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Identification

Personal identification

Full name
Tiago Matias Machado dos Santos Seara Paixão

Citation names

  • Paixão, Tiago

Author identifiers

Ciência ID
C41D-4B88-1D2C
ORCID iD
0000-0003-2361-3953
Google Scholar ID
7x0vA8EAAAAJ
Scopus Author Id
24773710200

Email addresses

  • tpaixao@igc.gulbenkian.pt (Professional)

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Education
Degree Classification
2007/09
Concluded
 - (Doutoramento)
Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
"The Stochastic Basis of Somatic Variation" (THESIS/DISSERTATION)
 Aprovado por Unanimidade
2001
Concluded
 Engenharia Fisica e Tecnologica (Licenciatura)
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Análise do modelo de Frenkel-Kontorova" (THESIS/DISSERTATION)
 15
Affiliation

Science

Category
Host institution 		Employer
2020 - Current Contracted Researcher (Research) Instituto Gulbenkian de Ciência, Portugal
2011 - 2017 Contracted Researcher (Research) Institute of Science and Technology Austria, Austria

Others

Category
Host institution 		Employer
2018 - 2019 Head of Clinical Research IB Lab GmbH (ImageBiopsy Lab), Austria
2008 - 2011 Postdoctoral fellow University of Houston, United States
2003 - 2007 PhD student Instituto Gulbenkian de Ciência, Portugal
2001 - 2002 Junior Researcher at the Non-Linear Dynamics Group at IST Universidade de Lisboa Instituto Superior Técnico, Portugal
Projects

Grant

Designation Funders
2013/01 - 2017/01 Speed of Adaptation in Genetics and Evolutionary computation (SAGE)
618091
 Seventh Framework Programme
2009/01/01 - 2009/12/31 A computational framework for the evolution of gene regulatory networks
SFRH/BPD/43753/2008
Researcher
University of Houston, United States
 Fundação para a Ciência e a Tecnologia
Concluded
2003 - 2007 The Stochastic basis of somatic variation
SFRH/BD/10550/2002
Instituto Gulbenkian de Ciência, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded

Other

Designation Funders
2021/01/01 - Current Comprehensive study of the mutational effects in E.coli
CPCA/A1/7350/2020
Principal investigator
Instituto Gulbenkian de Ciência, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
Outputs

