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.

Towards a runtime comparison of natural and artificial evolution
T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713.

Selection limits to adaptive walks on correlated landscapes
J. Heredia, B. Trubenova, D. Sudholt, T. Paixao, Genetics 205 (2017) 803–825.

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.

Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes
M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).

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).

Modelling and simulation details
M. Lukacisinova, S. Novak, T. Paixao, (2017).

Extensions of the model
M. Lukacisinova, S. Novak, T. Paixao, (2017).

Heuristic prediction for multiple stresses
M. Lukacisinova, S. Novak, T. Paixao, (2017).

Resistance frequencies for different combination strategies
M. Lukacisinova, S. Novak, T. Paixao, (2017).

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.

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.

The effect of gene interactions on the long-term response to selection
T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427.

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.

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.

Dynamics of transcription factor binding site evolution
M. Tugrul, T. Paixao, N.H. Barton, G. Tkadik, PLoS Genetics 11 (2015).

Model checking gene regulatory networks
M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, 9035 (2015) 469–483.

Other fitness models for comparison & for interacting TFBSs
M. Tugrul, T. Paixao, N.H. Barton, G. Tkadik, (2015).

Diverse forms of selection in evolution and computer science
N.H. Barton, S. Novak, T. Paixao, PNAS 111 (2014) 10398–10399.

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.