date_created: 2020-10-16T12:14:21Z
  date_updated: 2021-10-20T22:30:03Z
  embargo_to: open_access
  file_id: '8666'
  file_name: Thesis_ITomanek_final_201016.docx
  file_size: 25131884
  relation: source_file
- access_level: open_access
  checksum: f8edbc3b0f81a780e13ca1e561d42d8b
  content_type: application/pdf
  creator: itomanek
  date_created: 2020-10-16T12:14:21Z
  date_updated: 2021-10-20T22:30:03Z
  embargo: 2021-10-19
  file_id: '8667'
  file_name: Thesis_ITomanek_final_201016.pdf
  file_size: 15405675
  relation: main_file
file_date_updated: 2021-10-20T22:30:03Z
has_accepted_license: '1'
keyword:
- duplication
- amplification
- promoter
- CNV
- AMGET
- experimental evolution
- Escherichia coli
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '117'
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '7652'
    relation: research_data
    status: public
status: public
supervisor:
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
title: The evolution of gene expression by copy number and point mutations
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
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:<a href="https://doi.org/10.15479/AT:ISTA:8930">10.15479/AT:ISTA:8930</a>
  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. <a href="https://doi.org/10.15479/AT:ISTA:8930">https://doi.org/10.15479/AT:ISTA:8930</a>
  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. <a href="https://doi.org/10.15479/AT:ISTA:8930">https://doi.org/10.15479/AT:ISTA:8930</a>.
  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, <a href="https://doi.org/10.15479/AT:ISTA:8930">10.15479/AT:ISTA:8930</a>.
  mla: Kavcic, Bor. <i>Analysis Scripts and Research Data for the Paper “Minimal Biophysical
    Model of Combined Antibiotic Action.”</i> Institute of Science and Technology
    Austria, 2020, doi:<a href="https://doi.org/10.15479/AT:ISTA:8930">10.15479/AT:ISTA:8930</a>.
  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: '8951'
abstract:
- lang: eng
  text: Gene expression levels are influenced by multiple coexisting molecular mechanisms.
    Some of these interactions, such as those of transcription factors and promoters
    have been studied extensively. However, predicting phenotypes of gene regulatory
    networks remains a major challenge. Here, we use a well-defined synthetic gene
    regulatory network to study how network phenotypes depend on local genetic context,
    i.e. the genetic neighborhood of a transcription factor and its relative position.
    We show that one gene regulatory network with fixed topology can display not only
    quantitatively but also qualitatively different phenotypes, depending solely on
    the local genetic context of its components. Our results demonstrate that changes
    in local genetic context can place a single transcriptional unit within two separate
    regulons without the need for complex regulatory sequences. We propose that relative
    order of individual transcriptional units, with its potential for combinatorial
    complexity, plays an important role in shaping phenotypes of gene regulatory networks.
article_processing_charge: No
author:
- first_name: Anna A
  full_name: Nagy-Staron, Anna A
  id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87
  last_name: Nagy-Staron
  orcid: 0000-0002-1391-8377
citation:
  ama: Nagy-Staron AA. Sequences of gene regulatory network permutations for the article
    “Local genetic context shapes the function of a gene regulatory network.” 2020.
    doi:<a href="https://doi.org/10.15479/AT:ISTA:8951">10.15479/AT:ISTA:8951</a>
  apa: Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations
    for the article “Local genetic context shapes the function of a gene regulatory
    network.” Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:8951">https://doi.org/10.15479/AT:ISTA:8951</a>
  chicago: Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations
    for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory
    Network.’” Institute of Science and Technology Austria, 2020. <a href="https://doi.org/10.15479/AT:ISTA:8951">https://doi.org/10.15479/AT:ISTA:8951</a>.
  ieee: A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for
    the article ‘Local genetic context shapes the function of a gene regulatory network.’”
    Institute of Science and Technology Austria, 2020.
  ista: Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for
    the article ‘Local genetic context shapes the function of a gene regulatory network’,
    Institute of Science and Technology Austria, <a href="https://doi.org/10.15479/AT:ISTA:8951">10.15479/AT:ISTA:8951</a>.
  mla: Nagy-Staron, Anna A. <i>Sequences of Gene Regulatory Network Permutations for
    the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.”</i>
    Institute of Science and Technology Austria, 2020, doi:<a href="https://doi.org/10.15479/AT:ISTA:8951">10.15479/AT:ISTA:8951</a>.
  short: A.A. Nagy-Staron, (2020).