Publications

Conference paper
  1. Oliveto, P.S.; Paixão, T.; Heredia, J.P.; Sudholt, D.; Trubenová, B.. "When non-elitism outperforms elitism for crossing fitness valleys". 2016.
    10.1145/2908812.2908909
  2. Tiago Paixao; Jorge Pérez Heredia; Dirk Sudholt; Barbora Trubenova. "First Steps Towards a Runtime Comparison of Natural and Artificial Evolution". 2015.
    10.1145/2739480.2754758
  3. Tiago Paixão; Nick Barton. "A variance decomposition approach to the analysis of genetic algorithms". 2013.
    10.1145/2463372.2463470
  4. Nick Barton; Tiago Paixão. "Can quantitative and population genetics help us understand evolutionary computation?". 2013.
    10.1145/2463372.2463568
Journal article
  1. Susana Ramos; Viktoria Jeney; Ana Figueiredo; Tiago Paixão; Maria Rosário Sambo; Vatúsia Quinhentos; Rui Martins; et al. "Targeting circulating labile heme as a defense strategy against malaria". Life Science Alliance (2024): https://doi.org/10.26508/lsa.202302276.
    10.26508/lsa.202302276
  2. Caramalho, Iris; Matoso, Paula; Ligeiro, Dário; Paixão, Tiago; Sobral, Daniel; Fitas, Ana Laura; Limbert, Catarina; Demengeot, Jocelyne; Penha-Gonçalves, Carlos. "The rare DRB1*04:08-DQ8 haplotype is the main HLA class II genetic driver and discriminative factor of Early-onset Type 1 diabetes in the Portuguese population". Frontiers in Immunology 14 (2024): http://dx.doi.org/10.3389/fimmu.2023.1299609.
    10.3389/fimmu.2023.1299609
  3. Wu, Qian; Sacomboio, Euclides; Valente de Souza, Lara; Martins, Rui; Kitoko, Jamil; Cardoso, Sílvia; Ademolue, Temitope W.; et al. "Renal control of life-threatening malarial anemia". Cell Reports 42 2 (2023): 112057. http://dx.doi.org/10.1016/j.celrep.2023.112057.
    10.1016/j.celrep.2023.112057
  4. Smolle, Maria Anna; Goetz, Christoph; Maurer, Dietmar; Vielgut, Ines; Novak, Michael; Zier, Gerhard; Leithner, Andreas; et al. "Artificial intelligence-based computer-aided system for knee osteoarthritis assessment increases experienced orthopaedic surgeons’ agreement rate and accuracy". Knee Surgery, Sports Traumatology, Arthroscopy 31 3 (2022): 1053-1062. http://dx.doi.org/10.1007/s00167-022-07220-y.
    10.1007/s00167-022-07220-y
  5. Velho, Tiago R.; Ferreira, Ricardo; Willmann, Katharina; Pedroso, Dora; Paixão, Tiago; Pereira, Rafael Maniés; Junqueira, Nádia; et al. "Role of Omega-6 Fatty Acid Metabolism in Cardiac Surgery Postoperative Bleeding Risk". Critical Care Explorations 4 10 (2022): e0763. http://dx.doi.org/10.1097/cce.0000000000000763.
    10.1097/cce.0000000000000763
  6. Velho, Tiago R.; Pereira, Rafael Maniés; Paixão, Tiago; Guerra, Nuno Carvalho; Ferreira, Ricardo; Corte-Real, Hugo; Nobre, Ângelo; Moita, Luís Ferreira. "Sequential Organ Failure Assessment Score in the ICU As a Predictor of Long-Term Survival After Cardiac Surgery". Critical Care Explorations 4 5 (2022): e0682. http://dx.doi.org/10.1097/cce.0000000000000682.
    10.1097/cce.0000000000000682
  7. Gomes Pereira, Sónia; Sousa, Ana Laura; Nabais, Catarina; Paixão, Tiago; Holmes, Alexander J.; Schorb, Martin; Goshima, Gohta; et al. "The 3D architecture and molecular foundations of de novo centriole assembly via bicentrioles". Current Biology 31 19 (2021): 4340-4353.e7. http://dx.doi.org/10.1016/j.cub.2021.07.063.
    Published • 10.1016/j.cub.2021.07.063
  8. Ducrée, Jens; Etzrodt, Martin; Bartling, Sönke; Walshe, Ray; Harrington, Tomás; Wittek, Neslihan; Posth, Sebastian; et al. "Unchaining Collective Intelligence for Science, Research, and Technology Development by Blockchain-Boosted Community Participation". Frontiers in Blockchain 4 (2021): http://dx.doi.org/10.3389/fbloc.2021.631648.
    10.3389/fbloc.2021.631648
  9. Paiva, Rafael A.; Sousa, António G.G.; Ramos, Camila V.; Ávila, Mariana; Lilue, Jingtao; Paixão, Tiago; Martins, Vera C.. "Self-renewal of double-negative 3 early thymocytes enables thymus autonomy but compromises the ß-selection checkpoint". Cell Reports 35 2 (2021): 108967. http://dx.doi.org/10.1016/j.celrep.2021.108967.
