27 Publications

Mark all

[27]
2018 | Journal Article | IST-REx-ID: 723   OA
Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica 80, no. 5 (2018): 1604–33. https://doi.org/10.1007/s00453-017-0369-2.
View | Files available | DOI
 
[26]
2017 | Journal Article | IST-REx-ID: 1111
Heredia, Jorge, Barbora Trubenova, Dirk Sudholt, and Tiago Paixao. “Selection Limits to Adaptive Walks on Correlated Landscapes.” Genetics 205, no. 2 (2017): 803–25. https://doi.org/10.1534/genetics.116.189340.
View | DOI
 
[25]
2017 | Journal Article | IST-REx-ID: 1351
Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica 54, no. 8 (2017): 765–87. https://doi.org/10.1007/s00236-016-0278-x.
View | Files available | DOI
 
[24]
2017 | Conference Paper | IST-REx-ID: 1112
Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms,” 3–11. ACM, 2017. https://doi.org/10.1145/3040718.3040729.
View | DOI
 
[23]
2017 | Journal Article | IST-REx-ID: 954   OA
Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife 6 (2017). https://doi.org/10.7554/eLife.25192.
View | Files available | DOI
 
[22]
2017 | Journal Article | IST-REx-ID: 696   OA
Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology 13, no. 7 (2017): e1005609. https://doi.org/10.1371/journal.pcbi.1005609.
View | Files available | DOI
 
[21]
2017 | Journal Article | IST-REx-ID: 1336   OA
Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica 78, no. 2 (2017): 681–713. https://doi.org/10.1007/s00453-016-0212-1.
View | Files available | DOI
 
[20]
2016 | Conference Paper | IST-REx-ID: 1349   OA
Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” In Proceedings of the Genetic and Evolutionary Computation Conference 2016 , 1163–70. ACM, 2016. https://doi.org/10.1145/2908812.2908909.
View | Files available | DOI
 
[19]
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 113, no. 16 (2016): 4422–27. https://doi.org/10.1073/pnas.1518830113.
View | DOI | Download (ext.)
 
[18]
2015 | Journal Article | IST-REx-ID: 1666
Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gasper Tkacik. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics 11, no. 11 (2015). https://doi.org/10.1371/journal.pgen.1005639.
View | Files available | DOI
 
[17]
2015 | Journal Article | IST-REx-ID: 1542   OA
Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology 383 (2015): 28–43. https://doi.org/10.1016/j.jtbi.2015.07.011.
View | Files available | DOI
 
[16]
2015 | Conference Paper | IST-REx-ID: 1430   OA
Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62. ACM, 2015. https://doi.org/10.1145/2739480.2754758.
View | DOI | Download (ext.)
 
[15]
2015 | Conference Paper | IST-REx-ID: 1835   OA
Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_47.
View | Files available | DOI | Download (ext.)
 
[14]
2014 | Journal Article | IST-REx-ID: 2169   OA
Barton, Nicholas H, Sebastian Novak, and Tiago Paixao. “Diverse Forms of Selection in Evolution and Computer Science.” PNAS 111, no. 29 (2014): 10398–99. https://doi.org/10.1073/pnas.1410107111.
View | DOI | Download (ext.)
 
[13]
2014 | Journal Article | IST-REx-ID: 2252
Phadke, Sujal, Tiago Paixao, Tuan Pham, Stephanie Pham, and Rebecca Zufall. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” Journal of Heredity 105, no. 1 (2014): 130–35. https://doi.org/10.1093/jhered/est063.
View | DOI
 
[12]
2013 | Journal Article | IST-REx-ID: 2900
Azevedo, Ricardo, Rolf Lohaus, and Tiago Paixao. “Networking Networks.” Evolution & Development 10, no. 5 (2013): 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?” In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 1573–80. ACM, 2013. https://doi.org/10.1145/2463372.2463568.
View | Files available | DOI
 
[10]
2013 | Journal Article | IST-REx-ID: 2720   OA
Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics 195, no. 2 (2013): 527–40. https://doi.org/10.1534/genetics.113.153536 .
View | DOI | Download (ext.) | PubMed | Europe PMC
 
[9]
2013 | Conference Paper | IST-REx-ID: 2719
Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 845–52. ACM, 2013. https://doi.org/10.1145/2463372.2463470.
View | DOI
 
[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 6, no. 7 (2011). https://doi.org/10.1371/journal.pcbi.1000848.
View | DOI
 
[7]
2011 | Journal Article | IST-REx-ID: 2898
Paixao, Tiago, Sujal Phadke, Ricardo Azevedo, and Rebecca Zufall. “Sex Ratio Evolution under Probabilistic Sex Determination.” Evolution; International Journal of Organic Evolution 65, no. 7 (2011): 2050–60. https://doi.org/10.1111/j.1558-5646.2011.01266.x.
View | DOI
 
