Friedlander T, Prizak R, Guet CC, Barton NH, Tkadik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307.
LibreCat: https://research-explorer.ista.ac.at/record/1358
DOI: 10.1038/ncomms12307

Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a runtime comparison of natural and artificial evolution. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and evolutionary computation conference, 1455–1462.
LibreCat: https://research-explorer.ista.ac.at/record/1430
DOI: 10.1145/2739480.2754758

Paixao T, Badkobeh G, Barton NH, Çörüf D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes.  Journal of Theoretical Biology. 383, 28–43.
LibreCat: https://research-explorer.ista.ac.at/record/1542
DOI: 10.1016/j.jtbi.2015.07.011

Geiger B, Petrov T, Kubin G, Koeppl H. 2015. Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. 60(4), 1010–1022.
LibreCat: https://research-explorer.ista.ac.at/record/1840
DOI: 10.1109/TAC.2014.2364971

Tugrul M, Paixao T, Barton NH, Tkadik G. 2015. Other fitness models for comparison &; for interacting TFBSs, Public Library of Science,10.1371/journal.pgen.1005639.s001 .
LibreCat: https://research-explorer.ista.ac.at/record/9712
DOI: 10.1371/journal.pgen.1005639.s001

Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2015. Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria, Dryad,10.5061/dryad.cj910 .
LibreCat: https://research-explorer.ista.ac.at/record/9719
DOI: 10.5061/dryad.cj910

Tugrul M, Paixao T, Barton NH, Tkadik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).
LibreCat: https://research-explorer.ista.ac.at/record/1666
DOI: 10.1371/journal.pgen.1005639

Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model checking gene regulatory networks. 9035, 469–483.
LibreCat: https://research-explorer.ista.ac.at/record/1835
DOI: 10.1007/978-3-662-46681-0_47

Grabowska A, Wywia E, Dunin Horkawicz S, asica A, Wösten M, Nagy-Staron AA, Godlewska R, Bocian Ostrzycka K, Piekowska K, aniewski P, Bujnicki J, Van Putten J, Jagusztyn Krynicka E. 2014. Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. 9(9), e106247.
LibreCat: https://research-explorer.ista.ac.at/record/1894
DOI: 10.1371/journal.pone.0106247

Ganguly A, Petrov T, Koeppl H. 2014. Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. 69(3), 767–797.
LibreCat: https://research-explorer.ista.ac.at/record/2056
DOI: 10.1007/s00285-013-0738-7

Lagator M, Morgan A, Neve P, Colegrave N. 2014. Role of sex and migration in adaptation to sink environments. Evolution. 68(8), 2296–2305.
LibreCat: https://research-explorer.ista.ac.at/record/2083
DOI: 10.1111/evo.12440

Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and migration in adaptation to sink environments, Dryad,10.5061/dryad.s42n1 .
LibreCat: https://research-explorer.ista.ac.at/record/9747
DOI: 10.5061/dryad.s42n1

Lagator M, Colegrave N, Neve P. 2014. Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Proceedings of the Royal Society of London Series B Biological Sciences. 281(1794), 20141679.
LibreCat: https://research-explorer.ista.ac.at/record/2036
DOI: 10.1098/rspb.2014.1679

Lagator M, Colegrave N, Neve P. 2014. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses, Dryad,10.5061/dryad.85dn7 .
LibreCat: https://research-explorer.ista.ac.at/record/9741
DOI: 10.5061/dryad.85dn7

Dhar R, Bergmiller T, Wagner A. 2014. Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution. 68(6), 1775–1791.
LibreCat: https://research-explorer.ista.ac.at/record/9931
DOI: 10.1111/evo.12373
PMID: 24495000

Dhar R, Bergmiller T, Wagner A. 2014. Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes, Dryad,10.5061/dryad.jc402 .
LibreCat: https://research-explorer.ista.ac.at/record/9932
DOI: 10.5061/dryad.jc402

Milenkovi I, Petrov T, Kovács G. 2014. Patterns of hippocampal tau pathology differentiate neurodegenerative dementias. Dementia and Geriatric Cognitive Disorders. 38(5–6), 375–388.
LibreCat: https://research-explorer.ista.ac.at/record/1913
DOI: 10.1159/000365548
PMID: 25195847

