Tiago Paixao
Barton Group
Guet Group
32 Publications
2018 | Journal Article | IST-REx-ID: 723 |
Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica, vol. 80, no. 5, Springer, 2018, pp. 1604–33, doi:10.1007/s00453-017-0369-2.
[Published Version]
View
| Files available
| DOI
| WoS
2017 | Conference Paper | IST-REx-ID: 1112
Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms.” Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11, doi:10.1145/3040718.3040729.
View
| DOI
2017 | Research Data Reference | IST-REx-ID: 9849
Lukacisinova, Marta, et al. Modelling and Simulation Details. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s001.
[Published Version]
View
| Files available
| DOI
2017 | Research Data Reference | IST-REx-ID: 9850
Lukacisinova, Marta, et al. Extensions of the Model. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s002.
[Published Version]
View
| Files available
| DOI
2017 | Research Data Reference | IST-REx-ID: 9851
Lukacisinova, Marta, et al. Heuristic Prediction for Multiple Stresses. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s003.
[Published Version]
View
| Files available
| DOI
2017 | Research Data Reference | IST-REx-ID: 9852
Lukacisinova, Marta, et al. Resistance Frequencies for Different Combination Strategies. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s004.
[Published Version]
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| Files available
| DOI
2017 | Journal Article | IST-REx-ID: 1351 |
Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:10.1007/s00236-016-0278-x.
[Published Version]
View
| Files available
| DOI
| WoS
2017 | Journal Article | IST-REx-ID: 1336 |
Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica, vol. 78, no. 2, Springer, 2017, pp. 681–713, doi:10.1007/s00453-016-0212-1.
[Published Version]
View
| Files available
| DOI
| WoS
2017 | Journal Article | IST-REx-ID: 1111 |
Heredia, Jorge, et al. “Selection Limits to Adaptive Walks on Correlated Landscapes.” Genetics, vol. 205, no. 2, Genetics Society of America, 2017, pp. 803–25, doi:10.1534/genetics.116.189340.
[Published Version]
View
| DOI
| Download Published Version (ext.)
| WoS
| PubMed | Europe PMC
2017 | Journal Article | IST-REx-ID: 954 |
Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications, 2017, doi:10.7554/eLife.25192.
[Published Version]
View
| Files available
| DOI
| WoS
2017 | Journal Article | IST-REx-ID: 696 |
Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.
[Published Version]
View
| Files available
| DOI
2016 | Conference Paper | IST-REx-ID: 1349 |
Oliveto, Pietro, et al. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–70, doi:10.1145/2908812.2908909.
[Published Version]
View
| Files available
| DOI
2016 | Journal Article | IST-REx-ID: 1359 |
Paixao, Tiago, and Nicholas H. Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” PNAS, vol. 113, no. 16, National Academy of Sciences, 2016, pp. 4422–27, doi:10.1073/pnas.1518830113.
[Published Version]
View
| DOI
| Download Published Version (ext.)
| PubMed | Europe PMC
2015 | Conference Paper | IST-REx-ID: 1430 |
Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–62, doi:10.1145/2739480.2754758.
[Preprint]
View
| DOI
| Download Preprint (ext.)
2015 | Journal Article | IST-REx-ID: 1542 |
Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology, vol. 383, Elsevier, 2015, pp. 28–43, doi:10.1016/j.jtbi.2015.07.011.
[Published Version]
View
| Files available
| DOI
2015 | Research Data Reference | IST-REx-ID: 9712
Tugrul, Murat, et al. Other Fitness Models for Comparison & for Interacting TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001.
[Published Version]
View
| Files available
| DOI
2015 | Journal Article | IST-REx-ID: 1666 |
Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.
[Published Version]
View
| Files available
| DOI
2015 | Conference Paper | IST-REx-ID: 1835 |
Giacobbe, Mirco, et al. Model Checking Gene Regulatory Networks. Vol. 9035, Springer, 2015, pp. 469–83, doi:10.1007/978-3-662-46681-0_47.
[Preprint]
View
| Files available
| DOI
| Download Preprint (ext.)
