Tiago Paixao

Barton Group
Guet Group

32 Publications

Mark all

[32]
2018 | Published | Journal Article | IST-REx-ID: 723 | OA
Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 2018;80(5):1604-1633. doi:10.1007/s00453-017-0369-2
[Published Version] View | Files available | DOI | WoS
 
[31]
2017 | Published | Journal Article | IST-REx-ID: 954 | OA
Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192
[Published Version] View | Files available | DOI | WoS
 
[30]
2017 | Research Data Reference | IST-REx-ID: 9849
Lukacisinova M, Novak S, Paixao T. Modelling and simulation details. 2017. doi: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. Extensions of the model. 2017. doi: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. Heuristic prediction for multiple stresses. 2017. doi: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. Resistance frequencies for different combination strategies. 2017. doi:10.1371/journal.pcbi.1005609.s004
[Published Version] View | Files available | DOI
 
[26]
2017 | Published | Journal Article | IST-REx-ID: 1336 | OA
Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 2017;78(2):681-713. doi:10.1007/s00453-016-0212-1
[Published Version] View | Files available | DOI | WoS
 
[25]
2017 | Published | Journal Article | IST-REx-ID: 1351 | OA
Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking the evolution of gene regulatory networks. Acta Informatica. 2017;54(8):765-787. doi:10.1007/s00236-016-0278-x
[Published Version] View | Files available | DOI | WoS
 
[24]
2017 | Published | Journal Article | IST-REx-ID: 1111 | OA
Heredia J, Trubenova B, Sudholt D, Paixao T. Selection limits to adaptive walks on correlated landscapes. Genetics. 2017;205(2):803-825. doi:10.1534/genetics.116.189340
[Published Version] View | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[23]
2017 | Published | Conference Paper | IST-REx-ID: 1112
Paixao T, Pérez Heredia J. An application of stochastic differential equations to evolutionary algorithms. In: Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. ACM; 2017:3-11. doi:10.1145/3040718.3040729
View | DOI
 
[22]
2017 | Published | Journal Article | IST-REx-ID: 696 | OA
Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 2017;13(7). doi:10.1371/journal.pcbi.1005609
[Published Version] View | Files available | DOI
 
[21]
2016 | Published | Conference Paper | IST-REx-ID: 1349 | OA
Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. When non-elitism outperforms elitism for crossing fitness valleys. In: Proceedings of the Genetic and Evolutionary Computation Conference 2016 . ACM; 2016:1163-1170. doi:10.1145/2908812.2908909
[Published Version] View | Files available | DOI
 
[20]
2016 | Published | Journal Article | IST-REx-ID: 1359 | OA
Paixao T, Barton NH. The effect of gene interactions on the long-term response to selection. PNAS. 2016;113(16):4422-4427. doi:10.1073/pnas.1518830113
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[19]
2015 | Research Data Reference | IST-REx-ID: 9712
Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison & for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001
[Published Version] View | Files available | DOI
 
[18]
2015 | Published | Conference Paper | IST-REx-ID: 1430 | OA
Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime comparison of natural and artificial evolution. In: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. ACM; 2015:1455-1462. doi:10.1145/2739480.2754758
[Preprint] View | DOI | Download Preprint (ext.)
 
[17]
2015 | Published | Journal Article | IST-REx-ID: 1542 | OA
Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011
[Published Version] View | Files available | DOI
 
[16]
2015 | Published | Conference Paper | IST-REx-ID: 1835 | OA
Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking gene regulatory networks. 2015;9035:469-483. doi:10.1007/978-3-662-46681-0_47
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[15]
2015 | Published | Journal Article | IST-REx-ID: 1666 | OA
Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639
[Published Version] View | Files available | DOI
 
[14]
2014 | Published | Journal Article | IST-REx-ID: 2252
Phadke S, Paixao T, Pham T, Pham S, Zufall R. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. 2014;105(1):130-135. doi:10.1093/jhered/est063
View | DOI
 
[13]
2014 | Published | Journal Article | IST-REx-ID: 2169 | OA
Barton NH, Novak S, Paixao T. Diverse forms of selection in evolution and computer science. PNAS. 2014;111(29):10398-10399. doi:10.1073/pnas.1410107111
[Submitted Version] View | DOI | Download Submitted Version (ext.)
 
