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126 Publications
2017 | Thesis | IST-REx-ID: 202 | 
Pleska M. Biology of restriction-modification systems at the single-cell and population level. 2017. doi:10.15479/AT:ISTA:th_916
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2017 | Journal Article | IST-REx-ID: 1351 |
Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking the evolution of gene regulatory networks. Acta Informatica. 2017;54(8):765-787. doi:10.1007/s00236-016-0278-x
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2017 | Journal Article | IST-REx-ID: 1336 |
Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 2017;78(2):681-713. doi:10.1007/s00453-016-0212-1
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2017 | Journal Article | IST-REx-ID: 1084
Fang C, Nagy-Staron AA, Grafe M, et al. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 2017;104(1):16-31. doi:10.1111/mmi.13597
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2017 | Journal Article | IST-REx-ID: 954 |
Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192
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2017 | Journal Article | IST-REx-ID: 1007 |
Lang M, Sontag E. Zeros of nonlinear systems with input invariances. Automatica. 2017;81C:46-55. doi:10.1016/j.automatica.2017.03.030
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2017 | Research Data | IST-REx-ID: 5564 |
Steinrück M, Guet CC. Fastq files for “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection.” 2017. doi:10.15479/AT:ISTA:65
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2017 | Research Data | IST-REx-ID: 5560 |
Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. 2017. doi:10.15479/AT:ISTA:53
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2017 | Journal Article | IST-REx-ID: 665
Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 2017;356(6335):311-315. doi:10.1126/science.aaf4762
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2017 | Journal Article | IST-REx-ID: 1028 |
Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 2017;56(16):4608-4611. doi:10.1002/anie.201611998
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2017 | Journal Article | IST-REx-ID: 704 |
Steinrück M, Guet CC. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 2017;6. doi:10.7554/eLife.25100
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2017 | Journal Article | IST-REx-ID: 696 |
Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 2017;13(7). doi:10.1371/journal.pcbi.1005609
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2017 | Journal Article | IST-REx-ID: 735
Barone V, Lang M, Krens G, et al. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. 2017;43(2):198-211. doi:10.1016/j.devcel.2017.09.014
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2016 | Journal Article | IST-REx-ID: 1008
Gnügge R, Dharmarajan L, Lang M, Stelling J. An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. 2016;5(10):1098-1107. doi:10.1021/acssynbio.6b00013
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2016 | Journal Article | IST-REx-ID: 1170
Lang M, Stelling J. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 2016;38(6):B988-B1008. doi:10.1137/15M103306X
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2016 | Conference Paper | IST-REx-ID: 1220 |
Mikić 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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2016 | Journal Article | IST-REx-ID: 1290 |
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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2016 | Conference Paper | IST-REx-ID: 1320
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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2016 | Journal Article | IST-REx-ID: 1332 |
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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2016 | Journal Article | IST-REx-ID: 1342 |
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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2016 | Conference Paper | IST-REx-ID: 1349 |
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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2016 | Journal Article | IST-REx-ID: 1359 |
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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2016 | Journal Article | IST-REx-ID: 1427 |
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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2016 | Conference Paper | IST-REx-ID: 1524 |
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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2016 | Journal Article | IST-REx-ID: 1250 |
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
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2016 | Research Data Reference | IST-REx-ID: 9873
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
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2016 | Journal Article | IST-REx-ID: 5749 |
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
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2016 | Conference Paper | IST-REx-ID: 1093 |
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
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2016 | Conference Paper | IST-REx-ID: 1234 |
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
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2016 | Journal Article | IST-REx-ID: 1243
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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2016 | Journal Article | IST-REx-ID: 1358 |
Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 2016;7. doi:10.1038/ncomms12307
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2015 | Conference Paper | IST-REx-ID: 1430 |
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
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2015 | Journal Article | IST-REx-ID: 1542 |
Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011
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2015 | Journal Article | IST-REx-ID: 1840 |
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
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2015 | Research Data Reference | IST-REx-ID: 9712
Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison & for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001
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2015 | Research Data Reference | IST-REx-ID: 9719 |
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
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2015 | Journal Article | IST-REx-ID: 1666 |
Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639
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2015 | Conference Paper | IST-REx-ID: 1835 |
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
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2014 | Journal Article | IST-REx-ID: 1894 |
Grabowska A, Wywiał 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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2014 | Journal Article | IST-REx-ID: 2056 |
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
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2014 | Journal Article | IST-REx-ID: 2083 |
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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2014 | Research Data Reference | IST-REx-ID: 9747 |
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
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2014 | Journal Article | IST-REx-ID: 2036 |
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
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2014 | Research Data Reference | IST-REx-ID: 9741 |
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
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2014 | Journal Article | IST-REx-ID: 9931
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
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2014 | Research Data Reference | IST-REx-ID: 9932 |
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
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2014 | Journal Article | IST-REx-ID: 1913 |
Milenković 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
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2013 | Conference Paper | IST-REx-ID: 2718 |
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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2013 | Journal Article | IST-REx-ID: 2720 |
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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2013 | Conference Paper | IST-REx-ID: 2719
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
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