How to escape local optima in black box optimisation when non elitism outperforms elitism
P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 80 (2018) 1604–1633.
LibreCat: https://research-explorer.ista.ac.at/record/723
DOI: 10.1007/s00453-017-0369-2
WoS: 000428239300010

An application of stochastic differential equations to evolutionary algorithms
T. Paixao, J. Pérez Heredia, in:, Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11.
LibreCat: https://research-explorer.ista.ac.at/record/1112
DOI: 10.1145/3040718.3040729

Modelling and simulation details
M. Lukacisinova, S. Novak, T. Paixao, (2017).
LibreCat: https://research-explorer.ista.ac.at/record/9849
DOI: 10.1371/journal.pcbi.1005609.s001

Extensions of the model
M. Lukacisinova, S. Novak, T. Paixao, (2017).
LibreCat: https://research-explorer.ista.ac.at/record/9850
DOI: 10.1371/journal.pcbi.1005609.s002

Heuristic prediction for multiple stresses
M. Lukacisinova, S. Novak, T. Paixao, (2017).
LibreCat: https://research-explorer.ista.ac.at/record/9851
DOI: 10.1371/journal.pcbi.1005609.s003

Resistance frequencies for different combination strategies
M. Lukacisinova, S. Novak, T. Paixao, (2017).
LibreCat: https://research-explorer.ista.ac.at/record/9852
DOI: 10.1371/journal.pcbi.1005609.s004

Model checking the evolution of gene regulatory networks
M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta Informatica 54 (2017) 765–787.
LibreCat: https://research-explorer.ista.ac.at/record/1351
DOI: 10.1007/s00236-016-0278-x
WoS: 000414343200003

Towards a runtime comparison of natural and artificial evolution
T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713.
LibreCat: https://research-explorer.ista.ac.at/record/1336
DOI: 10.1007/s00453-016-0212-1
WoS: 000400379500013

Selection limits to adaptive walks on correlated landscapes
J. Heredia, B. Trubenova, D. Sudholt, T. Paixao, Genetics 205 (2017) 803–825.
LibreCat: https://research-explorer.ista.ac.at/record/1111
DOI: 10.1534/genetics.116.189340
WoS: 000394144900025
PMID: 27881471

On the mechanistic nature of epistasis in a canonical cis-regulatory element
M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).
LibreCat: https://research-explorer.ista.ac.at/record/954
DOI: 10.7554/eLife.25192
WoS: 000404024800001

Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes
M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).
LibreCat: https://research-explorer.ista.ac.at/record/696
DOI: 10.1371/journal.pcbi.1005609

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

The effect of gene interactions on the long-term response to selection
T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427.
LibreCat: https://research-explorer.ista.ac.at/record/1359
DOI: 10.1073/pnas.1518830113
PMID: 27044080

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

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

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

Diverse forms of selection in evolution and computer science
N.H. Barton, S. Novak, T. Paixao, PNAS 111 (2014) 10398–10399.
LibreCat: https://research-explorer.ista.ac.at/record/2169
DOI: 10.1073/pnas.1410107111

Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila
S. Phadke, T. Paixao, T. Pham, S. Pham, R. Zufall, Journal of Heredity 105 (2014) 130–135.
LibreCat: https://research-explorer.ista.ac.at/record/2252
DOI: 10.1093/jhered/est063

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

Networking networks
R. Azevedo, R. Lohaus, T. Paixao, Evolution &; Development 10 (2013) 514–515.
LibreCat: https://research-explorer.ista.ac.at/record/2900

Sex ratio evolution under probabilistic sex determination
T. Paixao, S. Phadke, R. Azevedo, R. Zufall, Evolution; International Journal of Organic Evolution 65 (2011) 2050–2060.
LibreCat: https://research-explorer.ista.ac.at/record/2898
DOI: 10.1111/j.1558-5646.2011.01266.x

Redundancy and the Evolution of Cis Regulatory Element Multiplicity
T. Paixao, R. Azevedo, PLoS Computational Biology 6 (2011).
LibreCat: https://research-explorer.ista.ac.at/record/2897
DOI: 10.1371/journal.pcbi.1000848

Within host competition selects for plasmid encoded toxin–antitoxin systems
T. Cooper, T. Paixao, J. Heinemann, Proc R Soc B 277 (2010) 3149–3155.
LibreCat: https://research-explorer.ista.ac.at/record/2899
DOI: 10.1098/rspb.2010.0831

Networking networks
R. Azevedo, R. Lohaus, T. Paixao, Evolution &; Development 10 (2008) 514–515.
LibreCat: https://research-explorer.ista.ac.at/record/2892
DOI: 10.1111/j.1525-142X.2008.00265.x

When three is not a crowd a Crossregulation Model of the dynamics and repertoire selection of regulatory C T cells
J. Carneiro, K. Leon, Í. Caramalho, C. Van Den Dool, R. Gardner, V. Oliveira, M. Bergman, N. Sepúlveda, T. Paixao, J. Faro, J. Demengeot, Immunological Reviews 216 (2007) 48–68.
LibreCat: https://research-explorer.ista.ac.at/record/2893
DOI: 10.1111/j.1600-065X.2007.00487.x

Quantitative insights into stochastic monoallelic expression of cytokine genes
T. Paixao, T. Carvalho, D. Calado, J. Carneiro, Immunology and Cell Biology 85 (2007) 315–322.
LibreCat: https://research-explorer.ista.ac.at/record/2896
DOI: 10.1038/sj.icb.7100057

Stochastic Monoallelic Expression of IL 10 in T Cells
D. Calado, T. Paixao, D. Holmberg, M. Haury, Journal of Immunology 177 (2006) 5358–5364.
LibreCat: https://research-explorer.ista.ac.at/record/2894
DOI: 10.4049/jimmunol.177.8.5358 

Immunological self tolerance: Lessons from mathematical modeling
J. Carneiro, T. Paixao, D. Milutinovic, J. Sousa, K. Leon, R. Gardner, J. Faro, Journal of Computational and Applied Mathematics 184 (2005) 77–100.
LibreCat: https://research-explorer.ista.ac.at/record/2895
DOI: 10.1016/j.cam.2004.10.025