    10.1016/j.celrep.2021.108967
  10. Nagy-Staron, Anna; Tomasek, Kathrin; Caruso Carter, Caroline; Sonnleitner, Elisabeth; Kavcic, Bor; Paixão, Tiago; Guet, Calin C. "Local genetic context shapes the function of a gene regulatory network". eLife 10 (2021): e65993. http://dx.doi.org/10.7554/elife.65993.
    Open access • Published • 10.7554/elife.65993
  11. Paixao, T.; DiFranco, M.D.; Ljuhar, R.; Ljuhar, D.; Goetz, C.; Bertalan, Z.; Dimai, H.P.; Nehrer, S.. "A novel quantitative metric for joint space width: data from the Osteoarthritis Initiative (OAI)". Osteoarthritis and Cartilage (2020): http://dx.doi.org/10.1016/j.joca.2020.04.003.
    Published • 10.1016/j.joca.2020.04.003
  12. Paixao, T.; Ljuhar, R.; Carrino, J.A.; Goetz, C.; Nehrer, S.. "Application of machine learning for the prediction of cartilage loss: data from the osteoarthritis initiative & multicenter osteoarthritis study". Osteoarthritis and Cartilage 28 (2020): S318. http://dx.doi.org/10.1016/j.joca.2020.02.491.
    Published • 10.1016/j.joca.2020.02.491
  13. Nehrer, Stefan; Ljuhar, Richard; Steindl, Peter; Simon, Rene; Maurer, Dietmar; Ljuhar, Davul; Bertalan, Zsolt; et al. "Automated Knee Osteoarthritis Assessment Increases Physicians’ Agreement Rate and Accuracy: Data from the Osteoarthritis Initiative". CARTILAGE (2019): http://dx.doi.org/10.1177/1947603519888793.
    Published • 10.1177/1947603519888793
  14. Marta Lukacišinová; Claus O. Wilke; Sebastian Novak; Tiago Paixão. "Stress-induced mutagenesis: Stress diversity facilitates the persistence of mutator genes". PLOS Computational Biology 13 7 (2017): e1005609-e1005609. https://doi.org/10.1371%2Fjournal.pcbi.1005609.
    10.1371/journal.pcbi.1005609
  15. Mato Lagator; Tiago Paixão; Nicholas H Barton; Jonathan P Bollback; 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.
    10.7554/eLife.25192
  16. Paixão T; Barton NH. "The effect of gene interactions on the long-term response to selection.". (2016): http://europepmc.org/abstract/med/27044080.
    10.1073/pnas.1518830113
  17. Perez Heredia, Jorge; Trubenova, Barbora; Sudholt, Dirk; Paixao, Tiago; Pérez Heredia J; Trubenová B; Sudholt D; Paixão T. "Selection Limits to Adaptive Walks on Correlated Landscapes.". Genetics (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:27881471&KeyUID=MEDLINE:27881471.
  18. Giacobbe, M.; Guet, C.C.; Gupta, A.; Henzinger, T.A.; Paixão, T.; Petrov, T.. "Model checking the evolution of gene regulatory networks". Acta Informatica (2016): 1-23. http://www.scopus.com/inward/record.url?eid=2-s2.0-84983499661&partnerID=MN8TOARS.
    10.1007/s00236-016-0278-x
  19. Murat Tugrul; Tiago Paixão; Nicholas H. Barton; Gašper Tkacik; Justin C. Fay. "Dynamics of Transcription Factor Binding Site Evolution". PLoS Genet 11 11 (2015): e1005639-e1005639. http://dx.doi.org/10.1371/journal.pgen.1005639.
    10.1371/journal.pgen.1005639
  20. Tiago Paixão; Golnaz Badkobeh; Nick Barton; Dogan Çörüs; Duc-Cuong Dang; Tobias Friedrich; Per Kristian Lehre; et al. "Toward a unifying framework for evolutionary processes". Journal of Theoretical Biology 383 (2015): 28-43. http://dx.doi.org/10.1016/j.jtbi.2015.07.011.
    10.1016/j.jtbi.2015.07.011
  21. N. H. Barton; S. Novak; T. Paixao. "Diverse forms of selection in evolution and computer science". Proceedings of the National Academy of Sciences 111 29 (2014): 10398-10399. http://dx.doi.org/10.1073/pnas.1410107111.
    10.1073/pnas.1410107111
  22. S. S. Phadke; T. Paixao; T. Pham; S. Pham; R. A. Zufall. "Genetic Background Alters Dominance Relationships between mat Alleles in the Ciliate Tetrahymena thermophila". Journal of Heredity 105 1 (2013): 130-135. http://dx.doi.org/10.1093/jhered/est063.
    10.1093/jhered/est063
  23. H.-A. Long; T. Paixao; R. B. R. Azevedo; R. A. Zufall. "Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena thermophila". Genetics 195 2 (2013): 527-540. http://dx.doi.org/10.1534/genetics.113.153536.
