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Lukacisinova, M., Novak, S., &; Paixao, T. (2017). Heuristic prediction for multiple stresses. Public Library of Science.https://doi.org/10.1371/journal.pcbi.1005609.s003 
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Lukacisinova, M., Novak, S., &; Paixao, T. (2017). Resistance frequencies for different combination strategies. Public Library of Science.https://doi.org/10.1371/journal.pcbi.1005609.s004 
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Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S.,https://doi.org/10.1371/journal.pgen.1007122.s018__Ackermann, M. (2017). Source data for figures and tables. Public Library of Science.https://doi.org/10.1371/journal.pgen.1007122.s018 
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Pleska, M., &; Guet, C. C. (2017). Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. The Royal Society.https://doi.org/10.1098/rsbl.2017.0646 
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Pleska, M. (2017). Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria.https://doi.org/10.15479/AT:ISTA:th_916 
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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 
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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 
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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 
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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 
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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 
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Steinrück, M., &; Guet, C. C. (2017). Fastq files for “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection.”https://doi.org/10.15479/AT:ISTA:65__Institute of Science and Technology Austria.https://doi.org/10.15479/AT:ISTA:65 
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Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R.,https://doi.org/10.15479/AT:ISTA:53__Guet, C. C. (2017). Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. Institute of Science and Technology Austria.https://doi.org/10.15479/AT:ISTA:53 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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PMID: 27044080

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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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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 
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PMID: 24495000