Tiago Paixao
Barton Group
Guet Group
32 Publications
2018 | Journal Article | IST-REx-ID: 723 |
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]
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| Files available
| DOI
| WoS
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]
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| Files available
| DOI
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]
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| Files available
| DOI
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]
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| Files available
| DOI
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]
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| Files available
| DOI
2017 | Journal Article | IST-REx-ID: 1351 |
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]
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| Files available
| DOI
| WoS
2017 | Journal Article | IST-REx-ID: 1336 |
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
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. Genetics Society of America, pp. 803–825, 2017.
[Published Version]
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| DOI
| Download Published Version (ext.)
| WoS
| PubMed | Europe PMC
2017 | Journal Article | IST-REx-ID: 954 |
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]
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| Files available
| DOI
| WoS
2017 | Journal Article | IST-REx-ID: 696 |
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]
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| Files available
| DOI
2016 | Conference Paper | IST-REx-ID: 1349 |
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]
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| Files available
| DOI
2016 | Journal Article | IST-REx-ID: 1359 |
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]
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| DOI
| Download Published Version (ext.)
| PubMed | Europe PMC
2015 | Conference Paper | IST-REx-ID: 1430 |
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]
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| DOI
| Download Preprint (ext.)
2015 | Journal Article | IST-REx-ID: 1542 |
T. Paixao et al., “Toward a unifying framework for evolutionary processes,” Journal of Theoretical Biology, vol. 383. Elsevier, pp. 28–43, 2015.
[Published Version]
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| Files available
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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]
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| Files available
| DOI
2015 | Journal Article | IST-REx-ID: 1666 |
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]
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| DOI
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.
[Preprint]
View
| Files available
| DOI
| Download Preprint (ext.)
2014 | Journal Article | IST-REx-ID: 2169 |
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]
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| DOI
| Download Submitted Version (ext.)
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
2013 | Conference Paper | IST-REx-ID: 2718 |
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]
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| Files available
| DOI
2013 | Journal Article | IST-REx-ID: 2720 |
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]
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| DOI
| Download Submitted Version (ext.)
| PubMed | Europe PMC
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.)
32 Publications
2018 | Journal Article | IST-REx-ID: 723 |
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
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
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
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
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
2017 | Journal Article | IST-REx-ID: 1351 |
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
2017 | Journal Article | IST-REx-ID: 1336 |
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
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. Genetics Society of America, pp. 803–825, 2017.
[Published Version]
View
| DOI
| Download Published Version (ext.)
| WoS
| PubMed | Europe PMC
2017 | Journal Article | IST-REx-ID: 954 |
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
2017 | Journal Article | IST-REx-ID: 696 |
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
2016 | Conference Paper | IST-REx-ID: 1349 |
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
2016 | Journal Article | IST-REx-ID: 1359 |
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
2015 | Conference Paper | IST-REx-ID: 1430 |
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.)
2015 | Journal Article | IST-REx-ID: 1542 |
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
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
2015 | Journal Article | IST-REx-ID: 1666 |
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
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.
[Preprint]
View
| Files available
| DOI
| Download Preprint (ext.)
2014 | Journal Article | IST-REx-ID: 2169 |
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.)
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
2013 | Conference Paper | IST-REx-ID: 2718 |
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
2013 | Journal Article | IST-REx-ID: 2720 |
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
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.)