Linear distances between Markov chains
P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1093
DOI: 10.4230/LIPIcs.CONCUR.2016.20

Faster statistical model checking for unbounded temporal properties
P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Springer, 2016, pp. 112–129.
LibreCat: https://research-explorer.ista.ac.at/record/1234
DOI: 10.1007/978-3-662-49674-9_7

Bacterial autoimmunity due to a restriction-modification system
M. Pleska, L. Qian, R. Okura, T. Bergmiller, Y. Wakamoto, E. Kussell, C.C. Guet, Current Biology 26 (2016) 404–409.
LibreCat: https://research-explorer.ista.ac.at/record/1243
DOI: 10.1016/j.cub.2015.12.041

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

First steps towards a runtime comparison of natural and artificial evolution
T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–1462.
LibreCat: https://research-explorer.ista.ac.at/record/1430
DOI: 10.1145/2739480.2754758

Toward a unifying framework for evolutionary processes
T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüf, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova,  Journal of Theoretical Biology 383 (2015) 28–43.
LibreCat: https://research-explorer.ista.ac.at/record/1542
DOI: 10.1016/j.jtbi.2015.07.011

Optimal Kullback-Leibler aggregation via information bottleneck
B. Geiger, T. Petrov, G. Kubin, H. Koeppl, IEEE Transactions on Automatic Control 60 (2015) 1010–1022.
LibreCat: https://research-explorer.ista.ac.at/record/1840
DOI: 10.1109/TAC.2014.2364971

Other fitness models for comparison & for interacting TFBSs
M. Tugrul, T. Paixao, N.H. Barton, G. Tkadik, (2015).
LibreCat: https://research-explorer.ista.ac.at/record/9712
DOI: 10.1371/journal.pgen.1005639.s001

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

Dynamics of transcription factor binding site evolution
M. Tugrul, T. Paixao, N.H. Barton, G. Tkadik, PLoS Genetics 11 (2015).
LibreCat: https://research-explorer.ista.ac.at/record/1666
DOI: 10.1371/journal.pgen.1005639

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

Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA
A. Grabowska, E. Wywia, S. Dunin Horkawicz, A. asica, M. Wösten, A.A. Nagy-Staron, R. Godlewska, K. Bocian Ostrzycka, K. Piekowska, P. aniewski, J. Bujnicki, J. Van Putten, E. Jagusztyn Krynicka, PLoS One 9 (2014).
LibreCat: https://research-explorer.ista.ac.at/record/1894
DOI: 10.1371/journal.pone.0106247

Markov chain aggregation and its applications to combinatorial reaction networks
A. Ganguly, T. Petrov, H. Koeppl, Journal of Mathematical Biology 69 (2014) 767–797.
LibreCat: https://research-explorer.ista.ac.at/record/2056
DOI: 10.1007/s00285-013-0738-7

Role of sex and migration in adaptation to sink environments
M. Lagator, A. Morgan, P. Neve, N. Colegrave, Evolution 68 (2014) 2296–2305.
LibreCat: https://research-explorer.ista.ac.at/record/2083
DOI: 10.1111/evo.12440

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

Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses
M. Lagator, N. Colegrave, P. Neve, Proceedings of the Royal Society of London Series B Biological Sciences 281 (2014).
LibreCat: https://research-explorer.ista.ac.at/record/2036
DOI: 10.1098/rspb.2014.1679

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

Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes
R. Dhar, T. Bergmiller, A. Wagner, Evolution 68 (2014) 1775–1791.
LibreCat: https://research-explorer.ista.ac.at/record/9931
DOI: 10.1111/evo.12373
PMID: 24495000

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

Patterns of hippocampal tau pathology differentiate neurodegenerative dementias
I. Milenkovi, T. Petrov, G. Kovács, Dementia and Geriatric Cognitive Disorders 38 (2014) 375–388.
LibreCat: https://research-explorer.ista.ac.at/record/1913
DOI: 10.1159/000365548
PMID: 25195847

Can quantitative and population genetics help us understand evolutionary computation?
N.H. Barton, T. Paixao, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–1580.
LibreCat: https://research-explorer.ista.ac.at/record/2718
DOI: 10.1145/2463372.2463568

Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila
H. Long, T. Paixao, R. Azevedo, R. Zufall, Genetics 195 (2013) 527–540.
LibreCat: https://research-explorer.ista.ac.at/record/2720
DOI: 10.1534/genetics.113.153536
PMID: 23934880

A variance decomposition approach to the analysis of genetic algorithms
T. Paixao, N.H. Barton, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–852.
LibreCat: https://research-explorer.ista.ac.at/record/2719
DOI: 10.1145/2463372.2463470

Dynamic persistence of antibiotic-stressed mycobacteria
Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler, J. Mckinney, Science 339 (2013) 91–95.
LibreCat: https://research-explorer.ista.ac.at/record/499
DOI: 10.1126/science.1229858

Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection
D. Refardt, T. Bergmiller, R. Kümmerli, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013).
LibreCat: https://research-explorer.ista.ac.at/record/2853
DOI: 10.1098/rspb.2012.3035
PMID: 23516238

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

The propagation approach for computing biochemical reaction networks
T.A. Henzinger, M. Mateescu, IEEE ACM Transactions on Computational Biology and Bioinformatics 10 (2012) 310–322.
LibreCat: https://research-explorer.ista.ac.at/record/2302
DOI: 10.1109/TCBB.2012.91
PMID: 22778152

Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions
N. Hadizadeh Yazdi, C.C. Guet, R. Johnson, J. Marko, Molecular Microbiology 86 (2012) 1318–1333.
LibreCat: https://research-explorer.ista.ac.at/record/2943
DOI: 10.1111/mmi.12071

Patterns of evolutionary conservation of essential genes correlate with their compensability
T. Bergmiller, M. Ackermann, O. Silander, PLoS Genetics 8 (2012).
LibreCat: https://research-explorer.ista.ac.at/record/3130
DOI: 10.1371/journal.pgen.1002803

Delayed continuous time Markov chains for genetic regulatory circuits
C.C. Guet, A. Gupta, T.A. Henzinger, M. Mateescu, A. Sezgin, in:, Springer, 2012, pp. 294–309.
LibreCat: https://research-explorer.ista.ac.at/record/3136
DOI: 10.1007/978-3-642-31424-7_24

Noise underlies switching behavior of the bacterial flagellum
H. Park, P. Oikonomou, C.C. Guet, P. Cluzel, Biophysical Journal 101 (2011) 2336–2340.
LibreCat: https://research-explorer.ista.ac.at/record/6496
DOI: 10.1016/j.bpj.2011.09.040
PMID: 22098731

Lumpability abstractions of rule-based systems
J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, in:, Open Publishing Association, 2010, pp. 142–161.
LibreCat: https://research-explorer.ista.ac.at/record/3719
arXiv: 1011.0496

SABRE: A tool for the stochastic analysis of biochemical reaction networks
F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2010, pp. 193–194.
LibreCat: https://research-explorer.ista.ac.at/record/3847
DOI: 10.1109/QEST.2010.33

Fast adaptive uniformization of the chemical master equation
F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2009, pp. 118–127.
LibreCat: https://research-explorer.ista.ac.at/record/3843
DOI: 10.1109/HiBi.2009.23