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Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level
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Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli
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Predicting bacterial promoter function and evolution from random sequences
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The physiology and genetics of bacterial responses to antibiotic combinations
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Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells
G. Glover, M. Voliotis, U. apiska, B.M. Invergo, D. Soanes, P. O’Neill, K. Moore, N. Nikolic, P. Petrov, D.S. Milner, S. Roy, K. Heesom, T.A. Richards, K. Tsaneva-Atanasova, S. Pagliara, Communications Biology 5 (2022).

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Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose
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Sequential and switchable patterning for studying cellular processes under spatiotemporal control
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High potency of sequential therapy with only beta-lactam antibiotics
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Pathogenic Escherichia coli hijack the host immune response
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Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to C
K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, BioRxiv (n.d.).

Design and application of light-regulated receptor tyrosine kinases
S. Kainrath, H.L. Janovjak, in:, D. Niopek (Ed.), Photoswitching Proteins, Springer Nature, 2020, pp. 233–246.

Gene regulation across scales – how biophysical constraints shape evolution
R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020.

Normative models of enhancer function
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The relation between crosstalk and gene regulation form revisited
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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.

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.

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.

A modular degron library for synthetic circuits in mammalian cells
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Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision
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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).

Supporting text and results
J. Ruess, M. Pleska, C.C. Guet, G. Tkadik, (2019).

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.

Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system
N. Nikolic, Current Genetics 65 (2019) 133–138.

Harmonic dynamics of the Abelian sandpile
M. Lang, M. Shkolnikov, Proceedings of the National Academy of Sciences 116 (2019) 2821–2830.

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.

Fabrication and operation of microfluidic hanging drop networks
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How to escape local optima in black box optimisation when non elitism outperforms elitism
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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.

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).

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).

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.

Optical functionalization of human class A orphan G-protein-coupled receptors
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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.

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.

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).

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.

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.

Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen
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Regulatory network structure determines patterns of intermolecular epistasis
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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).

MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations
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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).

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).

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).

Mathematical model
N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).

Modelling and simulation details
M. Lukacisinova, S. Novak, T. Paixao, (2017).

Extensions of the model
M. Lukacisinova, S. Novak, T. Paixao, (2017).

Supplementary methods
N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).

Heuristic prediction for multiple stresses
M. Lukacisinova, S. Novak, T. Paixao, (2017).

Resistance frequencies for different combination strategies
M. Lukacisinova, S. Novak, T. Paixao, (2017).

Source data for figures and tables
N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).

Effects of mutations in phage restriction sites during escape from restriction–modification
M. Pleska, C.C. Guet, Biology Letters 13 (2017).

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.

Model checking the evolution of gene regulatory networks
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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.

Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis
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On the mechanistic nature of epistasis in a canonical cis-regulatory element
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Zeros of nonlinear systems with input invariances
M. Lang, E. Sontag, Automatica 81C (2017) 46–55.

Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity
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Green-light-induced inactivation of receptor signaling using cobalamin-binding domains
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Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection
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Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes
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An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate
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An orthogonal permease–inducer–repressor feedback loop shows bistability
R. Gnügge, L. Dharmarajan, M. Lang, J. Stelling, ACS Synthetic Biology 5 (2016) 1098–1107.

Modular parameter identification of biomolecular networks
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Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency
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Compounds that select against the tetracycline-resistance efflux pump
L. Stone, M. Baym, T. Lieberman, R.P. Chait, J. Clardy, R. Kishony, Nature Chemical Biology 12 (2016) 902–904.

Scale-invariant systems realize nonlinear differential operators
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Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments
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Spatiotemporal microbial evolution on antibiotic landscapes
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When non-elitism outperforms elitism for crossing fitness valleys
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The effect of gene interactions on the long-term response to selection
T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427.

Epistatic interactions in the arabinose cis-regulatory element
M. Lagator, C. Igler, A. Moreno, C.C. Guet, J.P. Bollback, Molecular Biology and Evolution 33 (2016) 761–769.

Efficient reduction of kappa models by static inspection of the rule-set
A. Beica, C.C. Guet, T. Petrov, in:, Springer, 2016, pp. 173–191.

Genetic manipulation of glycogen allocation affects replicative lifespan in E coli
A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann, PLoS Genetics 12 (2016).

Quantification of the growth rate reduction as a consequence of age-specific mortality
A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann, (2016).

Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria
S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, Molecular Biology and Evolution 33 (2016) 770–782.

Linear distances between Markov chains
P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.

