Tiago Paixao

Barton Group
Guet Group

32 Publications

Mark all

[32]
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. Springer, pp. 1604–1633, 2018.
[Published Version] View | Files available | DOI | WoS
 
[31]
2017 | Conference Paper | IST-REx-ID: 1112
T. Paixao and J. Pérez Heredia, “An application of stochastic differential equations to evolutionary algorithms,” in Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, Copenhagen, Denmark, 2017, pp. 3–11.
View | DOI
 
[30]
2017 | Research Data Reference | IST-REx-ID: 9849
M. Lukacisinova, S. Novak, and T. Paixao, “Modelling and simulation details.” Public Library of Science, 2017.
[Published Version] View | Files available | DOI
 
[29]
2017 | Research Data Reference | IST-REx-ID: 9850
M. Lukacisinova, S. Novak, and T. Paixao, “Extensions of the model.” Public Library of Science, 2017.
[Published Version] View | Files available | DOI
 
[28]
2017 | Research Data Reference | IST-REx-ID: 9851
M. Lukacisinova, S. Novak, and T. Paixao, “Heuristic prediction for multiple stresses.” Public Library of Science, 2017.
[Published Version] View | Files available | DOI
 
[27]
2017 | Research Data Reference | IST-REx-ID: 9852
M. Lukacisinova, S. Novak, and T. Paixao, “Resistance frequencies for different combination strategies.” Public Library of Science, 2017.
[Published Version] View | Files available | DOI
 
[26]
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. Springer, pp. 765–787, 2017.
[Published Version] View | Files available | DOI | WoS
 
[25]
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. Springer, pp. 681–713, 2017.
[Published Version] View | Files available | DOI | WoS
 
[24]
2017 | Journal Article | IST-REx-ID: 1111 | OA
J. Heredia, B. Trubenova, D. Sudholt, and T. Paixao, “Selection limits to adaptive walks on correlated landscapes,” Genetics, vol. 205, no. 2. Genetics Society of America, pp. 803–825, 2017.
[Published Version] View | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[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. eLife Sciences Publications, 2017.
[Published Version] View | Files available | DOI | WoS
 
[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. Public Library of Science, 2017.
[Published Version] View | Files available | DOI
 
[21]
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.
[Published Version] View | Files available | DOI
 
[20]
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. National Academy of Sciences, pp. 4422–4427, 2016.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[19]
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.
[Preprint] View | DOI | Download Preprint (ext.)
 
[18]
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. Elsevier, pp. 28–43, 2015.
[Published Version] View | Files available | DOI
 
[17]
2015 | Research Data Reference | IST-REx-ID: 9712
M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison & for interacting TFBSs.” Public Library of Science, 2015.
[Published Version] View | Files available | DOI
 
[16]
2015 | Journal Article | IST-REx-ID: 1666 | OA
M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public Library of Science, 2015.
[Published Version] View | Files available | DOI
 
[15]
2015 | Conference Paper | IST-REx-ID: 1835 | OA
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.
[Preprint] View | Files available | DOI | Download Preprint (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. National Academy of Sciences, pp. 10398–10399, 2014.
[Submitted Version] View | DOI | Download Submitted Version (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. Oxford University Press, pp. 130–135, 2014.
View | DOI
 
[12]
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.
[Submitted Version] View | Files available | DOI
 
[11]
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. Genetics Society of America, pp. 527–540, 2013.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[10]
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
 
[9]
2013 | Journal Article | IST-REx-ID: 2900
R. Azevedo, R. Lohaus, and T. Paixao, “Networking networks,” Evolution & Development, vol. 10, no. 5. Wiley-Blackwell, pp. 514–515, 2013.
View | Download (ext.)
 