    10.1534/genetics.113.153536
  24. Paixao, Tiago; Barton, Nick; Blum, C. "A Variance Decomposition Approach to the Analysis of Genetic Algorithms". Gecco'13: Proceedings of the 2013 Genetic and Evolutionary Computation Conference (2013): 845-852. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000321981300106&KeyUID=WOS:000321981300106.
  25. Barton, Nick; Paixao, Tiago; Blum, C. "Can Quantitative and Population Genetics Help us Understand Evolutionary Computation?". Gecco'13: Proceedings of the 2013 Genetic and Evolutionary Computation Conference (2013): 1573-1580. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000321981300197&KeyUID=WOS:000321981300197.
  26. Tiago Paixão; Sujal S. Phadke; Ricardo B. R. Azevedo; Rebecca A. Zufall. "SEX RATIO EVOLUTION UNDER PROBABILISTIC SEX DETERMINATION". Evolution 65 7 (2011): 2050-2060. http://dx.doi.org/10.1111/j.1558-5646.2011.01266.x.
    10.1111/j.1558-5646.2011.01266.x
  27. Tiago Paixão; Ricardo B. R. Azevedo; Philip E. Bourne. "Redundancy and the Evolution of Cis-Regulatory Element Multiplicity". PLoS Comput Biol 6 7 (2010): e1000848-e1000848. http://dx.doi.org/10.1371/journal.pcbi.1000848.
    10.1371/journal.pcbi.1000848
  28. T. F. Cooper; T. Paixao; J. A. Heinemann. "Within-host competition selects for plasmid-encoded toxin-antitoxin systems". Proceedings of the Royal Society B: Biological Sciences 277 1697 (2010): 3149-3155. http://dx.doi.org/10.1098/rspb.2010.0831.
    10.1098/rspb.2010.0831
  29. Ricardo B. R. Azevedo; Rolf Lohaus; Tiago Paixão. "Networking networks". Evolution & Development 10 5 (2008): 514-515. http://dx.doi.org/10.1111/j.1525-142x.2008.00265.x.
    10.1111/j.1525-142x.2008.00265.x
  30. Azevedo, R.B.R.; Lohaus, R.; Paixão, T.. "Networking networks". Evolution and Development 10 5 (2008): 514-515. http://www.scopus.com/inward/record.url?eid=2-s2.0-51249093403&partnerID=MN8TOARS.
    10.1111/j.1525-142X.2008.00265.x
  31. Tiago Paixão; Tiago P Carvalho; Dinis P Calado; Jorge Carneiro. "Quantitative insights into stochastic monoallelic expression of cytokine genes". Immunol Cell Biol 85 4 (2007): 315-322. http://dx.doi.org/10.1038/sj.icb.7100057.
    10.1038/sj.icb.7100057
  32. Carneiro, Jorge; Leon, Kalet; Caramalho, Iris; van den Dool, Carline; Gardner, Rui; Oliveira, Vanessa; Bergman, Marie-Louise; 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 1 (2007): 48-68. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000244885500005&KeyUID=WOS:000244885500005.
    10.1111/j.1600-065x.2007.00487.x
  33. Calado, Dinis Pedro; Paixao, Tiago; Holmberg, Dan; Haury, Matthias; Calado, D.P.; Paixão, T.; Holmberg, D.; et al. "Stochastic monoallelic expression of IL-10 in T cells". Journal of Immunology 177 8 (2006): 5358-5364. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000241093100048&KeyUID=WOS:000241093100048.
    10.4049/jimmunol.177.8.5358
  34. Jorge Carneiro; Tiago Paixão; Dejan Milutinovic; João Sousa; Kalet Leon; Rui Gardner; Jose Faro. "Immunological self-tolerance: Lessons from mathematical modeling". Journal of Computational and Applied Mathematics 184 1 (2005): 77-100. http://dx.doi.org/10.1016/j.cam.2004.10.025.
    10.1016/j.cam.2004.10.025
Preprint
  1. Ravi Vishwakarma; Gabriele Maria Sgarlata; David Soriano-Panos; Rita Rasteiro; Tiago Maie; Tiago Paixao; Remi Tournebize; Lounes Chikhi. "Life history traits influence the dynamics of genetic diversity in a refugium population undergoing expansion and contraction". 2024. https://doi.org/10.1101/2024.03.28.586951.
    10.1101/2024.03.28.586951
  2. Qian Wu; Euclides Sacomboio; Lara Valente de Souza; Rui Martins; Sílvia Cardoso; Temitope W. Ademolue; Tiago Paixão; et al. "A Protective Inter-Organ Communication Response Against Life-Threatening Malarial Anemia". 2022. https://doi.org/10.1101/2022.01.12.475857.
    10.1101/2022.01.12.475857