Faster statistical model checking for unbounded temporal properties
P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Springer, 2016, pp. 112–129.

Bacterial autoimmunity due to a restriction-modification system
M. Pleska, L. Qian, R. Okura, T. Bergmiller, Y. Wakamoto, E. Kussell, C.C. Guet, Current Biology 26 (2016) 404–409.

Intrinsic limits to gene regulation by global crosstalk
T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkadik, Nature Communications 7 (2016).

First steps towards a runtime comparison of natural and artificial evolution
T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–1462.

Toward a unifying framework for evolutionary processes
T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüf, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova,  Journal of Theoretical Biology 383 (2015) 28–43.

Optimal Kullback-Leibler aggregation via information bottleneck
B. Geiger, T. Petrov, G. Kubin, H. Koeppl, IEEE Transactions on Automatic Control 60 (2015) 1010–1022.

Other fitness models for comparison & for interacting TFBSs
M. Tugrul, T. Paixao, N.H. Barton, G. Tkadik, (2015).

Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria
S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, (2015).

Dynamics of transcription factor binding site evolution
M. Tugrul, T. Paixao, N.H. Barton, G. Tkadik, PLoS Genetics 11 (2015).

Model checking gene regulatory networks
M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, 9035 (2015) 469–483.

Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA
A. Grabowska, E. Wywia, S. Dunin Horkawicz, A. asica, M. Wösten, A.A. Nagy-Staron, R. Godlewska, K. Bocian Ostrzycka, K. Piekowska, P. aniewski, J. Bujnicki, J. Van Putten, E. Jagusztyn Krynicka, PLoS One 9 (2014).

Markov chain aggregation and its applications to combinatorial reaction networks
A. Ganguly, T. Petrov, H. Koeppl, Journal of Mathematical Biology 69 (2014) 767–797.

Role of sex and migration in adaptation to sink environments
M. Lagator, A. Morgan, P. Neve, N. Colegrave, Evolution 68 (2014) 2296–2305.

Data from: Role of sex and migration in adaptation to sink environments
M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014).

Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses
M. Lagator, N. Colegrave, P. Neve, Proceedings of the Royal Society of London Series B Biological Sciences 281 (2014).

Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses
M. Lagator, N. Colegrave, P. Neve, (2014).

Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes
R. Dhar, T. Bergmiller, A. Wagner, Evolution 68 (2014) 1775–1791.

Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes
R. Dhar, T. Bergmiller, A. Wagner, (2014).

Patterns of hippocampal tau pathology differentiate neurodegenerative dementias
I. Milenkovi, T. Petrov, G. Kovács, Dementia and Geriatric Cognitive Disorders 38 (2014) 375–388.

Can quantitative and population genetics help us understand evolutionary computation?
N.H. Barton, T. Paixao, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–1580.

Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila
H. Long, T. Paixao, R. Azevedo, R. Zufall, Genetics 195 (2013) 527–540.

A variance decomposition approach to the analysis of genetic algorithms
T. Paixao, N.H. Barton, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–852.

Dynamic persistence of antibiotic-stressed mycobacteria
Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler, J. Mckinney, Science 339 (2013) 91–95.

Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection
D. Refardt, T. Bergmiller, R. Kümmerli, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013).

Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection
D. Refardt, T. Bergmiller, R. Kümmerli, (2013).

The propagation approach for computing biochemical reaction networks
T.A. Henzinger, M. Mateescu, IEEE ACM Transactions on Computational Biology and Bioinformatics 10 (2012) 310–322.

Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions
N. Hadizadeh Yazdi, C.C. Guet, R. Johnson, J. Marko, Molecular Microbiology 86 (2012) 1318–1333.

Patterns of evolutionary conservation of essential genes correlate with their compensability
T. Bergmiller, M. Ackermann, O. Silander, PLoS Genetics 8 (2012).

Delayed continuous time Markov chains for genetic regulatory circuits
C.C. Guet, A. Gupta, T.A. Henzinger, M. Mateescu, A. Sezgin, in:, Springer, 2012, pp. 294–309.

Noise underlies switching behavior of the bacterial flagellum
H. Park, P. Oikonomou, C.C. Guet, P. Cluzel, Biophysical Journal 101 (2011) 2336–2340.

Lumpability abstractions of rule-based systems
J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, in:, Open Publishing Association, 2010, pp. 142–161.

SABRE: A tool for the stochastic analysis of biochemical reaction networks
F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2010, pp. 193–194.

Fast adaptive uniformization of the chemical master equation
F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2009, pp. 118–127.