Publications

Please also check Google Scholar and ORCID

Publications

Wu, Q., Sacomboio, E., Valente de Souza, L., Martins, R., Kitoko, J., Cardoso, S., Ademolue, T. W., Paixão, T., Lehtimäki, J., Figueiredo, A., Norden, C., Tharaux, P.-L., Weiss, G., Wang, F., Ramos, S., & Soares, M. P. (2023). Renal control of life-threatening malarial anemia. Cell Reports, 42(2), 112057. https://doi.org/10.1016/j.celrep.2023.112057

Gonçalves, C., Kareklas, K., Teles, M. C., Varela, S. A. M., Costa, J., Leite, R. B., Paixão, T., & Oliveira, R. F. (2022). Phenotypic architecture of sociality and its associated genetic polymorphisms in zebrafish. Genes, Brain and Behavior, n/a(n/a), e12809. https://doi.org/10.1111/gbb.12809

Ramos, S., Ademolue, T. W., Jentho, E., Wu, Q., Guerra, J., Martins, R., Pires, G., Weis, S., Carlos, A. R., Mahú, I., Seixas, E., Duarte, D., Rajas, F., Cardoso, S., Sousa, A. G. G., Lilue, J., Paixão, T., Mithieux, G., Nogueira, F., & Soares, M. P. (2022). A hypometabolic defense strategy against malaria. Cell Metabolism, 34(8), 1183–1200.e12. https://doi.org/10.1016/j.cmet.2022.06.011

Smolle, M. A., Goetz, C., Maurer, D., Vielgut, I., Novak, M., Zier, G., Leithner, A., Nehrer, S., Paixao, T., Ljuhar, R., & Sadoghi, P. (2022). Artificial intelligence-based computer-aided system for knee osteoarthritis assessment increases experienced orthopaedic surgeons’ agreement rate and accuracy. Knee Surgery, Sports Traumatology, Arthroscopy. https://doi.org/10.1007/s00167-022-07220-y

Velho, T. R., Ferreira, R., Willmann, K., Pedroso, D., Paixão, T., Pereira, R. M., Junqueira, N., Guerra, N. C., Brito, D., Almeida, A. G., Nobre, Â., Köcher, T., Pinto, F., & Moita, L. F. (2022). Role of Omega-6 Fatty Acid Metabolism in Cardiac Surgery Postoperative Bleeding Risk. Critical Care Explorations, 4(10), e0763. https://doi.org/10.1097/CCE.0000000000000763

Velho, T. R., Pereira, R. M., Paixão, T., Guerra, N. C., Ferreira, R., Corte-Real, H., Nobre, Â., & Moita, L. F. (2022). Sequential Organ Failure Assessment Score in the ICU As a Predictor of Long-Term Survival After Cardiac Surgery. Critical Care Explorations, 4(5), e0682. https://doi.org/10.1097/CCE.0000000000000682

Wu, Q., Sacomboio, E., Souza, L. V. de, Martins, R., Cardoso, S., Ademolue, T. W., Paixão, T., Lehtimäki, J., Norden, C., Tharaux, P.-L., Weiss, G., Wang, F., Ramos, S., & Soares, M. P. (2022). A Protective Inter-Organ Communication Response Against Life-Threatening Malarial Anemia (p. 2022.01.12.475857). bioRxiv. https://doi.org/10.1101/2022.01.12.475857

Ducrée, J., Etzrodt, M., Bartling, S., Walshe, R., Harrington, T., Wittek, N., Posth, S., Wittek, K., Ionita, A., Prinz, W., Kogias, D., Paixão, T., Peterfi, I., & Lawton, J. (2021). Unchaining Collective Intelligence for Science, Research, and Technology Development by Blockchain-Boosted Community Participation. Frontiers in Blockchain, 4. https://doi.org/10.3389/fbloc.2021.631648

Gomes Pereira, S., Sousa, A. L., Nabais, C., Paixão, T., Holmes, A. J., Schorb, M., Goshima, G., Tranfield, E. M., Becker, J. D., & Bettencourt-Dias, M. (2021). The 3D architecture and molecular foundations of de novo centriole assembly via bicentrioles. Current Biology. https://doi.org/10.1016/j.cub.2021.07.063

Gonçalves, C., Kareklas, K., Teles, M. C., Varela, S. A. M., Costa, J., Leite, R. B., Paixão, T., & Oliveira, R. F. (2021). Phenotypic architecture of sociality and its associated genetic polymorphisms in zebrafish (p. 2021.07.29.454277). https://doi.org/10.1101/2021.07.29.454277

Nagy-Staron, A., Tomasek, K., Caruso Carter, C., Sonnleitner, E., Kavčič, B., Paixão, T., & Guet, C. C. (2021). Local genetic context shapes the function of a gene regulatory network. eLife, 10, e65993. https://doi.org/10.7554/eLife.65993

