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89 Publications

2015 | Conference Paper | IST-REx-ID: 1430 | OA
T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards a runtime comparison of natural and artificial evolution,” in Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, Madrid, Spain, 2015, pp. 1455–1462.
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2014 | Journal Article | IST-REx-ID: 2036 | OA
M. Lagator, N. Colegrave, and P. 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, vol. 281, no. 1794, 2014.
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2014 | Journal Article | IST-REx-ID: 2056 | OA
A. Ganguly, T. Petrov, and H. Koeppl, “Markov chain aggregation and its applications to combinatorial reaction networks,” Journal of Mathematical Biology, vol. 69, no. 3, pp. 767–797, 2014.
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2014 | Journal Article | IST-REx-ID: 2083 | OA
M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Role of sex and migration in adaptation to sink environments,” Evolution, vol. 68, no. 8, pp. 2296–2305, 2014.
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2014 | Journal Article | IST-REx-ID: 1894 | OA
A. Grabowska et al., “Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA,” PLoS One, vol. 9, no. 9, 2014.
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2014 | Journal Article | IST-REx-ID: 1913 | OA
I. Milenković, T. Petrov, and G. Kovács, “Patterns of hippocampal tau pathology differentiate neurodegenerative dementias,” Dementia and Geriatric Cognitive Disorders, vol. 38, no. 5–6, pp. 375–388, 2014.
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2013 | Journal Article | IST-REx-ID: 499
Y. Wakamoto et al., “Dynamic persistence of antibiotic-stressed mycobacteria,” Science, vol. 339, no. 6115, pp. 91–95, 2013.
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2013 | Conference Paper | IST-REx-ID: 2718 | OA
N. H. Barton and T. Paixao, “Can quantitative and population genetics help us understand evolutionary computation?,” in Proceedings of the 15th annual conference on Genetic and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 1573–1580.
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2013 | Conference Paper | IST-REx-ID: 2719
T. Paixao and N. H. Barton, “A variance decomposition approach to the analysis of genetic algorithms,” in Proceedings of the 15th annual conference on Genetic and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 845–852.
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2013 | Journal Article | IST-REx-ID: 2720 | OA
H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila,” Genetics, vol. 195, no. 2, pp. 527–540, 2013.
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2013 | Journal Article | IST-REx-ID: 2853 | OA
D. Refardt, T. Bergmiller, and R. 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, vol. 280, no. 1759, 2013.
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2012 | Journal Article | IST-REx-ID: 2302
T. A. Henzinger and M. Mateescu, “The propagation approach for computing biochemical reaction networks,” IEEE ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 2, pp. 310–322, 2012.
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2012 | Journal Article | IST-REx-ID: 2943 | OA
N. Hadizadeh Yazdi, C. C. Guet, R. Johnson, and J. Marko, “Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions,” Molecular Microbiology, vol. 86, no. 6, pp. 1318–1333, 2012.
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2012 | Journal Article | IST-REx-ID: 3130 | OA
T. Bergmiller, M. Ackermann, and O. Silander, “Patterns of evolutionary conservation of essential genes correlate with their compensability,” PLoS Genetics, vol. 8, no. 6, 2012.
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2012 | Conference Paper | IST-REx-ID: 3136
C. C. Guet, A. Gupta, T. A. Henzinger, M. Mateescu, and A. Sezgin, “Delayed continuous time Markov chains for genetic regulatory circuits,” presented at the CAV: Computer Aided Verification, Berkeley, CA, USA, 2012, vol. 7358, pp. 294–309.
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2011 | Journal Article | IST-REx-ID: 6496 | OA
H. Park, P. Oikonomou, C. C. Guet, and P. Cluzel, “Noise underlies switching behavior of the bacterial flagellum,” Biophysical Journal, vol. 101, no. 10, pp. 2336–2340, 2011.
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2010 | Conference Paper | IST-REx-ID: 3719 | OA
J. Feret, T. A. Henzinger, H. Koeppl, and T. Petrov, “Lumpability abstractions of rule-based systems,” presented at the MECBIC: Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany, 2010, vol. 40, pp. 142–161.
View | Files available | arXiv
 
2010 | Conference Paper | IST-REx-ID: 3847 | OA
F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “SABRE: A tool for the stochastic analysis of biochemical reaction networks,” presented at the QEST: Quantitative Evaluation of Systems, Williamsburg, USA, 2010, pp. 193–194.
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2009 | Conference Paper | IST-REx-ID: 3843 | OA
F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Fast adaptive uniformization of the chemical master equation,” presented at the HIBI: High-Performance Computational Systems Biology, Trento, Italy, 2009, vol. 4, no. 6, pp. 118–127.
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