[6]
2010 | Journal Article | IST-REx-ID: 2899
Cooper, Tim, Tiago Paixao, and Jack Heinemann. “Within Host Competition Selects for Plasmid Encoded Toxin–Antitoxin Systems.” Proc R Soc B 277, no. 1697 (2010): 3149–55. https://doi.org/10.1098/rspb.2010.0831.
View | DOI
 
[5]
2008 | Journal Article | IST-REx-ID: 2892
Azevedo, Ricardo, Rolf Lohaus, and Tiago Paixao. “Networking Networks.” Evolution & Development 10, no. 5 (2008): 514–15. https://doi.org/10.1111/j.1525-142X.2008.00265.x.
View | DOI
 
[4]
2007 | Journal Article | IST-REx-ID: 2893
Carneiro, Jorge, Kalet Leon, Íris Caramalho, Carline Van Den Dool, Rui Gardner, Vanessa Oliveira, Marie Bergman, et al. “When Three Is Not a Crowd a Crossregulation Model of the Dynamics and Repertoire Selection of Regulatory CD4 T Cells.” Immunological Reviews 216, no. 1 (2007): 48–68. https://doi.org/10.1111/j.1600-065X.2007.00487.x.
View | DOI
 
[3]
2007 | Journal Article | IST-REx-ID: 2896
Paixao, Tiago, Tiago Carvalho, Dinis Calado, and Jorge Carneiro. “Quantitative Insights into Stochastic Monoallelic Expression of Cytokine Genes.” Immunology and Cell Biology 85, no. 4 (2007): 315–22. https://doi.org/10.1038/sj.icb.7100057.
View | DOI
 
[2]
2006 | Journal Article | IST-REx-ID: 2894
Calado, Dinis, Tiago Paixao, Dan Holmberg, and Matthias Haury. “Stochastic Monoallelic Expression of IL 10 in T Cells.” Journal of Immunology 177, no. 8 (2006): 5358–64. https://doi.org/10.4049/jimmunol.177.8.5358 .
View | DOI
 
[1]
2005 | Journal Article | IST-REx-ID: 2895
Carneiro, Jorge, Tiago Paixao, Dejan Milutinovic, João Sousa, Kalet Leon, Rui Gardner, and Jose Faro. “Immunological Self Tolerance: Lessons from Mathematical Modeling.” Journal of Computational and Applied Mathematics 184, no. 1 (2005): 77–100. https://doi.org/10.1016/j.cam.2004.10.025.
View | DOI
 

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27 Publications

Mark all

[27]
2018 | Journal Article | IST-REx-ID: 723   OA
Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica 80, no. 5 (2018): 1604–33. https://doi.org/10.1007/s00453-017-0369-2.
View | Files available | DOI
 
[26]
2017 | Journal Article | IST-REx-ID: 1111
Heredia, Jorge, Barbora Trubenova, Dirk Sudholt, and Tiago Paixao. “Selection Limits to Adaptive Walks on Correlated Landscapes.” Genetics 205, no. 2 (2017): 803–25. https://doi.org/10.1534/genetics.116.189340.
View | DOI
 
[25]
2017 | Journal Article | IST-REx-ID: 1351
Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica 54, no. 8 (2017): 765–87. https://doi.org/10.1007/s00236-016-0278-x.
View | Files available | DOI
 
[24]
2017 | Conference Paper | IST-REx-ID: 1112
Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms,” 3–11. ACM, 2017. https://doi.org/10.1145/3040718.3040729.
View | DOI
 
[23]
2017 | Journal Article | IST-REx-ID: 954   OA
Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife 6 (2017). https://doi.org/10.7554/eLife.25192.
View | Files available | DOI
 
[22]
2017 | Journal Article | IST-REx-ID: 696   OA
Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology 13, no. 7 (2017): e1005609. https://doi.org/10.1371/journal.pcbi.1005609.
View | Files available | DOI
 
[21]
2017 | Journal Article | IST-REx-ID: 1336   OA
Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica 78, no. 2 (2017): 681–713. https://doi.org/10.1007/s00453-016-0212-1.
View | Files available | DOI
 
[20]
2016 | Conference Paper | IST-REx-ID: 1349   OA
Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” In Proceedings of the Genetic and Evolutionary Computation Conference 2016 , 1163–70. ACM, 2016. https://doi.org/10.1145/2908812.2908909.
View | Files available | DOI
 
[19]
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 113, no. 16 (2016): 4422–27. https://doi.org/10.1073/pnas.1518830113.
View | DOI | Download (ext.)
 
[18]
2015 | Journal Article | IST-REx-ID: 1666
Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gasper Tkacik. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics 11, no. 11 (2015). https://doi.org/10.1371/journal.pgen.1005639.
View | Files available | DOI
 
[17]
2015 | Journal Article | IST-REx-ID: 1542   OA
Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology 383 (2015): 28–43. https://doi.org/10.1016/j.jtbi.2015.07.011.
View | Files available | DOI
 
[16]
2015 | Conference Paper | IST-REx-ID: 1430   OA
Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62. ACM, 2015. https://doi.org/10.1145/2739480.2754758.
View | DOI | Download (ext.)
 