[12]
2013 | Published | Conference Paper | IST-REx-ID: 2718 | OA
Barton NH, Paixao T. Can quantitative and population genetics help us understand evolutionary computation? In: Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation. ACM; 2013:1573-1580. doi:10.1145/2463372.2463568
[Submitted Version] View | Files available | DOI
 
[11]
2013 | Published | Conference Paper | IST-REx-ID: 2719
Paixao T, Barton NH. A variance decomposition approach to the analysis of genetic algorithms. In: Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation. ACM; 2013:845-852. doi:10.1145/2463372.2463470
View | DOI
 
[10]
2013 | Published | Journal Article | IST-REx-ID: 2720 | OA
Long H, Paixao T, Azevedo R, Zufall R. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 2013;195(2):527-540. doi:10.1534/genetics.113.153536
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[9]
2013 | Published | Journal Article | IST-REx-ID: 2900
Azevedo R, Lohaus R, Paixao T. Networking networks. Evolution & Development. 2013;10(5):514-515.
View | Download (ext.)
 
[8]
2011 | Published | Journal Article | IST-REx-ID: 2897
Paixao T, Azevedo R. Redundancy and the Evolution of Cis Regulatory Element Multiplicity. PLoS Computational Biology. 2011;6(7). doi:10.1371/journal.pcbi.1000848
View | DOI
 
[7]
2011 | Published | Journal Article | IST-REx-ID: 2898
Paixao T, Phadke S, Azevedo R, Zufall R. Sex ratio evolution under probabilistic sex determination. Evolution; International Journal of Organic Evolution. 2011;65(7):2050-2060. doi:10.1111/j.1558-5646.2011.01266.x
View | DOI
 
[6]
2010 | Published | Journal Article | IST-REx-ID: 2899
Cooper T, Paixao T, Heinemann J. Within host competition selects for plasmid encoded toxin–antitoxin systems. Proc R Soc B. 2010;277(1697):3149-3155. doi:10.1098/rspb.2010.0831
View | DOI
 
[5]
2008 | Published | Journal Article | IST-REx-ID: 2892
Azevedo R, Lohaus R, Paixao T. Networking networks. Evolution & Development. 2008;10(5):514-515. doi:10.1111/j.1525-142X.2008.00265.x
View | DOI
 
[4]
2007 | Published | Journal Article | IST-REx-ID: 2893
Carneiro J, Leon K, Caramalho Í, et al. When three is not a crowd a Crossregulation Model of the dynamics and repertoire selection of regulatory CD4 T cells. Immunological Reviews. 2007;216(1):48-68. doi:10.1111/j.1600-065X.2007.00487.x
View | DOI
 
[3]
2007 | Published | Journal Article | IST-REx-ID: 2896
Paixao T, Carvalho T, Calado D, Carneiro J. Quantitative insights into stochastic monoallelic expression of cytokine genes. Immunology and Cell Biology. 2007;85(4):315-322. doi:10.1038/sj.icb.7100057
View | DOI
 
[2]
2006 | Published | Journal Article | IST-REx-ID: 2894
Calado D, Paixao T, Holmberg D, Haury M. Stochastic Monoallelic Expression of IL 10 in T Cells. Journal of Immunology. 2006;177(8):5358-5364. doi:10.4049/jimmunol.177.8.5358
View | DOI
 
[1]
2005 | Published | Journal Article | IST-REx-ID: 2895
Carneiro J, Paixao T, Milutinovic D, et al. Immunological self tolerance: Lessons from mathematical modeling. Journal of Computational and Applied Mathematics. 2005;184(1):77-100. doi:10.1016/j.cam.2004.10.025
View | DOI
 
