27 Publications

Mark all

[27]
2018 | Journal Article | IST-REx-ID: 723   OA
Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2018). How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica, 80(5), 1604–1633. https://doi.org/10.1007/s00453-017-0369-2
View | Files available | DOI
 
[26]
2017 | Journal Article | IST-REx-ID: 1111
Heredia, J., Trubenova, B., Sudholt, D., & Paixao, T. (2017). Selection limits to adaptive walks on correlated landscapes. Genetics, 205(2), 803–825. https://doi.org/10.1534/genetics.116.189340
View | DOI
 
[25]
2017 | Journal Article | IST-REx-ID: 1351
Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2017). Model checking the evolution of gene regulatory networks. Acta Informatica, 54(8), 765–787. https://doi.org/10.1007/s00236-016-0278-x
View | Files available | DOI
 
[24]
2017 | Conference Paper | IST-REx-ID: 1112
Paixao, T., & Pérez Heredia, J. (2017). An application of stochastic differential equations to evolutionary algorithms (pp. 3–11). Presented at the FOGA: Foundations of Genetic Algorithms, Copenhagen, Denmark: ACM. https://doi.org/10.1145/3040718.3040729
View | DOI
 
[23]
2017 | Journal Article | IST-REx-ID: 954   OA
Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C. (2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element. ELife, 6. https://doi.org/10.7554/eLife.25192
View | Files available | DOI
 
[22]
2017 | Journal Article | IST-REx-ID: 696
Lukacisinova, M., Novak, S., & Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology, 13(7). https://doi.org/10.1371/journal.pcbi.1005609
View | Files available | DOI
 
[21]
2017 | Journal Article | IST-REx-ID: 1336   OA
Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. Algorithmica, 78(2), 681–713. https://doi.org/10.1007/s00453-016-0212-1
View | Files available | DOI
 
[20]
2016 | Conference Paper | IST-REx-ID: 1349   OA
Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., & Trubenova, B. (2016). When non-elitism outperforms elitism for crossing fitness valleys. In Proceedings of the Genetic and Evolutionary Computation Conference 2016 (pp. 1163–1170). Denver, CO, USA: ACM. https://doi.org/10.1145/2908812.2908909
View | Files available | DOI
 
[19]
2016 | Journal Article | IST-REx-ID: 1359   OA
Paixao, T., & Barton, N. H. (2016). The effect of gene interactions on the long-term response to selection. PNAS, 113(16), 4422–4427. https://doi.org/10.1073/pnas.1518830113
View | DOI | Download (ext.)
 
[18]
2015 | Journal Article | IST-REx-ID: 1666
Tugrul, M., Paixao, T., Barton, N. H., & Tkacik, G. (2015). Dynamics of transcription factor binding site evolution. PLoS Genetics, 11(11). https://doi.org/10.1371/journal.pgen.1005639
View | Files available | DOI
 
[17]
2015 | Journal Article | IST-REx-ID: 1542   OA
Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology, 383, 28–43. https://doi.org/10.1016/j.jtbi.2015.07.011
View | Files available | DOI
 
[16]
2015 | Conference Paper | IST-REx-ID: 1430   OA
Paixao, T., Sudholt, D., Heredia, J., & Trubenova, B. (2015). First steps towards a runtime comparison of natural and artificial evolution. In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation (pp. 1455–1462). Madrid, Spain: ACM. https://doi.org/10.1145/2739480.2754758
View | DOI | Download (ext.)
 
[15]
2015 | Conference Paper | IST-REx-ID: 1835   OA
Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2015). Model checking gene regulatory networks. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_47
View | Files available | DOI | Download (ext.)
 
[14]
2014 | Journal Article | IST-REx-ID: 2169   OA
Barton, N. H., Novak, S., & Paixao, T. (2014). Diverse forms of selection in evolution and computer science. PNAS, 111(29), 10398–10399. https://doi.org/10.1073/pnas.1410107111
View | DOI | Download (ext.)
 
[13]
2014 | Journal Article | IST-REx-ID: 2252
Phadke, S., Paixao, T., Pham, T., Pham, S., & Zufall, R. (2014). Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity, 105(1), 130–135. https://doi.org/10.1093/jhered/est063
View | DOI
 
[12]
2013 | Journal Article | IST-REx-ID: 2900
Azevedo, R., Lohaus, R., & Paixao, T. (2013). Networking networks. Evolution & Development, 10(5), 514–515.
View | Download (ext.)
 
