Tiago Paixao

Barton Group
Guet Group

32 Publications

Mark all

[32]
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.
[Published Version] View | Files available | DOI | WoS
 
[31]
2017 | Conference Paper | IST-REx-ID: 1112
Paixao T, Pérez Heredia J. 2017. An application of stochastic differential equations to evolutionary algorithms. Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. FOGA: Foundations of Genetic Algorithms, 3–11.
View | DOI
 
[30]
2017 | Research Data Reference | IST-REx-ID: 9849
Lukacisinova M, Novak S, Paixao T. 2017. Modelling and simulation details, Public Library of Science, 10.1371/journal.pcbi.1005609.s001.
[Published Version] View | Files available | DOI
 
[29]
2017 | Research Data Reference | IST-REx-ID: 9850
Lukacisinova M, Novak S, Paixao T. 2017. Extensions of the model, Public Library of Science, 10.1371/journal.pcbi.1005609.s002.
[Published Version] View | Files available | DOI
 
[28]
2017 | Research Data Reference | IST-REx-ID: 9851
Lukacisinova M, Novak S, Paixao T. 2017. Heuristic prediction for multiple stresses, Public Library of Science, 10.1371/journal.pcbi.1005609.s003.
[Published Version] View | Files available | DOI
 
[27]
2017 | Research Data Reference | IST-REx-ID: 9852
Lukacisinova M, Novak S, Paixao T. 2017. Resistance frequencies for different combination strategies, Public Library of Science, 10.1371/journal.pcbi.1005609.s004.
[Published Version] View | Files available | DOI
 
[26]
2017 | Journal Article | IST-REx-ID: 1351 | OA
Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787.
[Published Version] View | Files available | DOI | WoS
 
[25]
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.
[Published Version] View | Files available | DOI | WoS
 
[24]
2017 | Journal Article | IST-REx-ID: 1111 | OA
Heredia J, Trubenova B, Sudholt D, Paixao T. 2017. Selection limits to adaptive walks on correlated landscapes. Genetics. 205(2), 803–825.
[Published Version] View | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[23]
2017 | Journal Article | IST-REx-ID: 954 | OA
Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192.
[Published Version] View | Files available | DOI | WoS
 
[22]
2017 | Journal Article | IST-REx-ID: 696 | OA
Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609.
[Published Version] View | Files available | DOI
 
[21]
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. Proceedings of the Genetic and Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation conference, 1163–1170.
[Published Version] View | Files available | DOI
 
[20]
2016 | Journal Article | IST-REx-ID: 1359 | OA
Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 4422–4427.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[19]
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. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and evolutionary computation conference, 1455–1462.
[Preprint] View | DOI | Download Preprint (ext.)
 
[18]
2015 | Journal Article | IST-REx-ID: 1542 | OA
Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 383, 28–43.
[Published Version] View | Files available | DOI
 
[17]
2015 | Research Data Reference | IST-REx-ID: 9712
Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison & for interacting TFBSs, Public Library of Science, 10.1371/journal.pgen.1005639.s001.
[Published Version] View | Files available | DOI
 
[16]
2015 | Journal Article | IST-REx-ID: 1666 | OA
Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).
[Published Version] View | Files available | DOI
 
[15]
2015 | Conference Paper | IST-REx-ID: 1835 | OA
Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model checking gene regulatory networks. 9035, 469–483.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[14]
2014 | Journal Article | IST-REx-ID: 2169 | OA
Barton NH, Novak S, Paixao T. 2014. Diverse forms of selection in evolution and computer science. PNAS. 111(29), 10398–10399.
[Submitted Version] View | DOI | Download Submitted Version (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.
View | DOI
 
[12]
2013 | Conference Paper | IST-REx-ID: 2718 | OA
Barton NH, Paixao T. 2013. Can quantitative and population genetics help us understand evolutionary computation? Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 1573–1580.
[Submitted Version] View | Files available | DOI
 
[11]
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.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[10]
2013 | Conference Paper | IST-REx-ID: 2719
Paixao T, Barton NH. 2013. A variance decomposition approach to the analysis of genetic algorithms. Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 845–852.
View | DOI
 
[9]
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.)
 
