Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Data from: Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.”https://doi.org/10.5061/dryad.jc402__Dryad, 2014.https://doi.org/10.5061/dryad.jc402 .
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Milenkovi, Ivan, Tatjana Petrov, and Gábor Kovács. “Patterns of Hippocampal Tau Pathology Differentiate Neurodegenerative Dementias.”https://doi.org/10.1159/000365548__Dementia and Geriatric Cognitive Disorders. Karger Publishers, 2014.https://doi.org/10.1159/000365548 .
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Barton, Nicholas H, and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?”https://doi.org/10.1145/2463372.2463568__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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Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.”https://doi.org/10.1534/genetics.113.153536__Genetics. Genetics Society of America, 2013.https://doi.org/10.1534/genetics.113.153536 .
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Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.”https://doi.org/10.1145/2463372.2463470__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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Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.”https://doi.org/10.1126/science.1229858__Science. American Association for the Advancement of Science, 2013.https://doi.org/10.1126/science.1229858 .
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Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.”https://doi.org/10.1098/rspb.2012.3035__Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society, 2013.https://doi.org/10.1098/rspb.2012.3035 .
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Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Data from: Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.”https://doi.org/10.5061/dryad.b1q2n__Dryad, 2013.https://doi.org/10.5061/dryad.b1q2n .
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Henzinger, Thomas A, and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.”https://doi.org/10.1109/TCBB.2012.91__IEEE ACM Transactions on Computational Biology and Bioinformatics. IEEE, 2012.https://doi.org/10.1109/TCBB.2012.91 .
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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.”https://doi.org/10.1111/mmi.12071__Molecular Microbiology. Wiley-Blackwell, 2012.https://doi.org/10.1111/mmi.12071 .
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Bergmiller, Tobias, Martin Ackermann, and Olin Silander. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.”https://doi.org/10.1371/journal.pgen.1002803__PLoS Genetics. Public Library of Science, 2012.https://doi.org/10.1371/journal.pgen.1002803 .
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Guet, Calin C, Ashutosh Gupta, Thomas A Henzinger, Maria Mateescu, and Ali Sezgin. “Delayed Continuous Time Markov Chains for Genetic Regulatory Circuits,”https://doi.org/10.1007/978-3-642-31424-7_24__7358:294–309. Springer, 2012.https://doi.org/10.1007/978-3-642-31424-7_24 .
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Park, Heungwon, Panos Oikonomou, Calin C Guet, and Philippe Cluzel. “Noise Underlies Switching Behavior of the Bacterial Flagellum.”https://doi.org/10.1016/j.bpj.2011.09.040__Biophysical Journal. Elsevier, 2011.https://doi.org/10.1016/j.bpj.2011.09.040 .
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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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arXiv: 1011.0496

Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “SABRE: A Tool for the Stochastic Analysis of Biochemical Reaction Networks,”https://doi.org/10.1109/QEST.2010.33__193–94. IEEE, 2010.https://doi.org/10.1109/QEST.2010.33 .
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Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “Fast Adaptive Uniformization of the Chemical Master Equation,”https://doi.org/10.1109/HiBi.2009.23__4:118–27. IEEE, 2009.https://doi.org/10.1109/HiBi.2009.23 .
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