27 Publications

Mark all

[27]
2018 | Journal Article | IST-REx-ID: 723   OA
P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How to escape local optima in black box optimisation when non elitism outperforms elitism,” Algorithmica, vol. 80, no. 5, pp. 1604–1633, 2018.
View | Files available | DOI
 
[26]
2017 | Journal Article | IST-REx-ID: 1111
J. Heredia, B. Trubenova, D. Sudholt, and T. Paixao, “Selection limits to adaptive walks on correlated landscapes,” Genetics, vol. 205, no. 2, pp. 803–825, 2017.
View | DOI
 
[25]
2017 | Journal Article | IST-REx-ID: 1351   OA
M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking the evolution of gene regulatory networks,” Acta Informatica, vol. 54, no. 8, pp. 765–787, 2017.
View | Files available | DOI
 
[24]
2017 | Conference Paper | IST-REx-ID: 1112
T. Paixao and J. Pérez Heredia, “An application of stochastic differential equations to evolutionary algorithms,” presented at the FOGA: Foundations of Genetic Algorithms, Copenhagen, Denmark, 2017, pp. 3–11.
View | DOI
 
[23]
2017 | Journal Article | IST-REx-ID: 954   OA
M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife, vol. 6, 2017.
View | Files available | DOI
 
[22]
2017 | Journal Article | IST-REx-ID: 696   OA
M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” PLoS Computational Biology, vol. 13, no. 7, p. e1005609, 2017.
View | Files available | DOI
 
[21]
2017 | Journal Article | IST-REx-ID: 1336   OA
T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” Algorithmica, vol. 78, no. 2, pp. 681–713, 2017.
View | Files available | DOI
 
[20]
2016 | Conference Paper | IST-REx-ID: 1349   OA
P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism outperforms elitism for crossing fitness valleys,” in Proceedings of the Genetic and Evolutionary Computation Conference 2016 , Denver, CO, USA, 2016, pp. 1163–1170.
View | Files available | DOI
 
[19]
2016 | Journal Article | IST-REx-ID: 1359   OA
T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term response to selection,” PNAS, vol. 113, no. 16, pp. 4422–4427, 2016.
View | DOI | Download (ext.)
 
[18]
2015 | Journal Article | IST-REx-ID: 1666
M. Tugrul, T. Paixao, N. H. Barton, and G. Tkacik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11, 2015.
View | Files available | DOI
 
[17]
2015 | Journal Article | IST-REx-ID: 1542   OA
T. Paixao et al., “Toward a unifying framework for evolutionary processes,” Journal of Theoretical Biology, vol. 383, pp. 28–43, 2015.
View | Files available | DOI
 
[16]
2015 | Conference Paper | IST-REx-ID: 1430   OA
T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards a runtime comparison of natural and artificial evolution,” in Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, Madrid, Spain, 2015, pp. 1455–1462.
View | DOI | Download (ext.)
 
[15]
2015 | Conference Paper | IST-REx-ID: 1835
M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking gene regulatory networks,” vol. 9035. Springer, pp. 469–483, 2015.
View | Files available | DOI | Download (ext.)
 
[14]
2014 | Journal Article | IST-REx-ID: 2169   OA
N. H. Barton, S. Novak, and T. Paixao, “Diverse forms of selection in evolution and computer science,” PNAS, vol. 111, no. 29, pp. 10398–10399, 2014.
View | DOI | Download (ext.)
 
[13]
2014 | Journal Article | IST-REx-ID: 2252
S. Phadke, T. Paixao, T. Pham, S. Pham, and R. Zufall, “Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila,” Journal of Heredity, vol. 105, no. 1, pp. 130–135, 2014.
View | DOI
 
[12]
2013 | Journal Article | IST-REx-ID: 2900
R. Azevedo, R. Lohaus, and T. Paixao, “Networking networks,” Evolution & Development, vol. 10, no. 5, pp. 514–515, 2013.
View | Download (ext.)
 
[11]
2013 | Conference Paper | IST-REx-ID: 2718   OA
N. H. Barton and T. Paixao, “Can quantitative and population genetics help us understand evolutionary computation?,” in Proceedings of the 15th annual conference on Genetic and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 1573–1580.
View | Files available | DOI
 
[10]
2013 | Journal Article | IST-REx-ID: 2720   OA
H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila,” Genetics, vol. 195, no. 2, pp. 527–540, 2013.
View | DOI | Download (ext.) | PubMed | Europe PMC
 
[9]
2013 | Conference Paper | IST-REx-ID: 2719
T. Paixao and N. H. Barton, “A variance decomposition approach to the analysis of genetic algorithms,” in Proceedings of the 15th annual conference on Genetic and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 845–852.
View | DOI
 
