Miki G, Stoll A, Bevirt J, Grah R, Moore M. Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency. In: AIAA; 2016:1-19. doi:10.2514/6.2016-3764
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Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 2016;12(11):902-904. doi:10.1038/nchembio.2176
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Lang M, Sontag E. Scale-invariant systems realize nonlinear differential operators. In: Vol 2016-July. IEEE; 2016. doi:10.1109/ACC.2016.7526722
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Chait RP, Palmer A, Yelin I, Kishony R. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 2016;7. doi:10.1038/ncomms10333
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Baym M, Lieberman T, Kelsic E, et al. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 2016;353(6304):1147-1151. doi:10.1126/science.aag0822
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Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. When non-elitism outperforms elitism for crossing fitness valleys. In: Proceedings of the Genetic and Evolutionary Computation Conference 2016 . ACM; 2016:1163-1170. doi:10.1145/2908812.2908909
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Paixao T, Barton NH. The effect of gene interactions on the long-term response to selection. PNAS. 2016;113(16):4422-4427. doi:10.1073/pnas.1518830113
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PMID: 27044080

Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. 2016;33(3):761-769. doi:10.1093/molbev/msv269
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Beica A, Guet CC, Petrov T. Efficient reduction of kappa models by static inspection of the rule-set. In: Vol 9271. Springer; 2016:173-191. doi:10.1007/978-3-319-26916-0_10
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Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS Genetics. 2016;12(4). doi:10.1371/journal.pgen.1005974
LibreCat: https://research-explorer.ista.ac.at/record/1250
DOI: 10.1371/journal.pgen.1005974

Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Quantification of the growth rate reduction as a consequence of age-specific mortality. 2016. doi:10.1371/journal.pgen.1005974.s015
LibreCat: https://research-explorer.ista.ac.at/record/9873
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Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. Molecular Biology and Evolution. 2016;33(3):770-782. doi:10.1093/molbev/msv270
LibreCat: https://research-explorer.ista.ac.at/record/5749
DOI: 10.1093/molbev/msv270
PMID: 26609077

Daca P, Henzinger TA, Kretinsky J, Petrov T. Linear distances between Markov chains. In: Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.20
LibreCat: https://research-explorer.ista.ac.at/record/1093
DOI: 10.4230/LIPIcs.CONCUR.2016.20

Daca P, Henzinger TA, Kretinsky J, Petrov T. Faster statistical model checking for unbounded temporal properties. In: Vol 9636. Springer; 2016:112-129. doi:10.1007/978-3-662-49674-9_7
LibreCat: https://research-explorer.ista.ac.at/record/1234
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Pleska M, Qian L, Okura R, et al. Bacterial autoimmunity due to a restriction-modification system. Current Biology. 2016;26(3):404-409. doi:10.1016/j.cub.2015.12.041
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Friedlander T, Prizak R, Guet CC, Barton NH, Tkadik G. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 2016;7. doi:10.1038/ncomms12307
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Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime comparison of natural and artificial evolution. In: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. ACM; 2015:1455-1462. doi:10.1145/2739480.2754758
LibreCat: https://research-explorer.ista.ac.at/record/1430
DOI: 10.1145/2739480.2754758

Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. 10.1016/j.jtbi.2015.07.011__Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011
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. Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. 2015;60(4):1010-1022. doi:10.1109/TAC.2014.2364971
LibreCat: https://research-explorer.ista.ac.at/record/1840
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Tugrul M, Paixao T, Barton NH, Tkadik G. Other fitness models for comparison &; for interacting TFBSs. 2015. doi: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. Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria. 2015. doi:10.5061/dryad.cj910
LibreCat: https://research-explorer.ista.ac.at/record/9719
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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
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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
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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
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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
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Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration in adaptation to sink environments. 2014. doi:10.5061/dryad.s42n1
LibreCat: https://research-explorer.ista.ac.at/record/9747
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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

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

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

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
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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
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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
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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

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

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
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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
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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

Didier F, Henzinger TA, Mateescu M, Wolf V. Fast adaptive uniformization of the chemical master equation. In: Vol 4. IEEE; 2009:118-127. doi:10.1109/HiBi.2009.23
LibreCat: https://research-explorer.ista.ac.at/record/3843
DOI: 10.1109/HiBi.2009.23