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89 Publications

2017 | Journal Article | IST-REx-ID: 665
Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkacik G, Guet CC. 2017. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 356(6335), 311–315.
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2017 | Journal Article | IST-REx-ID: 696 | OA
Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7).
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2017 | Journal Article | IST-REx-ID: 704 | OA
Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 6.
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2017 | Journal Article | IST-REx-ID: 954 | OA
Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 6.
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2017 | Journal Article | IST-REx-ID: 1336 | OA
Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713.
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2017 | Journal Article | IST-REx-ID: 1351 | OA
Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787.
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2017 | Journal Article | IST-REx-ID: 1007 | OA
Lang M, Sontag E. 2017. Zeros of nonlinear systems with input invariances. Automatica. 81C, 46–55.
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2017 | Journal Article | IST-REx-ID: 1028 | OA
Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 56(16), 4608–4611.
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2017 | Journal Article | IST-REx-ID: 1084
Fang C, Nagy-Staron AA, 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. 104(1), 16–31.
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2016 | Conference Paper | IST-REx-ID: 1220 | OA
Mikić 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. AIAA: Aviation Technology, Integration, and Operations Conference 1–19.
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2016 | Conference Paper | IST-REx-ID: 1234 | OA
Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Faster statistical model checking for unbounded temporal properties. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 9636. 112–129.
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2016 | Journal Article | IST-REx-ID: 1243
Pleska M, Qian L, Okura R, Bergmiller T, Wakamoto Y, Kussell E, Guet CC. 2016. Bacterial autoimmunity due to a restriction-modification system. Current Biology. 26(3), 404–409.
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2016 | Journal Article | IST-REx-ID: 1250 | OA
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. 12(4).
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2016 | Journal Article | IST-REx-ID: 1290 | OA
Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. 2016. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 12(11), 902–904.
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2016 | Conference Paper | IST-REx-ID: 1320
Lang M, Sontag E. 2016. Scale-invariant systems realize nonlinear differential operators. ACC: American Control Conference vol. 2016–July.
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2016 | Journal Article | IST-REx-ID: 1332 | OA
Chait RP, Palmer A, Yelin I, Kishony R. 2016. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 7.
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2016 | Journal Article | IST-REx-ID: 1342 | OA
Baym M, Lieberman T, Kelsic E, Chait RP, Gross R, Yelin I, Kishony R. 2016. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 353(6304), 1147–1151.
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2016 | Conference Paper | IST-REx-ID: 1349 | OA
Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. 2016. When non-elitism outperforms elitism for crossing fitness valleys. Proceedings of the Genetic and Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation conference 1163–1170.
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2016 | Journal Article | IST-REx-ID: 1358 | OA
Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7.
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2016 | Journal Article | IST-REx-ID: 1359 | OA
Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 4422–4427.
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2016 | Journal Article | IST-REx-ID: 1427 | OA
Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. 2016. Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. 33(3), 761–769.
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2016 | Conference Paper | IST-REx-ID: 1524 | OA
Beica A, Guet CC, Petrov T. 2016. Efficient reduction of kappa models by static inspection of the rule-set. HSB: Hybrid Systems Biology, LNCS, vol. 9271. 173–191.
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2016 | Journal Article | IST-REx-ID: 1008
Gnügge R, Dharmarajan L, Lang M, Stelling J. 2016. An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. 5(10), 1098–1107.
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2016 | Conference Paper | IST-REx-ID: 1093 | OA
Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Linear distances between Markov chains. CONCUR: Concurrency Theory, LIPIcs, vol. 59.
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2016 | Journal Article | IST-REx-ID: 1170
Lang M, Stelling J. 2016. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 38(6), B988–B1008.
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2015 | Journal Article | IST-REx-ID: 5749 | OA
Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2015. Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria. Molecular Biology and Evolution. 33(3), 770–782.
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2015 | Journal Article | IST-REx-ID: 1542 | OA
Paixao T, Badkobeh G, Barton NH, Çörüş 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.
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2015 | Journal Article | IST-REx-ID: 1666 | OA
Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).
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2015 | Conference Paper | IST-REx-ID: 1835 | OA
Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model checking gene regulatory networks. 9035, 469–483.
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2015 | Journal Article | IST-REx-ID: 1840 | OA
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.
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2015 | Conference Paper | IST-REx-ID: 1430 | OA
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.
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2014 | Journal Article | IST-REx-ID: 2036 | OA
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.
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2014 | Journal Article | IST-REx-ID: 2056 | OA
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.
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2014 | Journal Article | IST-REx-ID: 2083 | OA
Lagator M, Morgan A, Neve P, Colegrave N. 2014. Role of sex and migration in adaptation to sink environments. Evolution. 68(8), 2296–2305.
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2014 | Journal Article | IST-REx-ID: 1894 | OA
Grabowska A, Wywiał E, Dunin Horkawicz S, Łasica A, Wösten M, Nagy-Staron AA, Godlewska R, Bocian Ostrzycka K, Pieńkowska K, Łaniewski 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).
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2014 | Journal Article | IST-REx-ID: 1913 | OA
Milenković I, Petrov T, Kovács G. 2014. Patterns of hippocampal tau pathology differentiate neurodegenerative dementias. Dementia and Geriatric Cognitive Disorders. 38(5–6), 375–388.
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2013 | Journal Article | IST-REx-ID: 499
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.
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2013 | Conference Paper | IST-REx-ID: 2718 | OA
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.
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2013 | Conference Paper | IST-REx-ID: 2719
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.
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2013 | Journal Article | IST-REx-ID: 2720 | OA
Long H, Paixao T, Azevedo R, Zufall R. 2013. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 195(2), 527–540.
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2013 | Journal Article | IST-REx-ID: 2853 | OA
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).
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2012 | Journal Article | IST-REx-ID: 2302
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.
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2012 | Journal Article | IST-REx-ID: 2943 | OA
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.
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2012 | Journal Article | IST-REx-ID: 3130 | OA
Bergmiller T, Ackermann M, Silander O. 2012. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 8(6).
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2012 | Conference Paper | IST-REx-ID: 3136
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.
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2011 | Journal Article | IST-REx-ID: 6496 | OA
Park H, Oikonomou P, Guet CC, Cluzel P. 2011. Noise underlies switching behavior of the bacterial flagellum. Biophysical Journal. 101(10), 2336–2340.
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2010 | Conference Paper | IST-REx-ID: 3719 | OA
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.
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2010 | Conference Paper | IST-REx-ID: 3847 | OA
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.
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2009 | Conference Paper | IST-REx-ID: 3843 | OA
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.
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