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32 Publications

Mark all

[32]
2018 | Published | Journal Article | IST-REx-ID: 723 | OA
Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 2018;80(5):1604-1633. doi:10.1007/s00453-017-0369-2
[Published Version] View | Files available | DOI | WoS
 
[31]
2017 | Published | Journal Article | IST-REx-ID: 954 | OA
Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192
[Published Version] View | Files available | DOI | WoS
 
[30]
2017 | Research Data Reference | IST-REx-ID: 9849
Lukacisinova M, Novak S, Paixao T. Modelling and simulation details. 2017. doi: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. Extensions of the model. 2017. doi: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. Heuristic prediction for multiple stresses. 2017. doi: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. Resistance frequencies for different combination strategies. 2017. doi:10.1371/journal.pcbi.1005609.s004
[Published Version] View | Files available | DOI
 
[26]
2017 | Published | Journal Article | IST-REx-ID: 1336 | OA
Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 2017;78(2):681-713. doi:10.1007/s00453-016-0212-1
[Published Version] View | Files available | DOI | WoS
 
[25]
2017 | Published | Journal Article | IST-REx-ID: 1351 | OA
Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking the evolution of gene regulatory networks. Acta Informatica. 2017;54(8):765-787. doi:10.1007/s00236-016-0278-x
[Published Version] View | Files available | DOI | WoS
 
[24]
2017 | Published | Journal Article | IST-REx-ID: 1111 | OA
Heredia J, Trubenova B, Sudholt D, Paixao T. Selection limits to adaptive walks on correlated landscapes. Genetics. 2017;205(2):803-825. doi:10.1534/genetics.116.189340
[Published Version] View | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[23]
2017 | Published | Conference Paper | IST-REx-ID: 1112
Paixao T, Pérez Heredia J. An application of stochastic differential equations to evolutionary algorithms. In: Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. ACM; 2017:3-11. doi:10.1145/3040718.3040729
View | DOI
 
[22]
2017 | Published | Journal Article | IST-REx-ID: 696 | OA
Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 2017;13(7). doi:10.1371/journal.pcbi.1005609
[Published Version] View | Files available | DOI
 
[21]
2016 | Published | Conference Paper | IST-REx-ID: 1349 | OA
Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. When non-elitism outperforms elitism for crossing fitness valleys. In: Proceedings of the Genetic and Evolutionary Computation Conference 2016 . ACM; 2016:1163-1170. doi:10.1145/2908812.2908909
[Published Version] View | Files available | DOI
 
[20]
2016 | Published | Journal Article | IST-REx-ID: 1359 | OA
Paixao T, Barton NH. The effect of gene interactions on the long-term response to selection. PNAS. 2016;113(16):4422-4427. doi:10.1073/pnas.1518830113
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[19]
2015 | Research Data Reference | IST-REx-ID: 9712
Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison & for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001
[Published Version] View | Files available | DOI
 
[18]
2015 | Published | Conference Paper | IST-REx-ID: 1430 | OA
Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime comparison of natural and artificial evolution. In: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. ACM; 2015:1455-1462. doi:10.1145/2739480.2754758
[Preprint] View | DOI | Download Preprint (ext.)
 
[17]
2015 | Published | Journal Article | IST-REx-ID: 1542 | OA
Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011
[Published Version] View | Files available | DOI
 
[16]
2015 | Published | Conference Paper | IST-REx-ID: 1835 | OA
Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking gene regulatory networks. 2015;9035:469-483. doi:10.1007/978-3-662-46681-0_47
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[15]
2015 | Published | Journal Article | IST-REx-ID: 1666 | OA
Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639
[Published Version] View | Files available | DOI
 
[14]
2014 | Published | Journal Article | IST-REx-ID: 2252
Phadke S, Paixao T, Pham T, Pham S, Zufall R. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. 2014;105(1):130-135. doi:10.1093/jhered/est063
View | DOI
 
[13]
2014 | Published | Journal Article | IST-REx-ID: 2169 | OA
Barton NH, Novak S, Paixao T. Diverse forms of selection in evolution and computer science. PNAS. 2014;111(29):10398-10399. doi:10.1073/pnas.1410107111
[Submitted Version] View | DOI | Download Submitted Version (ext.)
 