[11]
2013 | Conference Paper | IST-REx-ID: 2718   OA
Barton, N. H., & Paixao, T. (2013). Can quantitative and population genetics help us understand evolutionary computation? In Proceedings of the 15th annual conference on Genetic and evolutionary computation (pp. 1573–1580). Amsterdam, Netherlands: ACM. https://doi.org/10.1145/2463372.2463568
View | Files available | DOI
 
[10]
2013 | Journal Article | IST-REx-ID: 2720   OA
Long, H., Paixao, T., Azevedo, R., & Zufall, R. (2013). Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics, 195(2), 527–540. https://doi.org/10.1534/genetics.113.153536
View | DOI | Download (ext.) | PubMed | Europe PMC
 
[9]
2013 | Conference Paper | IST-REx-ID: 2719
Paixao, T., & Barton, N. H. (2013). A variance decomposition approach to the analysis of genetic algorithms. In Proceedings of the 15th annual conference on Genetic and evolutionary computation (pp. 845–852). Amsterdam, Netherlands: ACM. https://doi.org/10.1145/2463372.2463470
View | DOI
 
[8]
2011 | Journal Article | IST-REx-ID: 2897
Paixao, T., & Azevedo, R. (2011). Redundancy and the Evolution of Cis Regulatory Element Multiplicity. PLoS Computational Biology, 6(7). https://doi.org/10.1371/journal.pcbi.1000848
View | DOI
 
[7]
2011 | Journal Article | IST-REx-ID: 2898
Paixao, T., Phadke, S., Azevedo, R., & Zufall, R. (2011). Sex ratio evolution under probabilistic sex determination. Evolution; International Journal of Organic Evolution, 65(7), 2050–2060. https://doi.org/10.1111/j.1558-5646.2011.01266.x
View | DOI
 
[6]
2010 | Journal Article | IST-REx-ID: 2899
Cooper, T., Paixao, T., & Heinemann, J. (2010). Within host competition selects for plasmid encoded toxin–antitoxin systems. Proc R Soc B, 277(1697), 3149–3155. https://doi.org/10.1098/rspb.2010.0831
View | DOI
 
[5]
2008 | Journal Article | IST-REx-ID: 2892
Azevedo, R., Lohaus, R., & Paixao, T. (2008). Networking networks. Evolution & Development, 10(5), 514–515. https://doi.org/10.1111/j.1525-142X.2008.00265.x
View | DOI
 
[4]
2007 | Journal Article | IST-REx-ID: 2893
Carneiro, J., Leon, K., Caramalho, Í., Van Den Dool, C., Gardner, R., Oliveira, V., … Demengeot, J. (2007). When three is not a crowd a Crossregulation Model of the dynamics and repertoire selection of regulatory CD4 T cells. Immunological Reviews, 216(1), 48–68. https://doi.org/10.1111/j.1600-065X.2007.00487.x
View | DOI
 
[3]
2007 | Journal Article | IST-REx-ID: 2896
Paixao, T., Carvalho, T., Calado, D., & Carneiro, J. (2007). Quantitative insights into stochastic monoallelic expression of cytokine genes. Immunology and Cell Biology, 85(4), 315–322. https://doi.org/10.1038/sj.icb.7100057
View | DOI
 
[2]
2006 | Journal Article | IST-REx-ID: 2894
Calado, D., Paixao, T., Holmberg, D., & Haury, M. (2006). Stochastic Monoallelic Expression of IL 10 in T Cells. Journal of Immunology, 177(8), 5358–5364. https://doi.org/10.4049/jimmunol.177.8.5358
View | DOI
 
[1]
2005 | Journal Article | IST-REx-ID: 2895
Carneiro, J., Paixao, T., Milutinovic, D., Sousa, J., Leon, K., Gardner, R., & Faro, J. (2005). Immunological self tolerance: Lessons from mathematical modeling. Journal of Computational and Applied Mathematics, 184(1), 77–100. https://doi.org/10.1016/j.cam.2004.10.025
View | DOI
 