[8]
2011 | Journal Article | IST-REx-ID: 2897
T. Paixao and R. Azevedo, “Redundancy and the Evolution of Cis Regulatory Element Multiplicity,” PLoS Computational Biology, vol. 6, no. 7, 2011.
View | DOI
 
[7]
2011 | Journal Article | IST-REx-ID: 2898
T. Paixao, S. Phadke, R. Azevedo, and R. Zufall, “Sex ratio evolution under probabilistic sex determination,” Evolution; International Journal of Organic Evolution, vol. 65, no. 7, pp. 2050–2060, 2011.
View | DOI
 
[6]
2010 | Journal Article | IST-REx-ID: 2899
T. Cooper, T. Paixao, and J. Heinemann, “Within host competition selects for plasmid encoded toxin–antitoxin systems,” Proc R Soc B, vol. 277, no. 1697, pp. 3149–3155, 2010.
View | DOI
 
[5]
2008 | Journal Article | IST-REx-ID: 2892
R. Azevedo, R. Lohaus, and T. Paixao, “Networking networks,” Evolution & Development, vol. 10, no. 5, pp. 514–515, 2008.
View | DOI
 
[4]
2007 | Journal Article | IST-REx-ID: 2893
J. Carneiro et al., “When three is not a crowd a Crossregulation Model of the dynamics and repertoire selection of regulatory CD4 T cells,” Immunological Reviews, vol. 216, no. 1, pp. 48–68, 2007.
View | DOI
 
[3]
2007 | Journal Article | IST-REx-ID: 2896
T. Paixao, T. Carvalho, D. Calado, and J. Carneiro, “Quantitative insights into stochastic monoallelic expression of cytokine genes,” Immunology and Cell Biology, vol. 85, no. 4, pp. 315–322, 2007.
View | DOI
 
[2]
2006 | Journal Article | IST-REx-ID: 2894
D. Calado, T. Paixao, D. Holmberg, and M. Haury, “Stochastic Monoallelic Expression of IL 10 in T Cells,” Journal of Immunology, vol. 177, no. 8, pp. 5358–5364, 2006.
View | DOI
 
[1]
2005 | Journal Article | IST-REx-ID: 2895
J. Carneiro et al., “Immunological self tolerance: Lessons from mathematical modeling,” Journal of Computational and Applied Mathematics, vol. 184, no. 1, pp. 77–100, 2005.
View | DOI
 

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27 Publications

Mark all

[27]
2018 | Journal Article | IST-REx-ID: 723   OA
P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How to escape local optima in black box optimisation when non elitism outperforms elitism,” Algorithmica, vol. 80, no. 5, pp. 1604–1633, 2018.
View | Files available | DOI
 
[26]
2017 | Journal Article | IST-REx-ID: 1111
J. Heredia, B. Trubenova, D. Sudholt, and T. Paixao, “Selection limits to adaptive walks on correlated landscapes,” Genetics, vol. 205, no. 2, pp. 803–825, 2017.
View | DOI
 
[25]
2017 | Journal Article | IST-REx-ID: 1351   OA
M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking the evolution of gene regulatory networks,” Acta Informatica, vol. 54, no. 8, pp. 765–787, 2017.
View | Files available | DOI
 
[24]
2017 | Conference Paper | IST-REx-ID: 1112
T. Paixao and J. Pérez Heredia, “An application of stochastic differential equations to evolutionary algorithms,” presented at the FOGA: Foundations of Genetic Algorithms, Copenhagen, Denmark, 2017, pp. 3–11.
View | DOI
 
[23]
2017 | Journal Article | IST-REx-ID: 954   OA
M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife, vol. 6, 2017.
View | Files available | DOI
 
[22]
2017 | Journal Article | IST-REx-ID: 696   OA
M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” PLoS Computational Biology, vol. 13, no. 7, p. e1005609, 2017.
View | Files available | DOI
 
[21]
2017 | Journal Article | IST-REx-ID: 1336   OA
T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” Algorithmica, vol. 78, no. 2, pp. 681–713, 2017.
View | Files available | DOI
 
[20]
2016 | Conference Paper | IST-REx-ID: 1349   OA
P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism outperforms elitism for crossing fitness valleys,” in Proceedings of the Genetic and Evolutionary Computation Conference 2016 , Denver, CO, USA, 2016, pp. 1163–1170.
View | Files available | DOI
 
[19]
2016 | Journal Article | IST-REx-ID: 1359   OA
T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term response to selection,” PNAS, vol. 113, no. 16, pp. 4422–4427, 2016.
View | DOI | Download (ext.)
 