[12]
2013 | Published | Conference Paper | IST-REx-ID: 2718 | OA
Barton NH, Paixao T. Can quantitative and population genetics help us understand evolutionary computation? In: Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation. ACM; 2013:1573-1580. doi:10.1145/2463372.2463568
[Submitted Version] View | Files available | DOI
 
[11]
2013 | Published | Conference Paper | IST-REx-ID: 2719
Paixao T, Barton NH. A variance decomposition approach to the analysis of genetic algorithms. In: Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation. ACM; 2013:845-852. doi:10.1145/2463372.2463470
View | DOI
 
[10]
2013 | Published | Journal Article | IST-REx-ID: 2720 | OA
Long H, Paixao T, Azevedo R, Zufall R. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 2013;195(2):527-540. doi:10.1534/genetics.113.153536
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[9]
2013 | Published | Journal Article | IST-REx-ID: 2900
Azevedo R, Lohaus R, Paixao T. Networking networks. Evolution & Development. 2013;10(5):514-515.
View | Download (ext.)
 
[8]
2011 | Published | Journal Article | IST-REx-ID: 2897
Paixao T, Azevedo R. Redundancy and the Evolution of Cis Regulatory Element Multiplicity. PLoS Computational Biology. 2011;6(7). doi:10.1371/journal.pcbi.1000848
View | DOI
 
[7]
2011 | Published | Journal Article | IST-REx-ID: 2898
Paixao T, Phadke S, Azevedo R, Zufall R. Sex ratio evolution under probabilistic sex determination. Evolution; International Journal of Organic Evolution. 2011;65(7):2050-2060. doi:10.1111/j.1558-5646.2011.01266.x
View | DOI
 
[6]
2010 | Published | Journal Article | IST-REx-ID: 2899
Cooper T, Paixao T, Heinemann J. Within host competition selects for plasmid encoded toxin–antitoxin systems. Proc R Soc B. 2010;277(1697):3149-3155. doi:10.1098/rspb.2010.0831
View | DOI
 
[5]
2008 | Published | Journal Article | IST-REx-ID: 2892
Azevedo R, Lohaus R, Paixao T. Networking networks. Evolution & Development. 2008;10(5):514-515. doi:10.1111/j.1525-142X.2008.00265.x
View | DOI
 
[4]
2007 | Published | Journal Article | IST-REx-ID: 2893
Carneiro J, Leon K, Caramalho Í, et al. When three is not a crowd a Crossregulation Model of the dynamics and repertoire selection of regulatory CD4 T cells. Immunological Reviews. 2007;216(1):48-68. doi:10.1111/j.1600-065X.2007.00487.x
View | DOI
 
[3]
2007 | Published | Journal Article | IST-REx-ID: 2896
Paixao T, Carvalho T, Calado D, Carneiro J. Quantitative insights into stochastic monoallelic expression of cytokine genes. Immunology and Cell Biology. 2007;85(4):315-322. doi:10.1038/sj.icb.7100057
View | DOI
 
[2]
2006 | Published | Journal Article | IST-REx-ID: 2894
Calado D, Paixao T, Holmberg D, Haury M. Stochastic Monoallelic Expression of IL 10 in T Cells. Journal of Immunology. 2006;177(8):5358-5364. doi:10.4049/jimmunol.177.8.5358
View | DOI
 
[1]
2005 | Published | Journal Article | IST-REx-ID: 2895
Carneiro J, Paixao T, Milutinovic D, et al. Immunological self tolerance: Lessons from mathematical modeling. Journal of Computational and Applied Mathematics. 2005;184(1):77-100. doi:10.1016/j.cam.2004.10.025
View | DOI
 
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