[8]
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.
View | DOI
 
[7]
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).
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.
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.
View | DOI
 
[4]
2007 | Journal Article | IST-REx-ID: 2893
Carneiro J, Leon K, Caramalho Í, Van Den Dool C, Gardner R, Oliveira V, Bergman M, Sepúlveda N, Paixao T, Faro J, 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.
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.
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.
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.
View | DOI
 
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32 Publications

Mark all

[32]
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.
[Published Version] View | Files available | DOI | WoS
 
[31]
2017 | Conference Paper | IST-REx-ID: 1112
Paixao T, Pérez Heredia J. 2017. An application of stochastic differential equations to evolutionary algorithms. Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. FOGA: Foundations of Genetic Algorithms, 3–11.
View | DOI
 
[30]
2017 | Research Data Reference | IST-REx-ID: 9849
Lukacisinova M, Novak S, Paixao T. 2017. Modelling and simulation details, Public Library of Science, 10.1371/journal.pcbi.1005609.s001.
[Published Version] View | Files available | DOI
 
[29]
2017 | Research Data Reference | IST-REx-ID: 9850
Lukacisinova M, Novak S, Paixao T. 2017. Extensions of the model, Public Library of Science, 10.1371/journal.pcbi.1005609.s002.
[Published Version] View | Files available | DOI
 
[28]
2017 | Research Data Reference | IST-REx-ID: 9851
Lukacisinova M, Novak S, Paixao T. 2017. Heuristic prediction for multiple stresses, Public Library of Science, 10.1371/journal.pcbi.1005609.s003.
[Published Version] View | Files available | DOI
 
[27]
2017 | Research Data Reference | IST-REx-ID: 9852
Lukacisinova M, Novak S, Paixao T. 2017. Resistance frequencies for different combination strategies, Public Library of Science, 10.1371/journal.pcbi.1005609.s004.
[Published Version] View | Files available | DOI
 
[26]
2017 | Journal Article | IST-REx-ID: 1351 | OA
Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787.
[Published Version] View | Files available | DOI | WoS
 
[25]
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.
[Published Version] View | Files available | DOI | WoS
 
[24]
2017 | Journal Article | IST-REx-ID: 1111 | OA
Heredia J, Trubenova B, Sudholt D, Paixao T. 2017. Selection limits to adaptive walks on correlated landscapes. Genetics. 205(2), 803–825.
[Published Version] View | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[23]
2017 | Journal Article | IST-REx-ID: 954 | OA
Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192.
[Published Version] View | Files available | DOI | WoS
 
[22]
2017 | Journal Article | IST-REx-ID: 696 | OA
Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609.
[Published Version] View | Files available | DOI
 
[21]
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. Proceedings of the Genetic and Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation conference, 1163–1170.
[Published Version] View | Files available | DOI
 
[20]
2016 | Journal Article | IST-REx-ID: 1359 | OA
Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 4422–4427.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[19]
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. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and evolutionary computation conference, 1455–1462.
[Preprint] View | DOI | Download Preprint (ext.)
 
[18]
2015 | Journal Article | IST-REx-ID: 1542 | OA
Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 383, 28–43.
[Published Version] View | Files available | DOI
 
[17]
2015 | Research Data Reference | IST-REx-ID: 9712
Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison & for interacting TFBSs, Public Library of Science, 10.1371/journal.pgen.1005639.s001.
[Published Version] View | Files available | DOI
 
[16]
2015 | Journal Article | IST-REx-ID: 1666 | OA
Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).
[Published Version] View | Files available | DOI
 
[15]
2015 | Conference Paper | IST-REx-ID: 1835 | OA
Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model checking gene regulatory networks. 9035, 469–483.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[14]
2014 | Journal Article | IST-REx-ID: 2169 | OA
Barton NH, Novak S, Paixao T. 2014. Diverse forms of selection in evolution and computer science. PNAS. 111(29), 10398–10399.
[Submitted Version] View | DOI | Download Submitted Version (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.
View | DOI
 
[12]
2013 | Conference Paper | IST-REx-ID: 2718 | OA
Barton NH, Paixao T. 2013. Can quantitative and population genetics help us understand evolutionary computation? Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 1573–1580.
[Submitted Version] View | Files available | DOI
 
[11]
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.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[10]
2013 | Conference Paper | IST-REx-ID: 2719
Paixao T, Barton NH. 2013. A variance decomposition approach to the analysis of genetic algorithms. Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 845–852.
View | DOI
 
[9]
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.)
 
[8]
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.
View | DOI
 
[7]
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).
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.
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.
View | DOI
 
[4]
2007 | Journal Article | IST-REx-ID: 2893
Carneiro J, Leon K, Caramalho Í, Van Den Dool C, Gardner R, Oliveira V, Bergman M, Sepúlveda N, Paixao T, Faro J, 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.
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.
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.
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.
View | DOI
 
Marked Publication(s)

Search

Filter Publications

    • Display / Sort

    Citation Style: ISTA Annual Report

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