[18]
2015 | Journal Article | IST-REx-ID: 1666
M. Tugrul, T. Paixao, N. H. Barton, and G. Tkacik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11, 2015.
View | Files available | DOI
 
[17]
2015 | Journal Article | IST-REx-ID: 1542   OA
T. Paixao et al., “Toward a unifying framework for evolutionary processes,” Journal of Theoretical Biology, vol. 383, pp. 28–43, 2015.
View | Files available | DOI
 
[16]
2015 | Conference Paper | IST-REx-ID: 1430   OA
T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards a runtime comparison of natural and artificial evolution,” in Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, Madrid, Spain, 2015, pp. 1455–1462.
View | DOI | Download (ext.)
 
[15]
2015 | Conference Paper | IST-REx-ID: 1835
M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking gene regulatory networks,” vol. 9035. Springer, pp. 469–483, 2015.
View | Files available | DOI | Download (ext.)
 
[14]
2014 | Journal Article | IST-REx-ID: 2169   OA
N. H. Barton, S. Novak, and T. Paixao, “Diverse forms of selection in evolution and computer science,” PNAS, vol. 111, no. 29, pp. 10398–10399, 2014.
View | DOI | Download (ext.)
 
[13]
2014 | Journal Article | IST-REx-ID: 2252
S. Phadke, T. Paixao, T. Pham, S. Pham, and R. Zufall, “Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila,” Journal of Heredity, vol. 105, no. 1, pp. 130–135, 2014.
View | DOI
 
[12]
2013 | Journal Article | IST-REx-ID: 2900
R. Azevedo, R. Lohaus, and T. Paixao, “Networking networks,” Evolution & Development, vol. 10, no. 5, pp. 514–515, 2013.
View | Download (ext.)
 
[11]
2013 | Conference Paper | IST-REx-ID: 2718   OA
N. H. Barton and T. Paixao, “Can quantitative and population genetics help us understand evolutionary computation?,” in Proceedings of the 15th annual conference on Genetic and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 1573–1580.
View | Files available | DOI
 
[10]
2013 | Journal Article | IST-REx-ID: 2720   OA
H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila,” Genetics, vol. 195, no. 2, pp. 527–540, 2013.
View | DOI | Download (ext.) | PubMed | Europe PMC
 
[9]
2013 | Conference Paper | IST-REx-ID: 2719
T. Paixao and N. H. Barton, “A variance decomposition approach to the analysis of genetic algorithms,” in Proceedings of the 15th annual conference on Genetic and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 845–852.
View | DOI
 
[8]
2011 | Journal Article | IST-REx-ID: 2897
T. Paixao and R. Azevedo, “Redundancy and the Evolution of Cis Regulatory Element Multiplicity,” PLoS Computational Biology, vol. 6, no. 7, 2011.
View | DOI
 
[7]
2011 | Journal Article | IST-REx-ID: 2898
T. Paixao, S. Phadke, R. Azevedo, and R. Zufall, “Sex ratio evolution under probabilistic sex determination,” Evolution; International Journal of Organic Evolution, vol. 65, no. 7, pp. 2050–2060, 2011.
View | DOI
 
[6]
2010 | Journal Article | IST-REx-ID: 2899
T. Cooper, T. Paixao, and J. Heinemann, “Within host competition selects for plasmid encoded toxin–antitoxin systems,” Proc R Soc B, vol. 277, no. 1697, pp. 3149–3155, 2010.
View | DOI
 
[5]
2008 | Journal Article | IST-REx-ID: 2892
R. Azevedo, R. Lohaus, and T. Paixao, “Networking networks,” Evolution & Development, vol. 10, no. 5, pp. 514–515, 2008.
View | DOI
 
[4]
2007 | Journal Article | IST-REx-ID: 2893
J. Carneiro et al., “When three is not a crowd a Crossregulation Model of the dynamics and repertoire selection of regulatory CD4 T cells,” Immunological Reviews, vol. 216, no. 1, pp. 48–68, 2007.
View | DOI
 
[3]
2007 | Journal Article | IST-REx-ID: 2896
T. Paixao, T. Carvalho, D. Calado, and J. Carneiro, “Quantitative insights into stochastic monoallelic expression of cytokine genes,” Immunology and Cell Biology, vol. 85, no. 4, pp. 315–322, 2007.
View | DOI
 
[2]
2006 | Journal Article | IST-REx-ID: 2894
D. Calado, T. Paixao, D. Holmberg, and M. Haury, “Stochastic Monoallelic Expression of IL 10 in T Cells,” Journal of Immunology, vol. 177, no. 8, pp. 5358–5364, 2006.
View | DOI
 
[1]
2005 | Journal Article | IST-REx-ID: 2895
J. Carneiro et al., “Immunological self tolerance: Lessons from mathematical modeling,” Journal of Computational and Applied Mathematics, vol. 184, no. 1, pp. 77–100, 2005.
View | DOI
 

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Display / Sort

Citation Style: IEEE

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