Normative models of enhancer function
R. Grah, B. Zoller, G. Tkadik, BioRxiv (2020).
LibreCat: https://research-explorer.ista.ac.at/record/7675
DOI: 10.1101/2020.04.08.029405

The relation between crosstalk and gene regulation form revisited
R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020).
LibreCat: https://research-explorer.ista.ac.at/record/7569
DOI: 10.1371/journal.pcbi.1007642
WoS: 000526725200019

Sequences of gene regulatory network permutations for the article "Local genetic context shapes the function of a gene regulatory network"
A.A. Nagy-Staron, (2020).
LibreCat: https://research-explorer.ista.ac.at/record/8951
DOI: 10.15479/AT:ISTA:8951

Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation
R. Grah, (2020).
LibreCat: https://research-explorer.ista.ac.at/record/7383
DOI: 10.15479/AT:ISTA:7383

Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals
S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals, Institute of Science and Technology Austria, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/7680
DOI: 10.15479/AT:ISTA:7680

Gene amplification as a form of population-level gene expression regulation
I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkadik, C.C. Guet, Nature Ecology &; Evolution 4 (2020) 612–625.
LibreCat: https://research-explorer.ista.ac.at/record/7652
DOI: 10.1038/s41559-020-1132-7
WoS: 000519008300005

The evolution of gene expression by copy number and point mutations
I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations, Institute of Science and Technology Austria, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/8653
DOI: 10.15479/AT:ISTA:8653

A modular degron library for synthetic circuits in mammalian cells
H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, M. Fussenegger, Nature Communications 10 (2019).
LibreCat: https://research-explorer.ista.ac.at/record/6465
DOI: 10.1038/s41467-019-09974-5
WoS: 000466338600006

Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision
C. Igler, S.T. Abedon, Frontiers in Microbiology 10 (2019).
LibreCat: https://research-explorer.ista.ac.at/record/6717
DOI: 10.3389/fmicb.2019.01171
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Molecular noise of innate immunity shapes bacteria-phage ecologies
J. Ruess, M. Pleska, C.C. Guet, G. Tkadik, PLoS Computational Biology 15 (2019).
LibreCat: https://research-explorer.ista.ac.at/record/6784
DOI: 10.1371/journal.pcbi.1007168
WoS: 000481577700032

Supporting text and results
J. Ruess, M. Pleska, C.C. Guet, G. Tkadik, (2019).
LibreCat: https://research-explorer.ista.ac.at/record/9786
DOI: 10.1371/journal.pcbi.1007168.s001

Transient memory in gene regulation
C.C. Guet, T.A. Henzinger, C. Igler, T. Petrov, A. Sezgin, in:, 17th International Conference on Computational Methods in Systems Biology, Springer Nature, 2019, pp. 155–187.
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DOI: 10.1007/978-3-030-31304-3_9
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Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system
N. Nikolic, Current Genetics 65 (2019) 133–138.
LibreCat: https://research-explorer.ista.ac.at/record/138
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Harmonic dynamics of the Abelian sandpile
M. Lang, M. Shkolnikov, Proceedings of the National Academy of Sciences 116 (2019) 2821–2830.
LibreCat: https://research-explorer.ista.ac.at/record/196
DOI: 10.1073/pnas.1812015116
WoS: 000459074400013
PMID:  30728300
arXiv: 1806.10823

Data for the paper "Gene amplification as a form of population-level gene expression regulation"
I. Tomanek, (2019).
LibreCat: https://research-explorer.ista.ac.at/record/7016
DOI: 10.15479/AT:ISTA:7016

On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation
C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019.
LibreCat: https://research-explorer.ista.ac.at/record/6371
DOI: 10.15479/AT:ISTA:6371

Fabrication and operation of microfluidic hanging drop networks
P. Misun, A. Birchler, M. Lang, A. Hierlemann, O. Frey, Methods in Molecular Biology 1771 (2018) 183–202.
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DOI: 10.1007/978-1-4939-7792-5_15

How to escape local optima in black box optimisation when non elitism outperforms elitism
P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 80 (2018) 1604–1633.
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Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains
K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018) 40–52.
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Leaky resistance and the conditions for the existence of lytic bacteriophage
W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).
LibreCat: https://research-explorer.ista.ac.at/record/82
DOI: 10.1371/journal.pbio.2005971
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Numerical data used in figures
W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, (2018).
LibreCat: https://research-explorer.ista.ac.at/record/9810
DOI: 10.1371/journal.pbio.2005971.s008

Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity
M. Pleska, M. Lang, D. Refardt, B. Levin, C.C. Guet, Nature Ecology and Evolution 2 (2018) 359–366.
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DOI: 10.1038/s41559-017-0424-z
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Optical functionalization of human class A orphan G-protein-coupled receptors
M. Morri, I. Sanchez-Romero, A.-M. Tichy, S. Kainrath, E.J. Gerrard, P. Hirschfeld, J. Schwarz, H.L. Janovjak, Nature Communications 9 (2018).
LibreCat: https://research-explorer.ista.ac.at/record/5984
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Nonoptimal gene expression creates latent potential for antibiotic resistance
A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.
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DOI: 10.1093/molbev/msy163
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PMID: 30169679

Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations
N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, I. Moll, Nucleic Acids Research 46 (2018) 2918–2931.
LibreCat: https://research-explorer.ista.ac.at/record/438
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Time-lapse microscopy data
T. Bergmiller, N. Nikolic, (2018).
LibreCat: https://research-explorer.ista.ac.at/record/5569
DOI: 10.15479/AT:ISTA:74

