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Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., &; Petrov, T. (2017). Model checking the evolution of gene regulatory networks. Acta Informatica. Springer.https://doi.org/10.1007/s00236-016-0278-x 

Paixao, T., Pérez Heredia, J., Sudholt, D., &; Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. Algorithmica. Springer.https://doi.org/10.1007/s00453-016-0212-1 

Fang, C., Nagy-Staron, A. A., Grafe, M., Heermann, R., Jung, K., Gebhard, S., &; Mascher, T. (2017). Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. Wiley-Blackwell.https://doi.org/10.1111/mmi.13597 

Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., &; Guet, C. C. (2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element. ELife. eLife Sciences Publications.https://doi.org/10.7554/eLife.25192 

Lang, M., &; Sontag, E. (2017). Zeros of nonlinear systems with input invariances. Automatica. International Federation of Automatic Control.https://doi.org/10.1016/j.automatica.2017.03.030 

Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R.,https://doi.org/10.1126/science.aaf4762__Guet, C. C. (2017). Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. American Association for the Advancement of Science.https://doi.org/10.1126/science.aaf4762 

Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., &; Janovjak, H. L. (2017). Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. Wiley-Blackwell.https://doi.org/10.1002/anie.201611998 

Steinrück, M., &; Guet, C. C. (2017). Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. ELife. eLife Sciences Publications.https://doi.org/10.7554/eLife.25100 

Lukacisinova, M., Novak, S., &; Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. Public Library of Science.https://doi.org/10.1371/journal.pcbi.1005609 

Barone, V., Lang, M., Krens, G., Pradhan, S., Shamipour, S., Sako, K.,https://doi.org/10.1016/j.devcel.2017.09.014__Heisenberg, C.-P. J. (2017). An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. Cell Press.https://doi.org/10.1016/j.devcel.2017.09.014 

Gnügge, R., Dharmarajan, L., Lang, M., &; Stelling, J. (2016). An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. American Chemical Society.https://doi.org/10.1021/acssynbio.6b00013 

Lang, M., &; Stelling, J. (2016). Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics .https://doi.org/10.1137/15M103306X 

Miki, G., Stoll, A., Bevirt, J., Grah, R., &; Moore, M. (2016). Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency (pp. 1–19). Presented at the AIAA: Aviation Technology, Integration, and Operations Conference, Washington, D.C., USA: AIAA.https://doi.org/10.2514/6.2016-3764 

Stone, L., Baym, M., Lieberman, T., Chait, R. P., Clardy, J., &; Kishony, R. (2016). Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. Nature Publishing Group.https://doi.org/10.1038/nchembio.2176 

Lang, M., &; Sontag, E. (2016). Scale-invariant systems realize nonlinear differential operators (Vol. 2016–July). Presented at the ACC: American Control Conference, Boston, MA, USA: IEEE.https://doi.org/10.1109/ACC.2016.7526722 

Chait, R. P., Palmer, A., Yelin, I., &; Kishony, R. (2016). Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. Nature Publishing Group.https://doi.org/10.1038/ncomms10333 

Baym, M., Lieberman, T., Kelsic, E., Chait, R. P., Gross, R., Yelin, I., &; Kishony, R. (2016). Spatiotemporal microbial evolution on antibiotic landscapes. Science. American Association for the Advancement of Science.https://doi.org/10.1126/science.aag0822 

Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., &; Trubenova, B. (2016). When non-elitism outperforms elitism for crossing fitness valleys. In Proceedings of the Genetic and Evolutionary Computation Conference 2016  (pp. 1163–1170). Denver, CO, USA: ACM.https://doi.org/10.1145/2908812.2908909 

Paixao, T., &; Barton, N. H. (2016). The effect of gene interactions on the long-term response to selection. PNAS. National Academy of Sciences.https://doi.org/10.1073/pnas.1518830113 

Lagator, M., Igler, C., Moreno, A., Guet, C. C., &; Bollback, J. P. (2016). Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. Oxford University Press.https://doi.org/10.1093/molbev/msv269 

Beica, A., Guet, C. C., &; Petrov, T. (2016). Efficient reduction of kappa models by static inspection of the rule-set (Vol. 9271, pp. 173–191). Presented at the HSB: Hybrid Systems Biology, Madrid, Spain: Springer.https://doi.org/10.1007/978-3-319-26916-0_10 

Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., &; Ackermann, M. (2016). Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS Genetics. Public Library of Science.https://doi.org/10.1371/journal.pgen.1005974 

Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., &; Ackermann, M. (2016). Quantification of the growth rate reduction as a consequence of age-specific mortality. Public Library of Science.https://doi.org/10.1371/journal.pgen.1005974.s015 

Wielgoss, S., Bergmiller, T., Bischofberger, A. M., &; Hall, A. R. (2016). Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. Molecular Biology and Evolution. Oxford University Press.https://doi.org/10.1093/molbev/msv270 

Daca, P., Henzinger, T. A., Kretinsky, J., &; Petrov, T. (2016). Linear distances between Markov chains (Vol. 59). Presented at the CONCUR: Concurrency Theory, Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.https://doi.org/10.4230/LIPIcs.CONCUR.2016.20 

Daca, P., Henzinger, T. A., Kretinsky, J., &; Petrov, T. (2016). Faster statistical model checking for unbounded temporal properties (Vol. 9636, pp. 112–129). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Eindhoven, The Netherlands: Springer.https://doi.org/10.1007/978-3-662-49674-9_7 

Pleska, M., Qian, L., Okura, R., Bergmiller, T., Wakamoto, Y., Kussell, E., &; Guet, C. C. (2016). Bacterial autoimmunity due to a restriction-modification system. Current Biology. Cell Press.https://doi.org/10.1016/j.cub.2015.12.041 

Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., &; Tkadik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. Nature Communications. Nature Publishing Group.https://doi.org/10.1038/ncomms12307 

Paixao, T., Sudholt, D., Heredia, J., &; Trubenova, B. (2015). First steps towards a runtime comparison of natural and artificial evolution. In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation (pp. 1455–1462). Madrid, Spain: ACM.https://doi.org/10.1145/2739480.2754758 

Paixao, T., Badkobeh, G., Barton, N. H., Çörüf, D., Dang, D., Friedrich, T.,https://doi.org/10.1016/j.jtbi.2015.07.011__Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. https://doi.org/10.1016/j.jtbi.2015.07.011__Journal of Theoretical Biology. Elsevier.https://doi.org/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. IEEE.https://doi.org/10.1109/TAC.2014.2364971 

Tugrul, M., Paixao, T., Barton, N. H., &; Tkadik, G. (2015). Other fitness models for comparison &; for interacting TFBSs. Public Library of Science.https://doi.org/10.1371/journal.pgen.1005639.s001 

Wielgoss, S., Bergmiller, T., Bischofberger, A. M., &; Hall, A. R. (2015). Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria. Dryad.https://doi.org/10.5061/dryad.cj910 

Tugrul, M., Paixao, T., Barton, N. H., &; Tkadik, G. (2015). Dynamics of transcription factor binding site evolution. PLoS Genetics. Public Library of Science.https://doi.org/10.1371/journal.pgen.1005639 

Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., &; Petrov, T. (2015). Model checking gene regulatory networks. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer.https://doi.org/10.1007/978-3-662-46681-0_47 

Grabowska, A., Wywia, E., Dunin Horkawicz, S., asica, A., Wösten, M., Nagy-Staron, A. A.,https://doi.org/10.1371/journal.pone.0106247__Jagusztyn Krynicka, E. (2014). Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. Public Library of Science.https://doi.org/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. Springer.https://doi.org/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. Wiley.https://doi.org/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.https://doi.org/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. Royal Society, The.https://doi.org/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.https://doi.org/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. Wiley.https://doi.org/10.1111/evo.12373 

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.https://doi.org/10.5061/dryad.jc402 

Milenkovi, I., Petrov, T., &; Kovács, G. (2014). Patterns of hippocampal tau pathology differentiate neurodegenerative dementias. Dementia and Geriatric Cognitive Disorders. Karger Publishers.https://doi.org/10.1159/000365548 

Barton, N. H., &; Paixao, T. (2013). Can quantitative and population genetics help us understand evolutionary computation? In Proceedings of the 15th annual conference on Genetic and evolutionary computation (pp. 1573–1580). Amsterdam, Netherlands: ACM.https://doi.org/10.1145/2463372.2463568 

Long, H., Paixao, T., Azevedo, R., &; Zufall, R. (2013). Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. Genetics Society of America.https://doi.org/10.1534/genetics.113.153536 

Paixao, T., &; Barton, N. H. (2013). A variance decomposition approach to the analysis of genetic algorithms. In Proceedings of the 15th annual conference on Genetic and evolutionary computation (pp. 845–852). Amsterdam, Netherlands: ACM.https://doi.org/10.1145/2463372.2463470 

Wakamoto, Y., Dhar, N., Chait, R. P., Schneider, K., Signorino Gelo, F., Leibler, S., &; Mckinney, J. (2013). Dynamic persistence of antibiotic-stressed mycobacteria. Science. American Association for the Advancement of Science.https://doi.org/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. The Royal Society.https://doi.org/10.1098/rspb.2012.3035 

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.https://doi.org/10.5061/dryad.b1q2n 

Henzinger, T. A., &; Mateescu, M. (2012). The propagation approach for computing biochemical reaction networks. IEEE ACM Transactions on Computational Biology and Bioinformatics. IEEE.https://doi.org/10.1109/TCBB.2012.91 

Hadizadeh Yazdi, N., Guet, C. C., Johnson, R., &; Marko, J. (2012). Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. Molecular Microbiology. Wiley-Blackwell.https://doi.org/10.1111/mmi.12071 

Bergmiller, T., Ackermann, M., &; Silander, O. (2012). Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. Public Library of Science.https://doi.org/10.1371/journal.pgen.1002803 

Guet, C. C., Gupta, A., Henzinger, T. A., Mateescu, M., &; Sezgin, A. (2012). Delayed continuous time Markov chains for genetic regulatory circuits (Vol. 7358, pp. 294–309). Presented at the CAV: Computer Aided Verification, Berkeley, CA, USA: Springer.https://doi.org/10.1007/978-3-642-31424-7_24 

Park, H., Oikonomou, P., Guet, C. C., &; Cluzel, P. (2011). Noise underlies switching behavior of the bacterial flagellum. Biophysical Journal. Elsevier.https://doi.org/10.1016/j.bpj.2011.09.040 

Feret, J., Henzinger, T. A., Koeppl, H., &; Petrov, T. (2010). Lumpability abstractions of rule-based systems (Vol. 40, pp. 142–161). Presented at the MECBIC: Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany: Open Publishing Association.

Didier, F., Henzinger, T. A., Mateescu, M., &; Wolf, V. (2010). SABRE: A tool for the stochastic analysis of biochemical reaction networks (pp. 193–194). Presented at the QEST: Quantitative Evaluation of Systems, Williamsburg, USA: IEEE.https://doi.org/10.1109/QEST.2010.33 

Didier, F., Henzinger, T. A., Mateescu, M., &; Wolf, V. (2009). Fast adaptive uniformization of the chemical master equation (Vol. 4, pp. 118–127). Presented at the HIBI: High-Performance Computational Systems Biology, Trento, Italy: IEEE.https://doi.org/10.1109/HiBi.2009.23