Other

Other output
  1. Phenotypic architecture of sociality and its associated genetic polymorphisms in zebrafish. 2021. Claúdia Gonçalves; Kyriacos Kareklas; Magda C. Teles; Susana A. M. Varela; João Costa; Ricardo B. Leite; Tiago Paixão; Rui F. Oliveira. https://doi.org/10.1101/2021.07.29.454277.
    10.1101/2021.07.29.454277
  2. The 3D architecture and molecular foundations of de novo centriole assembly via bicentrioles. 2020. Sónia Gomes Pereira; Ana Laura Sousa; Catarina Nabais; Tiago Paixão; Alexander. J. Holmes; Martin Schorb; Gohta Goshima; et al. https://doi.org/10.1101/2020.12.21.423647.
    10.1101/2020.12.21.423647
  3. Model Checking Gene Regulatory Networks. 2015. Mirco Giacobbe; Calin C. Guet; Ashutosh Gupta; Thomas A. Henzinger; Tiago Paixão; Tatjana Petrov. http://dx.doi.org/10.1007/978-3-662-46681-0_47.
    10.1007/978-3-662-46681-0_47
  4. Emergent speciation by multiple Dobzhansky-Muller incompatibilities. 2014. Tiago Paixão; Kevin E. Bassler; Ricardo B. R. Azevedo.
    10.1101/008268
Activities

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2020/09/01 - Current Evolutionary analysis of metabolic models in E. Coli
Supervisor
Instituto Gulbenkian de Ciência, Portugal

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2022/11/09 Habitat loss and fragmentation: effects on genetic diversity and differentiation
(Thesis) Main arguer
 Gabriele Maria Sgarlata (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
2022/09/16 The Role of Competition in Microbial Evolution: A theoretical and computational study of recurrent mutations within complex ecosystems
(Thesis) Arguer
 Massimo Amicone (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
2022/05/04 Studies of Staphylococcus aureus cell cycle: New approaches for automated analysis
(Thesis) Arguer
 Bruno Saraiva (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
2021 Finite Mixture Models based on Scale Mixtures of Skew-Normal distributions applied to serological data
(Thesis) Arguer
 Tiago Domingues (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2018 Stability, Robustness, and Phenotype Accessibility in Boolean Gene Regulatory Networks
(Thesis) Main arguer
 Ricardo Pinho (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
2014 Variation in protein expression levels in cell populations
(Thesis) Main arguer
 Thiago Guzella (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
Distinctions

Other distinction

2008 Honorable Mention (3rd place) at the Reinhart Heinrich Doctoral Thesis Award