2014 | Journal Article | IST-REx-ID: 2169 |
Barton, Nicholas H., et al. “Diverse Forms of Selection in Evolution and Computer Science.” PNAS, vol. 111, no. 29, National Academy of Sciences, 2014, pp. 10398–99, doi:10.1073/pnas.1410107111.
[Submitted Version]
View
| DOI
| Download Submitted Version (ext.)
2014 | Journal Article | IST-REx-ID: 2252
Phadke, Sujal, et al. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” Journal of Heredity, vol. 105, no. 1, Oxford University Press, 2014, pp. 130–35, doi:10.1093/jhered/est063.
View
| DOI
2013 | Conference Paper | IST-REx-ID: 2718 |
Barton, Nicholas H., and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–80, doi:10.1145/2463372.2463568.
[Submitted Version]
View
| Files available
| DOI
2013 | Journal Article | IST-REx-ID: 2720 |
Long, Hongan, et al. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics, vol. 195, no. 2, Genetics Society of America, 2013, pp. 527–40, doi:10.1534/genetics.113.153536.
[Submitted Version]
View
| DOI
| Download Submitted Version (ext.)
| PubMed | Europe PMC
2013 | Conference Paper | IST-REx-ID: 2719
Paixao, Tiago, and Nicholas H. Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–52, doi:10.1145/2463372.2463470.
View
| DOI
2013 | Journal Article | IST-REx-ID: 2900
Azevedo, Ricardo, et al. “Networking Networks.” Evolution & Development, vol. 10, no. 5, Wiley-Blackwell, 2013, pp. 514–15.
View
| Download (ext.)
2011 | Journal Article | IST-REx-ID: 2898
Paixao, Tiago, et al. “Sex Ratio Evolution under Probabilistic Sex Determination.” Evolution; International Journal of Organic Evolution, vol. 65, no. 7, Wiley-Blackwell, 2011, pp. 2050–60, doi:10.1111/j.1558-5646.2011.01266.x.
View
| DOI
2011 | Journal Article | IST-REx-ID: 2897
Paixao, Tiago, and Ricardo Azevedo. “Redundancy and the Evolution of Cis Regulatory Element Multiplicity.” PLoS Computational Biology, vol. 6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pcbi.1000848.
View
| DOI
2010 | Journal Article | IST-REx-ID: 2899
Cooper, Tim, et al. “Within Host Competition Selects for Plasmid Encoded Toxin–Antitoxin Systems.” Proc R Soc B, vol. 277, no. 1697, Wiley-Blackwell, 2010, pp. 3149–55, doi:10.1098/rspb.2010.0831.
View
| DOI
2008 | Journal Article | IST-REx-ID: 2892
Azevedo, Ricardo, et al. “Networking Networks.” Evolution & Development, vol. 10, no. 5, Wiley-Blackwell, 2008, pp. 514–15, doi:10.1111/j.1525-142X.2008.00265.x.
View
| DOI
2007 | Journal Article | IST-REx-ID: 2893
Carneiro, Jorge, 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, 2007, pp. 48–68, doi:10.1111/j.1600-065X.2007.00487.x.
View
| DOI
2007 | Journal Article | IST-REx-ID: 2896
Paixao, Tiago, et al. “Quantitative Insights into Stochastic Monoallelic Expression of Cytokine Genes.” Immunology and Cell Biology, vol. 85, no. 4, Nature Publishing Group, 2007, pp. 315–22, doi:10.1038/sj.icb.7100057.
View
| DOI
2006 | Journal Article | IST-REx-ID: 2894
Calado, Dinis, et al. “Stochastic Monoallelic Expression of IL 10 in T Cells.” Journal of Immunology, vol. 177, no. 8, American Association of Immunologists, 2006, pp. 5358–64, doi:10.4049/jimmunol.177.8.5358 .
View
| DOI
2005 | Journal Article | IST-REx-ID: 2895
Carneiro, Jorge, et al. “Immunological Self Tolerance: Lessons from Mathematical Modeling.” Journal of Computational and Applied Mathematics, vol. 184, no. 1, Elsevier, 2005, pp. 77–100, doi:10.1016/j.cam.2004.10.025.