Barton NH, Paixao T. 2013. Can quantitative and population genetics help us understand evolutionary computation? Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 1573–1580.
LibreCat: https://research-explorer.ista.ac.at/record/2718
DOI: 10.1145/2463372.2463568

Long H, Paixao T, Azevedo R, Zufall R. 2013. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 195(2), 527–540.
LibreCat: https://research-explorer.ista.ac.at/record/2720
DOI: 10.1534/genetics.113.153536
PMID: 23934880

Paixao T, Barton NH. 2013. A variance decomposition approach to the analysis of genetic algorithms. Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 845–852.
LibreCat: https://research-explorer.ista.ac.at/record/2719
DOI: 10.1145/2463372.2463470

Wakamoto Y, Dhar N, Chait RP, Schneider K, Signorino Gelo F, Leibler S, Mckinney J. 2013. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 339(6115), 91–95.
LibreCat: https://research-explorer.ista.ac.at/record/499
DOI: 10.1126/science.1229858

Refardt D, Bergmiller T, Kümmerli R. 2013. Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection. Proceedings of the Royal Society of London Series B Biological Sciences. 280(1759).
LibreCat: https://research-explorer.ista.ac.at/record/2853
DOI: 10.1098/rspb.2012.3035
PMID: 23516238

Refardt D, Bergmiller T, Kümmerli R. 2013. Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection, Dryad,10.5061/dryad.b1q2n .
LibreCat: https://research-explorer.ista.ac.at/record/9751
DOI: 10.5061/dryad.b1q2n

Henzinger TA, Mateescu M. 2012. The propagation approach for computing biochemical reaction networks. IEEE ACM Transactions on Computational Biology and Bioinformatics. 10(2), 310–322.
LibreCat: https://research-explorer.ista.ac.at/record/2302
DOI: 10.1109/TCBB.2012.91
PMID: 22778152

Hadizadeh Yazdi N, Guet CC, Johnson R, Marko J. 2012. Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. Molecular Microbiology. 86(6), 1318–1333.
LibreCat: https://research-explorer.ista.ac.at/record/2943
DOI: 10.1111/mmi.12071

Bergmiller T, Ackermann M, Silander O. 2012. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 8(6), e1002803.
LibreCat: https://research-explorer.ista.ac.at/record/3130
DOI: 10.1371/journal.pgen.1002803

Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. 2012. Delayed continuous time Markov chains for genetic regulatory circuits. CAV: Computer Aided Verification, LNCS, vol. 7358, 294–309.
LibreCat: https://research-explorer.ista.ac.at/record/3136
DOI: 10.1007/978-3-642-31424-7_24

Park H, Oikonomou P, Guet CC, Cluzel P. 2011. Noise underlies switching behavior of the bacterial flagellum. Biophysical Journal. 101(10), 2336–2340.
LibreCat: https://research-explorer.ista.ac.at/record/6496
DOI: 10.1016/j.bpj.2011.09.040
PMID: 22098731

Feret J, Henzinger TA, Koeppl H, Petrov T. 2010. Lumpability abstractions of rule-based systems. MECBIC: Membrane Computing and Biologically Inspired Process Calculi, EPTCS, vol. 40, 142–161.
LibreCat: https://research-explorer.ista.ac.at/record/3719
arXiv: 1011.0496

Didier F, Henzinger TA, Mateescu M, Wolf V. 2010. SABRE: A tool for the stochastic analysis of biochemical reaction networks. QEST: Quantitative Evaluation of Systems, 193–194.
LibreCat: https://research-explorer.ista.ac.at/record/3847
DOI: 10.1109/QEST.2010.33

Didier F, Henzinger TA, Mateescu M, Wolf V. 2009. Fast adaptive uniformization of the chemical master equation. HIBI: High-Performance Computational Systems Biology vol. 4, 118–127.
LibreCat: https://research-explorer.ista.ac.at/record/3843
DOI: 10.1109/HiBi.2009.23