Tugrul M, Paixao T, Barton NH, Tkadik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639
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. Model checking gene regulatory networks. 2015;9035:469-483. doi:10.1007/978-3-662-46681-0_47
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, et al. Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0106247
LibreCat: https://research-explorer.ista.ac.at/record/1894
DOI: 10.1371/journal.pone.0106247

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

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

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

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

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

Barton NH, Paixao T. Can quantitative and population genetics help us understand evolutionary computation? In: Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation. ACM; 2013:1573-1580. doi:10.1145/2463372.2463568
LibreCat: https://research-explorer.ista.ac.at/record/2718
DOI: 10.1145/2463372.2463568

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

Paixao T, Barton NH. A variance decomposition approach to the analysis of genetic algorithms. In: Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation. ACM; 2013:845-852. doi:10.1145/2463372.2463470
LibreCat: https://research-explorer.ista.ac.at/record/2719
DOI: 10.1145/2463372.2463470

Wakamoto Y, Dhar N, Chait RP, et al. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 2013;339(6115):91-95. doi:10.1126/science.1229858
LibreCat: https://research-explorer.ista.ac.at/record/499
DOI: 10.1126/science.1229858

Refardt D, Bergmiller T, Kümmerli R. 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. 2013;280(1759). doi:10.1098/rspb.2012.3035
LibreCat: https://research-explorer.ista.ac.at/record/2853
DOI: 10.1098/rspb.2012.3035
PMID: 23516238

Henzinger TA, Mateescu M. The propagation approach for computing biochemical reaction networks. IEEE ACM Transactions on Computational Biology and Bioinformatics. 2012;10(2):310-322. doi:10.1109/TCBB.2012.91
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. Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. Molecular Microbiology. 2012;86(6):1318-1333. doi:10.1111/mmi.12071
LibreCat: https://research-explorer.ista.ac.at/record/2943
DOI: 10.1111/mmi.12071

Bergmiller T, Ackermann M, Silander O. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002803
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. Delayed continuous time Markov chains for genetic regulatory circuits. In: Vol 7358. Springer; 2012:294-309. doi:10.1007/978-3-642-31424-7_24
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. Noise underlies switching behavior of the bacterial flagellum. Biophysical Journal. 2011;101(10):2336-2340. doi:10.1016/j.bpj.2011.09.040
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. Lumpability abstractions of rule-based systems. In: Vol 40. Open Publishing Association; 2010:142-161.
LibreCat: https://research-explorer.ista.ac.at/record/3719
arXiv: 1011.0496

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