27 Publications

Mark all

[27]
2018 | Journal Article | IST-REx-ID: 723 | OA
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.
View | Files available | DOI
 
[26]
2017 | Journal Article | IST-REx-ID: 1336 | OA
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.
View | Files available | DOI
 
[25]
2017 | Journal Article | IST-REx-ID: 1351 | OA
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.
View | Files available | DOI
 
[24]
2017 | Journal Article | IST-REx-ID: 1111 | OA
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.
View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[23]
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
 
[22]
2017 | Journal Article | IST-REx-ID: 696 | OA
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.
View | Files available | DOI
 
[21]
2017 | Journal Article | IST-REx-ID: 954 | OA
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.
View | Files available | DOI
 
[20]
2016 | Journal Article | IST-REx-ID: 1359 | OA
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.
View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[19]
2016 | Conference Paper | IST-REx-ID: 1349 | OA
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.
View | Files available | DOI
 
[18]
2015 | Conference Paper | IST-REx-ID: 1835 | OA
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.
View | Files available | DOI | Download Preprint (ext.)
 
[17]
2015 | Conference Paper | IST-REx-ID: 1430 | OA
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.
View | DOI | Download Preprint (ext.)
 
[16]
2015 | Journal Article | IST-REx-ID: 1542 | OA
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.
View | Files available | DOI
 
[15]
2015 | Journal Article | IST-REx-ID: 1666 | OA
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.
View | Files available | DOI
 
[14]
2014 | Journal Article | IST-REx-ID: 2169 | OA
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.
View | DOI | Download Submitted Version (ext.)
 
[13]
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
 
[12]
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.)
 
[11]
2013 | Conference Paper | IST-REx-ID: 2718 | OA
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.
View | Files available | DOI
 
[10]
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
 
[9]
2013 | Journal Article | IST-REx-ID: 2720 | OA
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.
View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[8]
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
 
[7]
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
 
[6]
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
 
[5]
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
 
[4]
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
 
[3]
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
 
[2]
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
 
[1]
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
 

Search

Filter Publications

27 Publications

Mark all

[27]
2018 | Journal Article | IST-REx-ID: 723 | OA
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.
View | Files available | DOI
 
[26]
2017 | Journal Article | IST-REx-ID: 1336 | OA
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.
View | Files available | DOI
 
[25]
2017 | Journal Article | IST-REx-ID: 1351 | OA
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.
View | Files available | DOI
 
[24]
2017 | Journal Article | IST-REx-ID: 1111 | OA
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.
View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[23]
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
 
[22]
2017 | Journal Article | IST-REx-ID: 696 | OA
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.
View | Files available | DOI
 
[21]
2017 | Journal Article | IST-REx-ID: 954 | OA
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.
View | Files available | DOI
 
[20]
2016 | Journal Article | IST-REx-ID: 1359 | OA
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.
View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[19]
2016 | Conference Paper | IST-REx-ID: 1349 | OA
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.
View | Files available | DOI
 
[18]
2015 | Conference Paper | IST-REx-ID: 1835 | OA
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.
View | Files available | DOI | Download Preprint (ext.)
 
[17]
2015 | Conference Paper | IST-REx-ID: 1430 | OA
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.
View | DOI | Download Preprint (ext.)
 
[16]
2015 | Journal Article | IST-REx-ID: 1542 | OA
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.
View | Files available | DOI
 
[15]
2015 | Journal Article | IST-REx-ID: 1666 | OA
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.
View | Files available | DOI
 
[14]
2014 | Journal Article | IST-REx-ID: 2169 | OA
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.
View | DOI | Download Submitted Version (ext.)
 
[13]
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
 
[12]
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.)
 
[11]
2013 | Conference Paper | IST-REx-ID: 2718 | OA
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.
View | Files available | DOI
 
[10]
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
 
[9]
2013 | Journal Article | IST-REx-ID: 2720 | OA
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.
View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[8]
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
 
[7]
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
 
[6]
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
 
[5]
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
 
[4]
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
 
[3]
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
 
[2]
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
 
[1]
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
 

Search

Filter Publications