View
| DOI
32 Publications
2018 | Journal Article | IST-REx-ID: 723 |
Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica, vol. 80, no. 5, Springer, 2018, pp. 1604–33, doi:10.1007/s00453-017-0369-2.
[Published Version]
View
| Files available
| DOI
| WoS
2017 | Conference Paper | IST-REx-ID: 1112
Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms.” Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11, doi:10.1145/3040718.3040729.
View
| DOI
2017 | Research Data Reference | IST-REx-ID: 9849
Lukacisinova, Marta, et al. Modelling and Simulation Details. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s001.
[Published Version]
View
| Files available
| DOI
2017 | Research Data Reference | IST-REx-ID: 9850
Lukacisinova, Marta, et al. Extensions of the Model. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s002.
[Published Version]
View
| Files available
| DOI
2017 | Research Data Reference | IST-REx-ID: 9851
Lukacisinova, Marta, et al. Heuristic Prediction for Multiple Stresses. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s003.
[Published Version]
View
| Files available
| DOI
2017 | Research Data Reference | IST-REx-ID: 9852
Lukacisinova, Marta, et al. Resistance Frequencies for Different Combination Strategies. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s004.
[Published Version]
View
| Files available
| DOI
2017 | Journal Article | IST-REx-ID: 1351 |
Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:10.1007/s00236-016-0278-x.
[Published Version]
View
| Files available
| DOI
| WoS
2017 | Journal Article | IST-REx-ID: 1336 |
Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica, vol. 78, no. 2, Springer, 2017, pp. 681–713, doi:10.1007/s00453-016-0212-1.
[Published Version]
View
| Files available
| DOI
| WoS
2017 | Journal Article | IST-REx-ID: 1111 |
Heredia, Jorge, et al. “Selection Limits to Adaptive Walks on Correlated Landscapes.” Genetics, vol. 205, no. 2, Genetics Society of America, 2017, pp. 803–25, doi:10.1534/genetics.116.189340.
[Published Version]
View
| DOI
| Download Published Version (ext.)
| WoS
| PubMed | Europe PMC
2017 | Journal Article | IST-REx-ID: 954 |
Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications, 2017, doi:10.7554/eLife.25192.
[Published Version]
View
| Files available
| DOI
| WoS
2017 | Journal Article | IST-REx-ID: 696 |
Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.
[Published Version]
View
| Files available
| DOI
2016 | Conference Paper | IST-REx-ID: 1349 |
Oliveto, Pietro, et al. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–70, doi:10.1145/2908812.2908909.
[Published Version]
View
| Files available
| DOI
2016 | Journal Article | IST-REx-ID: 1359 |
Paixao, Tiago, and Nicholas H. Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” PNAS, vol. 113, no. 16, National Academy of Sciences, 2016, pp. 4422–27, doi:10.1073/pnas.1518830113.
[Published Version]
View
| DOI
| Download Published Version (ext.)
| PubMed | Europe PMC
2015 | Conference Paper | IST-REx-ID: 1430 |
Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–62, doi:10.1145/2739480.2754758.
[Preprint]
View
| DOI
| Download Preprint (ext.)
2015 | Journal Article | IST-REx-ID: 1542 |
Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology, vol. 383, Elsevier, 2015, pp. 28–43, doi:10.1016/j.jtbi.2015.07.011.
[Published Version]
View
| Files available
| DOI
2015 | Research Data Reference | IST-REx-ID: 9712
Tugrul, Murat, et al. Other Fitness Models for Comparison & for Interacting TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001.
[Published Version]
View
| Files available
| DOI
2015 | Journal Article | IST-REx-ID: 1666 |
Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.
[Published Version]
View
| Files available
| DOI
2015 | Conference Paper | IST-REx-ID: 1835 |
Giacobbe, Mirco, et al. Model Checking Gene Regulatory Networks. Vol. 9035, Springer, 2015, pp. 469–83, doi:10.1007/978-3-662-46681-0_47.
[Preprint]
View
| Files available
| DOI
| Download Preprint (ext.)
