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126 Publications
2015 | Research Data Reference | IST-REx-ID: 9719 | 
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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2015 | Journal Article | IST-REx-ID: 1666 |
Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, 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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2015 | Conference Paper | IST-REx-ID: 1835 |
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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2014 | Journal Article | IST-REx-ID: 1894 |
Grabowska, A., Wywiał, E., Dunin Horkawicz, S., Łasica, A., Wösten, M., Nagy-Staron, A. A., … 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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2014 | Journal Article | IST-REx-ID: 2056 |
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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2014 | Journal Article | IST-REx-ID: 2083 |
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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2014 | Research Data Reference | IST-REx-ID: 9747 |
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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2014 | Journal Article | IST-REx-ID: 2036 |
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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2014 | Research Data Reference | IST-REx-ID: 9741 |
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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2014 | Journal Article | IST-REx-ID: 9931
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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2014 | Research Data Reference | IST-REx-ID: 9932 |
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
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2014 | Journal Article | IST-REx-ID: 1913 |
Milenković, 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
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| PubMed | Europe PMC
2013 | Conference Paper | IST-REx-ID: 2718 |
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
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2013 | Journal Article | IST-REx-ID: 2720 |
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
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2013 | Conference Paper | IST-REx-ID: 2719
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
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2013 | Journal Article | IST-REx-ID: 499
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
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2013 | Journal Article | IST-REx-ID: 2853 |
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
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2013 | Research Data Reference | IST-REx-ID: 9751 |
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
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2012 | Journal Article | IST-REx-ID: 2302
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
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2012 | Journal Article | IST-REx-ID: 2943 |
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
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2012 | Journal Article | IST-REx-ID: 3130 |
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
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2012 | Conference Paper | IST-REx-ID: 3136
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
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2011 | Journal Article | IST-REx-ID: 6496 |
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
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2010 | Conference Paper | IST-REx-ID: 3719 |
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.
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2010 | Conference Paper | IST-REx-ID: 3847 |
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
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2009 | Conference Paper | IST-REx-ID: 3843 |
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
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