M. Lang and E. Sontag, “Scale-invariant systems realize nonlinear differential operators,” presented at the ACC: American Control Conference, Boston, MA, USA, 2016, vol. 2016–July.
LibreCat: https://research-explorer.ista.ac.at/record/1320
DOI: 10.1109/ACC.2016.7526722

R. P. Chait, A. Palmer, I. Yelin, and R. Kishony, “Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments,” Nature Communications, vol. 7. Nature Publishing Group, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1332
DOI: 10.1038/ncomms10333

M. Baym et al., “Spatiotemporal microbial evolution on antibiotic landscapes,” Science, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1147–1151, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1342
DOI: 10.1126/science.aag0822

P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism outperforms elitism for crossing fitness valleys,” in Proceedings of the Genetic and Evolutionary Computation Conference 2016 , Denver, CO, USA, 2016, pp. 1163–1170.
LibreCat: https://research-explorer.ista.ac.at/record/1349
DOI: 10.1145/2908812.2908909

T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term response to selection,” PNAS, vol. 113, no. 16. National Academy of Sciences, pp. 4422–4427, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1359
DOI: 10.1073/pnas.1518830113
PMID: 27044080

M. Lagator, C. Igler, A. Moreno, C. C. Guet, and J. P. Bollback, “Epistatic interactions in the arabinose cis-regulatory element,” Molecular Biology and Evolution, vol. 33, no. 3. Oxford University Press, pp. 761–769, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1427
DOI: 10.1093/molbev/msv269

A. Beica, C. C. Guet, and T. Petrov, “Efficient reduction of kappa models by static inspection of the rule-set,” presented at the HSB: Hybrid Systems Biology, Madrid, Spain, 2016, vol. 9271, pp. 173–191.
LibreCat: https://research-explorer.ista.ac.at/record/1524
DOI: 10.1007/978-3-319-26916-0_10

A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann, “Genetic manipulation of glycogen allocation affects replicative lifespan in E coli,” PLoS Genetics, vol. 12, no. 4. Public Library of Science, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1250
DOI: 10.1371/journal.pgen.1005974

A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann, “Quantification of the growth rate reduction as a consequence of age-specific mortality.” Public Library of Science, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/9873
DOI: 10.1371/journal.pgen.1005974.s015

S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria,” Molecular Biology and Evolution, vol. 33, no. 3. Oxford University Press, pp. 770–782, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/5749
DOI: 10.1093/molbev/msv270
PMID: 26609077

P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Linear distances between Markov chains,” presented at the CONCUR: Concurrency Theory, Quebec City; Canada, 2016, vol. 59.
LibreCat: https://research-explorer.ista.ac.at/record/1093
DOI: 10.4230/LIPIcs.CONCUR.2016.20

P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Faster statistical model checking for unbounded temporal properties,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Eindhoven, The Netherlands, 2016, vol. 9636, pp. 112–129.
LibreCat: https://research-explorer.ista.ac.at/record/1234
DOI: 10.1007/978-3-662-49674-9_7

M. Pleska et al., “Bacterial autoimmunity due to a restriction-modification system,” Current Biology, vol. 26, no. 3. Cell Press, pp. 404–409, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1243
DOI: 10.1016/j.cub.2015.12.041

T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkadik, “Intrinsic limits to gene regulation by global crosstalk,” Nature Communications, vol. 7. Nature Publishing Group, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1358
DOI: 10.1038/ncomms12307

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.
LibreCat: https://research-explorer.ista.ac.at/record/1430
DOI: 10.1145/2739480.2754758

T. Paixao et al., “Toward a unifying framework for evolutionary processes,”  Journal of Theoretical Biology, vol. 383. Elsevier, pp. 28–43, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/1542
DOI: 10.1016/j.jtbi.2015.07.011

B. Geiger, T. Petrov, G. Kubin, and H. Koeppl, “Optimal Kullback-Leibler aggregation via information bottleneck,” IEEE Transactions on Automatic Control, vol. 60, no. 4. IEEE, pp. 1010–1022, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/1840
DOI: 10.1109/TAC.2014.2364971

M. Tugrul, T. Paixao, N. H. Barton, and G. Tkadik, “Other fitness models for comparison &; for interacting TFBSs.” Public Library of Science, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/9712
DOI: 10.1371/journal.pgen.1005639.s001

S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria.” Dryad, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/9719
DOI: 10.5061/dryad.cj910

M. Tugrul, T. Paixao, N. H. Barton, and G. Tkadik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public Library of Science, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/1666
DOI: 10.1371/journal.pgen.1005639

M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking gene regulatory networks,” vol. 9035. Springer, pp. 469–483, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/1835
DOI: 10.1007/978-3-662-46681-0_47