2014 | Journal Article | IST-REx-ID: 2169 |
Barton, Nicholas H., et al. “Diverse Forms of Selection in Evolution and Computer Science.” PNAS, vol. 111, no. 29, National Academy of Sciences, 2014, pp. 10398–99, doi:10.1073/pnas.1410107111.
[Submitted Version]
View
| DOI
| Download Submitted Version (ext.)
2014 | Journal Article | IST-REx-ID: 2252
Phadke, Sujal, et al. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” Journal of Heredity, vol. 105, no. 1, Oxford University Press, 2014, pp. 130–35, doi:10.1093/jhered/est063.
View
| DOI
2013 | Conference Paper | IST-REx-ID: 2718 |
Barton, Nicholas H., and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–80, doi:10.1145/2463372.2463568.
[Submitted Version]
View
| Files available
| DOI
2013 | Journal Article | IST-REx-ID: 2720 |
Long, Hongan, et al. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics, vol. 195, no. 2, Genetics Society of America, 2013, pp. 527–40, doi:10.1534/genetics.113.153536.
[Submitted Version]
View
| DOI
| Download Submitted Version (ext.)
| PubMed | Europe PMC
2013 | Conference Paper | IST-REx-ID: 2719
Paixao, Tiago, and Nicholas H. Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–52, doi:10.1145/2463372.2463470.
View
| DOI
2013 | Journal Article | IST-REx-ID: 2900
Azevedo, Ricardo, et al. “Networking Networks.” Evolution & Development, vol. 10, no. 5, Wiley-Blackwell, 2013, pp. 514–15.
View
| Download (ext.)
2011 | Journal Article | IST-REx-ID: 2898
Paixao, Tiago, et al. “Sex Ratio Evolution under Probabilistic Sex Determination.” Evolution; International Journal of Organic Evolution, vol. 65, no. 7, Wiley-Blackwell, 2011, pp. 2050–60, doi:10.1111/j.1558-5646.2011.01266.x.
View
| DOI
2011 | Journal Article | IST-REx-ID: 2897
Paixao, Tiago, and Ricardo Azevedo. “Redundancy and the Evolution of Cis Regulatory Element Multiplicity.” PLoS Computational Biology, vol. 6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pcbi.1000848.
View
| DOI
2010 | Journal Article | IST-REx-ID: 2899
Cooper, Tim, et al. “Within Host Competition Selects for Plasmid Encoded Toxin–Antitoxin Systems.” Proc R Soc B, vol. 277, no. 1697, Wiley-Blackwell, 2010, pp. 3149–55, doi:10.1098/rspb.2010.0831.
View
| DOI
2008 | Journal Article | IST-REx-ID: 2892
Azevedo, Ricardo, et al. “Networking Networks.” Evolution & Development, vol. 10, no. 5, Wiley-Blackwell, 2008, pp. 514–15, doi:10.1111/j.1525-142X.2008.00265.x.
View
| DOI
2007 | Journal Article | IST-REx-ID: 2893
Carneiro, Jorge, 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, 2007, pp. 48–68, doi:10.1111/j.1600-065X.2007.00487.x.
View
| DOI
2007 | Journal Article | IST-REx-ID: 2896
Paixao, Tiago, et al. “Quantitative Insights into Stochastic Monoallelic Expression of Cytokine Genes.” Immunology and Cell Biology, vol. 85, no. 4, Nature Publishing Group, 2007, pp. 315–22, doi:10.1038/sj.icb.7100057.
View
| DOI
2006 | Journal Article | IST-REx-ID: 2894
Calado, Dinis, et al. “Stochastic Monoallelic Expression of IL 10 in T Cells.” Journal of Immunology, vol. 177, no. 8, American Association of Immunologists, 2006, pp. 5358–64, doi:10.4049/jimmunol.177.8.5358 .
View
| DOI
2005 | Journal Article | IST-REx-ID: 2895
Carneiro, Jorge, et al. “Immunological Self Tolerance: Lessons from Mathematical Modeling.” Journal of Computational and Applied Mathematics, vol. 184, no. 1, Elsevier, 2005, pp. 77–100, doi:10.1016/j.cam.2004.10.025.
View
| DOI