[15]
2015 | Conference Paper | IST-REx-ID: 1835   OA
Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_47.
View | Files available | DOI | Download (ext.)
 
[14]
2014 | Journal Article | IST-REx-ID: 2169   OA
Barton, Nicholas H, Sebastian Novak, and Tiago Paixao. “Diverse Forms of Selection in Evolution and Computer Science.” PNAS 111, no. 29 (2014): 10398–99. https://doi.org/10.1073/pnas.1410107111.
View | DOI | Download (ext.)
 
[13]
2014 | Journal Article | IST-REx-ID: 2252
Phadke, Sujal, Tiago Paixao, Tuan Pham, Stephanie Pham, and Rebecca Zufall. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” Journal of Heredity 105, no. 1 (2014): 130–35. https://doi.org/10.1093/jhered/est063.
View | DOI
 
[12]
2013 | Journal Article | IST-REx-ID: 2900
Azevedo, Ricardo, Rolf Lohaus, and Tiago Paixao. “Networking Networks.” Evolution & Development 10, no. 5 (2013): 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?” In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 1573–80. ACM, 2013. https://doi.org/10.1145/2463372.2463568.
View | Files available | DOI
 
[10]
2013 | Journal Article | IST-REx-ID: 2720   OA
Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics 195, no. 2 (2013): 527–40. https://doi.org/10.1534/genetics.113.153536 .
View | DOI | Download (ext.) | PubMed | Europe PMC
 
[9]
2013 | Conference Paper | IST-REx-ID: 2719
Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 845–52. ACM, 2013. https://doi.org/10.1145/2463372.2463470.
View | DOI
 
[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 6, no. 7 (2011). https://doi.org/10.1371/journal.pcbi.1000848.
View | DOI
 
[7]
2011 | Journal Article | IST-REx-ID: 2898
Paixao, Tiago, Sujal Phadke, Ricardo Azevedo, and Rebecca Zufall. “Sex Ratio Evolution under Probabilistic Sex Determination.” Evolution; International Journal of Organic Evolution 65, no. 7 (2011): 2050–60. https://doi.org/10.1111/j.1558-5646.2011.01266.x.
View | DOI
 
[6]
2010 | Journal Article | IST-REx-ID: 2899
Cooper, Tim, Tiago Paixao, and Jack Heinemann. “Within Host Competition Selects for Plasmid Encoded Toxin–Antitoxin Systems.” Proc R Soc B 277, no. 1697 (2010): 3149–55. https://doi.org/10.1098/rspb.2010.0831.
View | DOI
 
[5]
2008 | Journal Article | IST-REx-ID: 2892
Azevedo, Ricardo, Rolf Lohaus, and Tiago Paixao. “Networking Networks.” Evolution & Development 10, no. 5 (2008): 514–15. https://doi.org/10.1111/j.1525-142X.2008.00265.x.
View | DOI
 
[4]
2007 | Journal Article | IST-REx-ID: 2893
Carneiro, Jorge, Kalet Leon, Íris Caramalho, Carline Van Den Dool, Rui Gardner, Vanessa Oliveira, Marie Bergman, et al. “When Three Is Not a Crowd a Crossregulation Model of the Dynamics and Repertoire Selection of Regulatory CD4 T Cells.” Immunological Reviews 216, no. 1 (2007): 48–68. https://doi.org/10.1111/j.1600-065X.2007.00487.x.
View | DOI
 
[3]
2007 | Journal Article | IST-REx-ID: 2896
Paixao, Tiago, Tiago Carvalho, Dinis Calado, and Jorge Carneiro. “Quantitative Insights into Stochastic Monoallelic Expression of Cytokine Genes.” Immunology and Cell Biology 85, no. 4 (2007): 315–22. https://doi.org/10.1038/sj.icb.7100057.
View | DOI
 
[2]
2006 | Journal Article | IST-REx-ID: 2894
Calado, Dinis, Tiago Paixao, Dan Holmberg, and Matthias Haury. “Stochastic Monoallelic Expression of IL 10 in T Cells.” Journal of Immunology 177, no. 8 (2006): 5358–64. https://doi.org/10.4049/jimmunol.177.8.5358 .
View | DOI
 
[1]
2005 | Journal Article | IST-REx-ID: 2895
Carneiro, Jorge, Tiago Paixao, Dejan Milutinovic, João Sousa, Kalet Leon, Rui Gardner, and Jose Faro. “Immunological Self Tolerance: Lessons from Mathematical Modeling.” Journal of Computational and Applied Mathematics 184, no. 1 (2005): 77–100. https://doi.org/10.1016/j.cam.2004.10.025.
View | DOI
 

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