Search

Filter Publications

Display / Sort

Citation Style: APA

Export / Embed

27 Publications

Mark all

[27]
2018 | Journal Article | IST-REx-ID: 723   OA
Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2018). How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica, 80(5), 1604–1633. https://doi.org/10.1007/s00453-017-0369-2
View | Files available | DOI
 
[26]
2017 | Journal Article | IST-REx-ID: 1111
Heredia, J., Trubenova, B., Sudholt, D., & Paixao, T. (2017). Selection limits to adaptive walks on correlated landscapes. Genetics, 205(2), 803–825. https://doi.org/10.1534/genetics.116.189340
View | DOI
 
[25]
2017 | Journal Article | IST-REx-ID: 1351
Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2017). Model checking the evolution of gene regulatory networks. Acta Informatica, 54(8), 765–787. https://doi.org/10.1007/s00236-016-0278-x
View | Files available | DOI
 
[24]
2017 | Conference Paper | IST-REx-ID: 1112
Paixao, T., & Pérez Heredia, J. (2017). An application of stochastic differential equations to evolutionary algorithms (pp. 3–11). Presented at the FOGA: Foundations of Genetic Algorithms, Copenhagen, Denmark: ACM. https://doi.org/10.1145/3040718.3040729
View | DOI
 
[23]
2017 | Journal Article | IST-REx-ID: 954   OA
Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C. (2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element. ELife, 6. https://doi.org/10.7554/eLife.25192
View | Files available | DOI
 
[22]
2017 | Journal Article | IST-REx-ID: 696
Lukacisinova, M., Novak, S., & Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology, 13(7). https://doi.org/10.1371/journal.pcbi.1005609
View | Files available | DOI
 
[21]
2017 | Journal Article | IST-REx-ID: 1336   OA
Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. Algorithmica, 78(2), 681–713. https://doi.org/10.1007/s00453-016-0212-1
View | Files available | DOI
 
[20]
2016 | Conference Paper | IST-REx-ID: 1349   OA
Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., & Trubenova, B. (2016). When non-elitism outperforms elitism for crossing fitness valleys. In Proceedings of the Genetic and Evolutionary Computation Conference 2016 (pp. 1163–1170). Denver, CO, USA: ACM. https://doi.org/10.1145/2908812.2908909
View | Files available | DOI
 
[19]
2016 | Journal Article | IST-REx-ID: 1359   OA
Paixao, T., & Barton, N. H. (2016). The effect of gene interactions on the long-term response to selection. PNAS, 113(16), 4422–4427. https://doi.org/10.1073/pnas.1518830113
View | DOI | Download (ext.)
 
[18]
2015 | Journal Article | IST-REx-ID: 1666
Tugrul, M., Paixao, T., Barton, N. H., & Tkacik, G. (2015). Dynamics of transcription factor binding site evolution. PLoS Genetics, 11(11). https://doi.org/10.1371/journal.pgen.1005639
View | Files available | DOI
 
[17]
2015 | Journal Article | IST-REx-ID: 1542   OA
Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology, 383, 28–43. https://doi.org/10.1016/j.jtbi.2015.07.011
View | Files available | DOI
 
[16]
2015 | Conference Paper | IST-REx-ID: 1430   OA
Paixao, T., Sudholt, D., Heredia, J., & Trubenova, B. (2015). First steps towards a runtime comparison of natural and artificial evolution. In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation (pp. 1455–1462). Madrid, Spain: ACM. https://doi.org/10.1145/2739480.2754758
View | DOI | Download (ext.)
 
[15]
2015 | Conference Paper | IST-REx-ID: 1835   OA
Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2015). Model checking gene regulatory networks. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_47
View | Files available | DOI | Download (ext.)
 
[14]
2014 | Journal Article | IST-REx-ID: 2169   OA
Barton, N. H., Novak, S., & Paixao, T. (2014). Diverse forms of selection in evolution and computer science. PNAS, 111(29), 10398–10399. https://doi.org/10.1073/pnas.1410107111
View | DOI | Download (ext.)
 
[13]
2014 | Journal Article | IST-REx-ID: 2252
Phadke, S., Paixao, T., Pham, T., Pham, S., & Zufall, R. (2014). Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity, 105(1), 130–135. https://doi.org/10.1093/jhered/est063
View | DOI
 
[12]
2013 | Journal Article | IST-REx-ID: 2900
Azevedo, R., Lohaus, R., & Paixao, T. (2013). Networking networks. Evolution & Development, 10(5), 514–515.
View | Download (ext.)
 