Statistical mechanics for metabolic networks during steady state growth
D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkadik, Nature Communications 9 (2018).
LibreCat: https://research-explorer.ista.ac.at/record/161
DOI: 10.1038/s41467-018-05417-9
WoS: 000440149300021

The influence of sequence context on the evolution of bacterial gene expression
M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial Gene Expression, Institute of Science and Technology Austria, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/26
DOI: 10.15479/AT:ISTA:th1059

Evolutionary potential of transcription factors for gene regulatory rewiring
C. Igler, M. Lagator, G. Tkadik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643.
LibreCat: https://research-explorer.ista.ac.at/record/67
DOI: 10.1038/s41559-018-0651-y
WoS: 000447947600021

Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring
C. Igler, M. Lagator, G. Tkadik, J.P. Bollback, C.C. Guet, (2018).
LibreCat: https://research-explorer.ista.ac.at/record/5585
DOI: 10.15479/AT:ISTA:108

Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen
S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie 129 (2017) 4679–4682.
LibreCat: https://research-explorer.ista.ac.at/record/538
DOI: 10.1002/ange.201611998

Regulatory network structure determines patterns of intermolecular epistasis
M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).
LibreCat: https://research-explorer.ista.ac.at/record/570
DOI: 10.7554/eLife.28921

Shaping bacterial population behavior through computer interfaced control of individual cells
R.P. Chait, J. Ruess, T. Bergmiller, G. Tkadik, C.C. Guet, Nature Communications 8 (2017).
LibreCat: https://research-explorer.ista.ac.at/record/613
DOI: 10.1038/s41467-017-01683-1

MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations
N. Nikolic, Z. Didara, I. Moll, PeerJ 2017 (2017).
LibreCat: https://research-explorer.ista.ac.at/record/624
DOI: 10.7717/peerj.3830

Bacterial flagella grow through an injection diffusion mechanism
T. Renault, A. Abraham, T. Bergmiller, G. Paradis, S. Rainville, E. Charpentier, C.C. Guet, Y. Tu, K. Namba, J. Keener, T. Minamino, M. Erhardt, ELife 6 (2017).
LibreCat: https://research-explorer.ista.ac.at/record/655
DOI: 10.7554/eLife.23136

Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations
N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, PLoS Genetics 13 (2017).
LibreCat: https://research-explorer.ista.ac.at/record/541
DOI: 10.1371/journal.pgen.1007122

Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification
M. Pleska, C.C. Guet, (2017).
LibreCat: https://research-explorer.ista.ac.at/record/9847
DOI: 10.6084/m9.figshare.5633917.v1

Mathematical model
N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).
LibreCat: https://research-explorer.ista.ac.at/record/9845
DOI: 10.1371/journal.pgen.1007122.s017

Modelling and simulation details
M. Lukacisinova, S. Novak, T. Paixao, (2017).
LibreCat: https://research-explorer.ista.ac.at/record/9849
DOI: 10.1371/journal.pcbi.1005609.s001

Extensions of the model
M. Lukacisinova, S. Novak, T. Paixao, (2017).
LibreCat: https://research-explorer.ista.ac.at/record/9850
DOI: 10.1371/journal.pcbi.1005609.s002

Supplementary methods
N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).
LibreCat: https://research-explorer.ista.ac.at/record/9846
DOI: 10.1371/journal.pgen.1007122.s016

Heuristic prediction for multiple stresses
M. Lukacisinova, S. Novak, T. Paixao, (2017).
LibreCat: https://research-explorer.ista.ac.at/record/9851
DOI: 10.1371/journal.pcbi.1005609.s003

Resistance frequencies for different combination strategies
M. Lukacisinova, S. Novak, T. Paixao, (2017).
LibreCat: https://research-explorer.ista.ac.at/record/9852
DOI: 10.1371/journal.pcbi.1005609.s004

Source data for figures and tables
N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).
LibreCat: https://research-explorer.ista.ac.at/record/9844
DOI: 10.1371/journal.pgen.1007122.s018

Effects of mutations in phage restriction sites during escape from restriction–modification
M. Pleska, C.C. Guet, Biology Letters 13 (2017).
LibreCat: https://research-explorer.ista.ac.at/record/561
DOI: 10.1098/rsbl.2017.0646
PMID: 29237814

Biology of restriction-modification systems at the single-cell and population level
M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell and Population Level, Institute of Science and Technology Austria, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/202
DOI: 10.15479/AT:ISTA:th_916

Model checking the evolution of gene regulatory networks
M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta Informatica 54 (2017) 765–787.
LibreCat: https://research-explorer.ista.ac.at/record/1351
DOI: 10.1007/s00236-016-0278-x
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Towards a runtime comparison of natural and artificial evolution
T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713.
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Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis
C. Fang, A.A. Nagy-Staron, M. Grafe, R. Heermann, K. Jung, S. Gebhard, T. Mascher, Molecular Microbiology 104 (2017) 16–31.
LibreCat: https://research-explorer.ista.ac.at/record/1084
DOI: 10.1111/mmi.13597
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On the mechanistic nature of epistasis in a canonical cis-regulatory element
M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).
LibreCat: https://research-explorer.ista.ac.at/record/954
DOI: 10.7554/eLife.25192
WoS: 000404024800001