contributor:
- contributor_type: project_member
  first_name: Anna A
  id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87
  last_name: Nagy-Staron
- contributor_type: project_member
  first_name: Kathrin
  id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
  last_name: Tomasek
- contributor_type: project_member
  first_name: Caroline
  last_name: Caruso Carter
- contributor_type: project_member
  first_name: Elisabeth
  last_name: Sonnleitner
- contributor_type: project_member
  first_name: Bor
  id: 350F91D2-F248-11E8-B48F-1D18A9856A87
  last_name: Kavcic
  orcid: 0000-0001-6041-254X
- contributor_type: project_member
  first_name: Tiago
  last_name: Paixão
- contributor_type: project_manager
  first_name: Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
date_created: 2020-12-20T10:00:26Z
date_published: 2020-12-21T00:00:00Z
date_updated: 2024-02-21T12:41:57Z
day: '21'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:8951
file:
- access_level: open_access
  checksum: f57862aeee1690c7effd2b1117d40ed1
  content_type: text/plain
  creator: bkavcic
  date_created: 2020-12-20T09:52:52Z
  date_updated: 2020-12-20T09:52:52Z
  file_id: '8952'
  file_name: readme.txt
  file_size: 523
  relation: main_file
  success: 1
- access_level: open_access
  checksum: f2c6d5232ec6d551b6993991e8689e9f
  content_type: application/octet-stream
  creator: bkavcic
  date_created: 2020-12-20T22:01:44Z
  date_updated: 2020-12-20T22:01:44Z
  file_id: '8954'
  file_name: GRNs Research depository.gb
  file_size: 379228
  relation: main_file
  success: 1
file_date_updated: 2020-12-20T22:01:44Z
has_accepted_license: '1'
keyword:
- Gene regulatory networks
- Gene expression
- Escherichia coli
- Synthetic Biology
month: '12'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '9283'
    relation: used_in_publication
    status: public
status: public
title: Sequences of gene regulatory network permutations for the article "Local genetic
  context shapes the function of a gene regulatory network"
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7016'
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: Isabella
  full_name: Tomanek, Isabella
  id: 3981F020-F248-11E8-B48F-1D18A9856A87
  last_name: Tomanek
  orcid: 0000-0001-6197-363X
citation:
  ama: Tomanek I. Data for the paper “Gene amplification as a form of population-level
    gene expression regulation.” 2019. doi:<a href="https://doi.org/10.15479/AT:ISTA:7016">10.15479/AT:ISTA:7016</a>
  apa: Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level
    gene expression regulation.” Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:7016">https://doi.org/10.15479/AT:ISTA:7016</a>
  chicago: Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of
    Population-Level Gene Expression Regulation.’” Institute of Science and Technology
    Austria, 2019. <a href="https://doi.org/10.15479/AT:ISTA:7016">https://doi.org/10.15479/AT:ISTA:7016</a>.
  ieee: I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level
    gene expression regulation.’” Institute of Science and Technology Austria, 2019.
  ista: Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level
    gene expression regulation’, Institute of Science and Technology Austria, <a href="https://doi.org/10.15479/AT:ISTA:7016">10.15479/AT:ISTA:7016</a>.
  mla: Tomanek, Isabella. <i>Data for the Paper “Gene Amplification as a Form of Population-Level
    Gene Expression Regulation.”</i> Institute of Science and Technology Austria,
    2019, doi:<a href="https://doi.org/10.15479/AT:ISTA:7016">10.15479/AT:ISTA:7016</a>.
  short: I. Tomanek, (2019).
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: 2019-11-13T09:07:31Z
date_published: 2019-11-13T00:00:00Z
date_updated: 2024-02-21T12:45:25Z
day: '13'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:7016
file:
- access_level: open_access
  checksum: 72441055043eda4cbf1398a422e2c118
  content_type: application/octet-stream
  creator: itomanek
  date_created: 2019-11-13T08:52:21Z
  date_updated: 2020-07-14T12:47:47Z
  description: Illumina whole genome sequence data for Locus 1 - amplified.
  file_id: '7017'
  file_name: D8_S35_R2_001.fastq
  file_size: 2456192500
  relation: main_file
  title: Locus1_amplified
- access_level: open_access
  checksum: a4ac50bf655d9c751f0305ade5c2ee16
  content_type: application/octet-stream
  creator: itomanek
  date_created: 2019-11-13T08:52:59Z
  date_updated: 2020-07-14T12:47:47Z
  description: Illumina whole genome sequence data for Locus 1 - ancestral.
  file_id: '7018'
  file_name: IT028_S11_R2_001.fastq
  file_size: 2833452234
  relation: main_file
  title: Locus1_ancestral
- access_level: open_access
  checksum: 5b227708ff478ca06e3f0448a4efdc2f
  content_type: application/octet-stream
  creator: itomanek
  date_created: 2019-11-13T08:54:10Z
  date_updated: 2020-07-14T12:47:47Z
  description: Illumina whole genome sequence data for Locus 1 - amplified, after
    DOG-selection.
  file_id: '7019'
  file_name: D8-DOG1_S47_R2_001.fastq
  file_size: 2878017264
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  title: microfluidics data
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has_accepted_license: '1'
keyword:
- Escherichia coli
- gene amplification
- galactose
- DOG
- experimental evolution
- Illumina sequence data
- FACS data
- microfluidics data
month: '11'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
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status: public
title: Data for the paper "Gene amplification as a form of population-level gene expression
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type: research_data
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---
_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:<a
    href="https://doi.org/10.15479/AT:ISTA:53">10.15479/AT:ISTA:53</a>
  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. <a href="https://doi.org/10.15479/AT:ISTA:53">https://doi.org/10.15479/AT:ISTA:53</a>
  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. <a href="https://doi.org/10.15479/AT:ISTA:53">https://doi.org/10.15479/AT:ISTA:53</a>.
  ieee: T. Bergmiller <i>et al.</i>, “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, <a href="https://doi.org/10.15479/AT:ISTA:53">10.15479/AT:ISTA:53</a>.
  mla: Bergmiller, Tobias, et al. <i>Biased Partitioning of the Multi-Drug Efflux
    Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity</i>. Institute of
    Science and Technology Austria, 2017, doi:<a href="https://doi.org/10.15479/AT:ISTA:53">10.15479/AT:ISTA:53</a>.
  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
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  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
license: https://creativecommons.org/publicdomain/zero/1.0/
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'
...