[11]
2013 | Conference Paper | IST-REx-ID: 2718   OA
Barton, N. H., & Paixao, T. (2013). Can quantitative and population genetics help us understand evolutionary computation? In Proceedings of the 15th annual conference on Genetic and evolutionary computation (pp. 1573–1580). Amsterdam, Netherlands: ACM. https://doi.org/10.1145/2463372.2463568
View | Files available | DOI
 
[10]
2013 | Journal Article | IST-REx-ID: 2720   OA
Long, H., Paixao, T., Azevedo, R., & Zufall, R. (2013). Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics, 195(2), 527–540. https://doi.org/10.1534/genetics.113.153536
View | DOI | Download (ext.) | PubMed | Europe PMC
 
[9]
2013 | Conference Paper | IST-REx-ID: 2719
Paixao, T., & Barton, N. H. (2013). A variance decomposition approach to the analysis of genetic algorithms. In Proceedings of the 15th annual conference on Genetic and evolutionary computation (pp. 845–852). Amsterdam, Netherlands: ACM. https://doi.org/10.1145/2463372.2463470
View | DOI
 
[8]
2011 | Journal Article | IST-REx-ID: 2897
Paixao, T., & Azevedo, R. (2011). Redundancy and the Evolution of Cis Regulatory Element Multiplicity. PLoS Computational Biology, 6(7). https://doi.org/10.1371/journal.pcbi.1000848
View | DOI
 
[7]
2011 | Journal Article | IST-REx-ID: 2898
Paixao, T., Phadke, S., Azevedo, R., & Zufall, R. (2011). Sex ratio evolution under probabilistic sex determination. Evolution; International Journal of Organic Evolution, 65(7), 2050–2060. https://doi.org/10.1111/j.1558-5646.2011.01266.x
View | DOI
 
[6]
2010 | Journal Article | IST-REx-ID: 2899
Cooper, T., Paixao, T., & Heinemann, J. (2010). Within host competition selects for plasmid encoded toxin–antitoxin systems. Proc R Soc B, 277(1697), 3149–3155. https://doi.org/10.1098/rspb.2010.0831
View | DOI
 
[5]
2008 | Journal Article | IST-REx-ID: 2892
Azevedo, R., Lohaus, R., & Paixao, T. (2008). Networking networks. Evolution & Development, 10(5), 514–515. https://doi.org/10.1111/j.1525-142X.2008.00265.x
View | DOI
 
[4]
2007 | Journal Article | IST-REx-ID: 2893
Carneiro, J., Leon, K., Caramalho, Í., Van Den Dool, C., Gardner, R., Oliveira, V., … Demengeot, J. (2007). When three is not a crowd a Crossregulation Model of the dynamics and repertoire selection of regulatory CD4 T cells. Immunological Reviews, 216(1), 48–68. https://doi.org/10.1111/j.1600-065X.2007.00487.x
View | DOI
 
[3]
2007 | Journal Article | IST-REx-ID: 2896
Paixao, T., Carvalho, T., Calado, D., & Carneiro, J. (2007). Quantitative insights into stochastic monoallelic expression of cytokine genes. Immunology and Cell Biology, 85(4), 315–322. https://doi.org/10.1038/sj.icb.7100057
View | DOI
 
[2]
2006 | Journal Article | IST-REx-ID: 2894
Calado, D., Paixao, T., Holmberg, D., & Haury, M. (2006). Stochastic Monoallelic Expression of IL 10 in T Cells. Journal of Immunology, 177(8), 5358–5364. https://doi.org/10.4049/jimmunol.177.8.5358
View | DOI
 
[1]
2005 | Journal Article | IST-REx-ID: 2895
Carneiro, J., Paixao, T., Milutinovic, D., Sousa, J., Leon, K., Gardner, R., & Faro, J. (2005). Immunological self tolerance: Lessons from mathematical modeling. Journal of Computational and Applied Mathematics, 184(1), 77–100. https://doi.org/10.1016/j.cam.2004.10.025
View | DOI
 

Search

Filter Publications

Display / Sort

Citation Style: APA

Export / Embed