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80 Publications

2016 | Journal Article | IST-REx-ID: 1008
Gnügge, Robert, Lekshmi Dharmarajan, Moritz Lang, and Jörg Stelling. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” ACS Synthetic Biology 5, no. 10 (2016): 1098–1107. https://doi.org/10.1021/acssynbio.6b00013.
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2016 | Journal Article | IST-REx-ID: 1250   OA
Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette Bigosch, and Martin Ackermann. “Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E Coli.” PLoS Genetics 12, no. 4 (2016). https://doi.org/10.1371/journal.pgen.1005974.
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2016 | Conference Paper | IST-REx-ID: 1320
Lang, Moritz, and Eduardo Sontag. “Scale-Invariant Systems Realize Nonlinear Differential Operators,” Vol. 2016–July. IEEE, 2016. https://doi.org/10.1109/ACC.2016.7526722.
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2016 | Journal Article | IST-REx-ID: 1332   OA
Chait, Remy P, Adam Palmer, Idan Yelin, and Roy Kishony. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” Nature Communications 7 (2016). https://doi.org/10.1038/ncomms10333.
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2016 | Conference Paper | IST-REx-ID: 1349   OA
Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” In Proceedings of the Genetic and Evolutionary Computation Conference 2016 , 1163–70. ACM, 2016. https://doi.org/10.1145/2908812.2908909.
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2016 | Journal Article | IST-REx-ID: 1243
Pleska, Maros, Long Qian, Reiko Okura, Tobias Bergmiller, Yuichi Wakamoto, Edo Kussell, and Calin C Guet. “Bacterial Autoimmunity Due to a Restriction-Modification System.” Current Biology 26, no. 3 (2016): 404–9. https://doi.org/10.1016/j.cub.2015.12.041.
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2016 | Conference Paper | IST-REx-ID: 1220   OA
Mikić, Gregor, Alex Stoll, Joe Bevirt, Rok Grah, and Mark Moore. “Fuselage Boundary Layer Ingestion Propulsion Applied to a Thin Haul Commuter Aircraft for Optimal Efficiency,” 1–19. AIAA, 2016. https://doi.org/10.2514/6.2016-3764.
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2016 | Journal Article | IST-REx-ID: 1427   OA
Lagator, Mato, Claudia Igler, Anaisa Moreno, Calin C Guet, and Jonathan P Bollback. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” Molecular Biology and Evolution 33, no. 3 (2016): 761–69. https://doi.org/10.1093/molbev/msv269.
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2016 | Journal Article | IST-REx-ID: 1170
Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” SIAM Journal on Scientific Computing 38, no. 6 (2016): B988–1008. https://doi.org/10.1137/15M103306X.
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2016 | Conference Paper | IST-REx-ID: 1093
Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Linear Distances between Markov Chains,” Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.20.
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2016 | Journal Article | IST-REx-ID: 1290   OA
Stone, Laura, Michael Baym, Tami Lieberman, Remy P Chait, Jon Clardy, and Roy Kishony. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” Nature Chemical Biology 12, no. 11 (2016): 902–4. https://doi.org/10.1038/nchembio.2176.
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2016 | Conference Paper | IST-REx-ID: 1524   OA
Beica, Andreea, Calin C Guet, and Tatjana Petrov. “Efficient Reduction of Kappa Models by Static Inspection of the Rule-Set,” 9271:173–91. Springer, 2016. https://doi.org/10.1007/978-3-319-26916-0_10.
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2016 | Journal Article | IST-REx-ID: 1358
Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gasper Tkacik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications 7 (2016). https://doi.org/10.1038/ncomms12307.
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2016 | Journal Article | IST-REx-ID: 1359   OA
Paixao, Tiago, and Nicholas H Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” PNAS 113, no. 16 (2016): 4422–27. https://doi.org/10.1073/pnas.1518830113.
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2016 | Journal Article | IST-REx-ID: 1342   OA
Baym, Michael, Tami Lieberman, Eric Kelsic, Remy P Chait, Rotem Gross, Idan Yelin, and Roy Kishony. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” Science 353, no. 6304 (2016): 1147–51. https://doi.org/10.1126/science.aag0822.
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2016 | Conference Paper | IST-REx-ID: 1234
Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Faster Statistical Model Checking for Unbounded Temporal Properties,” 9636:112–29. Springer, 2016. https://doi.org/10.1007/978-3-662-49674-9_7.
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2015 | Journal Article | IST-REx-ID: 1666   OA
Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gasper Tkacik. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics 11, no. 11 (2015). https://doi.org/10.1371/journal.pgen.1005639.
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2015 | Journal Article | IST-REx-ID: 1542   OA
Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology 383 (2015): 28–43. https://doi.org/10.1016/j.jtbi.2015.07.011.
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2015 | Journal Article | IST-REx-ID: 1840   OA
Geiger, Bernhard, Tatjana Petrov, Gernot Kubin, and Heinz Koeppl. “Optimal Kullback-Leibler Aggregation via Information Bottleneck.” IEEE Transactions on Automatic Control 60, no. 4 (2015): 1010–22. https://doi.org/10.1109/TAC.2014.2364971.