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. Public Library of Science, 2014.
LibreCat: https://research-explorer.ista.ac.at/record/1894
DOI: 10.1371/journal.pone.0106247

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. Springer, pp. 767–797, 2014.
LibreCat: https://research-explorer.ista.ac.at/record/2056
DOI: 10.1007/s00285-013-0738-7

M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Role of sex and migration in adaptation to sink environments,” Evolution, vol. 68, no. 8. Wiley, pp. 2296–2305, 2014.
LibreCat: https://research-explorer.ista.ac.at/record/2083
DOI: 10.1111/evo.12440

M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex and migration in adaptation to sink environments.” Dryad, 2014.
LibreCat: https://research-explorer.ista.ac.at/record/9747
DOI: 10.5061/dryad.s42n1

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. Royal Society, The, 2014.
LibreCat: https://research-explorer.ista.ac.at/record/2036
DOI: 10.1098/rspb.2014.1679

M. Lagator, N. Colegrave, and P. Neve, “Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses.” Dryad, 2014.
LibreCat: https://research-explorer.ista.ac.at/record/9741
DOI: 10.5061/dryad.85dn7

R. Dhar, T. Bergmiller, and A. Wagner, “Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes,” Evolution, vol. 68, no. 6. Wiley, pp. 1775–1791, 2014.
LibreCat: https://research-explorer.ista.ac.at/record/9931
DOI: 10.1111/evo.12373
PMID: 24495000

R. Dhar, T. Bergmiller, and A. Wagner, “Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes.” Dryad, 2014.
LibreCat: https://research-explorer.ista.ac.at/record/9932
DOI: 10.5061/dryad.jc402

I. Milenkovi, T. Petrov, and G. Kovács, “Patterns of hippocampal tau pathology differentiate neurodegenerative dementias,” Dementia and Geriatric Cognitive Disorders, vol. 38, no. 5–6. Karger Publishers, pp. 375–388, 2014.
LibreCat: https://research-explorer.ista.ac.at/record/1913
DOI: 10.1159/000365548
PMID: 25195847

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.
LibreCat: https://research-explorer.ista.ac.at/record/2718
DOI: 10.1145/2463372.2463568

H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila,” Genetics, vol. 195, no. 2. Genetics Society of America, pp. 527–540, 2013.
LibreCat: https://research-explorer.ista.ac.at/record/2720
DOI: 10.1534/genetics.113.153536
PMID: 23934880

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.
LibreCat: https://research-explorer.ista.ac.at/record/2719
DOI: 10.1145/2463372.2463470

Y. Wakamoto et al., “Dynamic persistence of antibiotic-stressed mycobacteria,” Science, vol. 339, no. 6115. American Association for the Advancement of Science, pp. 91–95, 2013.
LibreCat: https://research-explorer.ista.ac.at/record/499
DOI: 10.1126/science.1229858

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. The Royal Society, 2013.
LibreCat: https://research-explorer.ista.ac.at/record/2853
DOI: 10.1098/rspb.2012.3035
PMID: 23516238

D. Refardt, T. Bergmiller, and R. Kümmerli, “Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection.” Dryad, 2013.
LibreCat: https://research-explorer.ista.ac.at/record/9751
DOI: 10.5061/dryad.b1q2n

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. IEEE, pp. 310–322, 2012.
LibreCat: https://research-explorer.ista.ac.at/record/2302
DOI: 10.1109/TCBB.2012.91
PMID: 22778152

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. Wiley-Blackwell, pp. 1318–1333, 2012.
LibreCat: https://research-explorer.ista.ac.at/record/2943
DOI: 10.1111/mmi.12071

T. Bergmiller, M. Ackermann, and O. Silander, “Patterns of evolutionary conservation of essential genes correlate with their compensability,” PLoS Genetics, vol. 8, no. 6. Public Library of Science, 2012.
LibreCat: https://research-explorer.ista.ac.at/record/3130
DOI: 10.1371/journal.pgen.1002803

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.
LibreCat: https://research-explorer.ista.ac.at/record/3136
DOI: 10.1007/978-3-642-31424-7_24

H. Park, P. Oikonomou, C. C. Guet, and P. Cluzel, “Noise underlies switching behavior of the bacterial flagellum,” Biophysical Journal, vol. 101, no. 10. Elsevier, pp. 2336–2340, 2011.
LibreCat: https://research-explorer.ista.ac.at/record/6496
DOI: 10.1016/j.bpj.2011.09.040
PMID: 22098731

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.
LibreCat: https://research-explorer.ista.ac.at/record/3719
arXiv: 1011.0496

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.
LibreCat: https://research-explorer.ista.ac.at/record/3847
DOI: 10.1109/QEST.2010.33

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.
LibreCat: https://research-explorer.ista.ac.at/record/3843
DOI: 10.1109/HiBi.2009.23