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.
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.
View | DOI
 
[25]
2017 | Journal Article | IST-REx-ID: 1351
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.
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. FOGA: Foundations of Genetic Algorithms, Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms , 3–11.
View | DOI
 
[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.
View | Files available | DOI
 
[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.
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.
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. Proceedings of the Genetic and Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation conference 1163–1170.
View | Files available | DOI
 
[19]
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.
View | DOI | Download (ext.)
 
[18]
2015 | Journal Article | IST-REx-ID: 1666
Tugrul M, Paixao T, Barton NH, Tkacik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).
View | Files available | DOI
 
[17]
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.
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. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and evolutionary computation conference 1455–1462.
View | DOI | Download (ext.)
 
[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.
View | Files available | DOI | Download (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.
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.
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 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.
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.
View | DOI | Download (ext.) | PubMed | Europe PMC
 
[9]
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
 
[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).
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.
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
 

Search

Filter Publications

Display / Sort

Citation Style: IST Annual Report

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.
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.
View | DOI
 
[25]
2017 | Journal Article | IST-REx-ID: 1351
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.
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. FOGA: Foundations of Genetic Algorithms, Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms , 3–11.
View | DOI
 
[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.
View | Files available | DOI
 
[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.
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.
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. Proceedings of the Genetic and Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation conference 1163–1170.
View | Files available | DOI
 
[19]
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.
View | DOI | Download (ext.)
 
[18]
2015 | Journal Article | IST-REx-ID: 1666
Tugrul M, Paixao T, Barton NH, Tkacik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).
View | Files available | DOI
 
[17]
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.
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. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and evolutionary computation conference 1455–1462.
View | DOI | Download (ext.)
 
[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.
View | Files available | DOI | Download (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.
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.
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 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.
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.
View | DOI | Download (ext.) | PubMed | Europe PMC
 
[9]
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
 
[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).
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.
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
 

Search

Filter Publications

Display / Sort

Citation Style: IST Annual Report

Export / Embed