[8]
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. Wiley-Blackwell, pp. 2050–2060, 2011.
View | DOI
 
[7]
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. Public Library of Science, 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. Wiley-Blackwell, 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. Wiley-Blackwell, 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. Wiley-Blackwell, 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. Nature Publishing Group, 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. American Association of Immunologists, 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. Elsevier, pp. 77–100, 2005.
View | DOI
 
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32 Publications

Mark all

[32]
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. Springer, pp. 1604–1633, 2018.
[Published Version] View | Files available | DOI | WoS
 
[31]
2017 | Conference Paper | IST-REx-ID: 1112
T. Paixao and J. Pérez Heredia, “An application of stochastic differential equations to evolutionary algorithms,” in Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, Copenhagen, Denmark, 2017, pp. 3–11.
View | DOI
 
[30]
2017 | Research Data Reference | IST-REx-ID: 9849
M. Lukacisinova, S. Novak, and T. Paixao, “Modelling and simulation details.” Public Library of Science, 2017.
[Published Version] View | Files available | DOI
 
[29]
2017 | Research Data Reference | IST-REx-ID: 9850
M. Lukacisinova, S. Novak, and T. Paixao, “Extensions of the model.” Public Library of Science, 2017.
[Published Version] View | Files available | DOI
 
[28]
2017 | Research Data Reference | IST-REx-ID: 9851
M. Lukacisinova, S. Novak, and T. Paixao, “Heuristic prediction for multiple stresses.” Public Library of Science, 2017.
[Published Version] View | Files available | DOI
 
[27]
2017 | Research Data Reference | IST-REx-ID: 9852
M. Lukacisinova, S. Novak, and T. Paixao, “Resistance frequencies for different combination strategies.” Public Library of Science, 2017.
[Published Version] View | Files available | DOI
 
[26]
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. Springer, pp. 765–787, 2017.
[Published Version] View | Files available | DOI | WoS
 
[25]
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. Springer, pp. 681–713, 2017.
[Published Version] View | Files available | DOI | WoS
 
[24]
2017 | Journal Article | IST-REx-ID: 1111 | OA
J. Heredia, B. Trubenova, D. Sudholt, and T. Paixao, “Selection limits to adaptive walks on correlated landscapes,” Genetics, vol. 205, no. 2. Genetics Society of America, pp. 803–825, 2017.
[Published Version] View | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[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. eLife Sciences Publications, 2017.
[Published Version] View | Files available | DOI | WoS
 
[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. Public Library of Science, 2017.
[Published Version] View | Files available | DOI
 
[21]
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.
[Published Version] View | Files available | DOI
 
[20]
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. National Academy of Sciences, pp. 4422–4427, 2016.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[19]
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.
[Preprint] View | DOI | Download Preprint (ext.)
 
[18]
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. Elsevier, pp. 28–43, 2015.
[Published Version] View | Files available | DOI
 
[17]
2015 | Research Data Reference | IST-REx-ID: 9712
M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison & for interacting TFBSs.” Public Library of Science, 2015.
[Published Version] View | Files available | DOI
 
[16]
2015 | Journal Article | IST-REx-ID: 1666 | OA
M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public Library of Science, 2015.
[Published Version] View | Files available | DOI
 
[15]
2015 | Conference Paper | IST-REx-ID: 1835 | OA
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.
[Preprint] View | Files available | DOI | Download Preprint (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. National Academy of Sciences, pp. 10398–10399, 2014.
[Submitted Version] View | DOI | Download Submitted Version (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. Oxford University Press, pp. 130–135, 2014.
View | DOI
 
[12]
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.
[Submitted Version] View | Files available | DOI
 
[11]
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. Genetics Society of America, pp. 527–540, 2013.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[10]
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
 
[9]
2013 | Journal Article | IST-REx-ID: 2900
R. Azevedo, R. Lohaus, and T. Paixao, “Networking networks,” Evolution & Development, vol. 10, no. 5. Wiley-Blackwell, pp. 514–515, 2013.
View | Download (ext.)
 
[8]
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. Wiley-Blackwell, pp. 2050–2060, 2011.
View | DOI
 
[7]
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. Public Library of Science, 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. Wiley-Blackwell, 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. Wiley-Blackwell, 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. Wiley-Blackwell, 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. Nature Publishing Group, 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. American Association of Immunologists, 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. Elsevier, pp. 77–100, 2005.
View | DOI
 
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    Citation Style: IEEE

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