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2015 | Conference Paper | IST-REx-ID: 1430   OA
Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62. ACM, 2015. https://doi.org/10.1145/2739480.2754758.
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2015 | Conference Paper | IST-REx-ID: 1835   OA
Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_47.
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2015 | Journal Article | IST-REx-ID: 5749   OA
Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” Molecular Biology and Evolution 33, no. 3 (2015): 770–82. https://doi.org/10.1093/molbev/msv270.
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2014 | Journal Article | IST-REx-ID: 1894   OA
Grabowska, Anna, Ewa Wywiał, Stanislaw Dunin Horkawicz, Anna Łasica, Marc Wösten, Anna A Nagy-Staron, Renata Godlewska, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” PLoS One 9, no. 9 (2014). https://doi.org/10.1371/journal.pone.0106247.
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2014 | Journal Article | IST-REx-ID: 2056   OA
Ganguly, Arnab, Tatjana Petrov, and Heinz Koeppl. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” Journal of Mathematical Biology 69, no. 3 (2014): 767–97. https://doi.org/10.1007/s00285-013-0738-7.
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2014 | Journal Article | IST-REx-ID: 2083
Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Role of Sex and Migration in Adaptation to Sink Environments.” Evolution 68, no. 8 (2014): 2296–2305. https://doi.org/10.1111/evo.12440.
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2014 | Journal Article | IST-REx-ID: 1913
Milenković, Ivan, Tatjana Petrov, and Gábor Kovács. “Patterns of Hippocampal Tau Pathology Differentiate Neurodegenerative Dementias.” Dementia and Geriatric Cognitive Disorders 38, no. 5–6 (2014): 375–88. https://doi.org/10.1159/000365548.
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2014 | Journal Article | IST-REx-ID: 2036   OA
Lagator, Mato, Nick Colegrave, and Paul Neve. “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, no. 1794 (2014). https://doi.org/10.1098/rspb.2014.1679.
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2013 | Conference Paper | IST-REx-ID: 2718   OA
Barton, Nicholas H, and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 1573–80. ACM, 2013. https://doi.org/10.1145/2463372.2463568.
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2013 | Journal Article | IST-REx-ID: 2720   OA
Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics 195, no. 2 (2013): 527–40. https://doi.org/10.1534/genetics.113.153536 .
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2013 | Journal Article | IST-REx-ID: 499
Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.” Science 339, no. 6115 (2013): 91–95. https://doi.org/10.1126/science.1229858.
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2013 | Conference Paper | IST-REx-ID: 2719
Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 845–52. ACM, 2013. https://doi.org/10.1145/2463372.2463470.
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2013 | Journal Article | IST-REx-ID: 2853   OA
Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “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, no. 1759 (2013). https://doi.org/10.1098/rspb.2012.3035.
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2012 | Journal Article | IST-REx-ID: 2943   OA
Hadizadeh Yazdi, Nastaran, Calin C Guet, Reid Johnson, and John Marko. “Variation of the Folding and Dynamics of the Escherichia Coli Chromosome with Growth Conditions.” Molecular Microbiology 86, no. 6 (2012): 1318–33. https://doi.org/10.1111/mmi.12071.
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2012 | Conference Paper | IST-REx-ID: 3136
Guet, Calin C, Ashutosh Gupta, Thomas A Henzinger, Maria Mateescu, and Ali Sezgin. “Delayed Continuous Time Markov Chains for Genetic Regulatory Circuits,” 7358:294–309. Springer, 2012. https://doi.org/10.1007/978-3-642-31424-7_24.
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2012 | Journal Article | IST-REx-ID: 2302
Henzinger, Thomas A, and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.” IEEE ACM Transactions on Computational Biology and Bioinformatics 10, no. 2 (2012): 310–22. https://doi.org/10.1109/TCBB.2012.91.
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2012 | Journal Article | IST-REx-ID: 3130   OA
Bergmiller, Tobias, Martin Ackermann, and Olin Silander. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” PLoS Genetics 8, no. 6 (2012). https://doi.org/10.1371/journal.pgen.1002803.
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2011 | Journal Article | IST-REx-ID: 6496   OA
Park, Heungwon, Panos Oikonomou, Calin C Guet, and Philippe Cluzel. “Noise Underlies Switching Behavior of the Bacterial Flagellum.” Biophysical Journal 101, no. 10 (2011): 2336–40. https://doi.org/10.1016/j.bpj.2011.09.040.
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2010 | Conference Paper | IST-REx-ID: 3719   OA
Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability Abstractions of Rule-Based Systems,” 40:142–61. Open Publishing Association, 2010.
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2010 | Conference Paper | IST-REx-ID: 3847   OA
Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “SABRE: A Tool for the Stochastic Analysis of Biochemical Reaction Networks,” 193–94. IEEE, 2010. https://doi.org/10.1109/QEST.2010.33.
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2009 | Conference Paper | IST-REx-ID: 3843
Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “Fast Adaptive Uniformization of the Chemical Master Equation,” 4:118–27. IEEE, 2009. https://doi.org/10.1109/HiBi.2009.23.
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