Paiva, R. A., Sousa, A. G. G., Ramos, C. V., Ávila, M., Lilue, J., Paixão, T., & Martins, V. C. (2021). Self-renewal of double-negative 3 early thymocytes enables thymus autonomy but compromises the β-selection checkpoint. Cell Reports, 35(2), 108967. https://doi.org/10.1016/j.celrep.2021.108967

Paixao, T., DiFranco, M. D., Ljuhar, R., Ljuhar, D., Goetz, C., Bertalan, Z., Dimai, H. P., & Nehrer, S. (2020). A novel quantitative metric for joint space width: Data from the osteoarthritis initiative (OAI). Osteoarthritis and Cartilage, 0(0). https://doi.org/10.1016/j.joca.2020.04.003

Paixao, T., Ljuhar, R., Carrino, J. A., Goetz, C., & Nehrer, S. (2020). Application of machine learning for the prediction of cartilage loss: Data from the osteoarthritis initiative & multicenter osteoarthritis study. Osteoarthritis and Cartilage, 28, S318. https://doi.org/10.1016/j.joca.2020.02.491

Dimai, H. P., Paixao, T., Bertalan, Z., Ljuhar, R., Goetz, C., Ljuhar, D., Nehrer, S., & Fahrleitner-Pammer, A. (2019). Artificial Intelligence (AI) Can Detect Bone Marrow Lesions (BMLs) on Plain Radiographs. JOURNAL OF BONE AND MINERAL RESEARCH, 34, 199–199.

Nehrer, S., Ljuhar, R., Steindl, P., Simon, R., Maurer, D., Ljuhar, D., Bertalan, Z., Dimai, H. P., Goetz, C., & Paixao, T. (2019). Automated Knee Osteoarthritis Assessment Increases Physicians’ Agreement Rate and Accuracy: Data from the Osteoarthritis Initiative: CARTILAGE. https://doi.org/10.1177/1947603519888793

Oliveto, P. S., Paixão, T., Pérez Heredia, J., Sudholt, D., & Trubenová, B. (2018). How to Escape Local Optima in Black Box Optimisation: When Non-elitism Outperforms Elitism. Algorithmica, 80(5), 1604–1633. https://doi.org/10.1007/s00453-017-0369-2

Heredia, J. P., Trubenová, B., Sudholt, D., & Paixão, T. (2017). Selection Limits to Adaptive Walks on Correlated Landscapes. Genetics, 205(2), 803–825. https://doi.org/10.1534/genetics.116.189340

Lagator, M., Paixão, T., Barton, N. H., Bollback, J. P., & Guet, C. C. (2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife, 6, e25192. https://doi.org/10.7554/eLife.25192

Lukačišinová, M., Novak, S., & Paixão, T. (2017). Stress-induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLOS Computational Biology, 13(7), e1005609. https://doi.org/10.1371/journal.pcbi.1005609

Paixão, T., & Pérez Heredia, J. (2017). An Application of Stochastic Differential Equations to Evolutionary Algorithms. Proceedings of Foundations of Genetic Algorithms (FOGA 2017).

Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixão, T., & Petrov, T. (2016). Model checking the evolution of gene regulatory networks. Acta Informatica, 1–23. https://doi.org/10.1007/s00236-016-0278-x

Oliveto, P. S., Paixão, T., Pérez Heredia, J., Sudholt, D., & Trubenová, B. (2016). When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys. Proceedings of the Genetic and Evolutionary Computation Conference 2016, 1163–1170. https://doi.org/10.1145/2908812.2908909

Paixão, T., & Barton, N. H. (2016). The effect of gene interactions on the long-term response to selection. Proceedings of the National Academy of Sciences, 113(16), 4422–4427. https://doi.org/10.1073/pnas.1518830113

Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixão, T., & Petrov, T. (2015). Model Checking Gene Regulatory Networks. In C. Baier & C. Tinelli (Eds.), Tools and Algorithms for the Construction and Analysis of Systems (pp. 469–483). Springer Berlin Heidelberg. http://link.springer.com/chapter/10.1007/978-3-662-46681-0_47

Paixão, T., Badkobeh, G., Barton, N., Çörüş, D., Dang, D.-C., Friedrich, T., Lehre, P. K., Sudholt, D., Sutton, A. M., & Trubenová, B. (2015). Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology, 383, 28–43. https://doi.org/10.1016/j.jtbi.2015.07.011

Paixão, T., Bassler, K. E., & Azevedo, R. B. R. (2015). Emergent Speciation by Multiple Dobzhansky–Muller Incompatibilities. bioRxiv, 008268. https://doi.org/10.1101/008268

Tuğrul, M., Paixão, T., Barton, N. H., & Tkačik, G. (2015). Dynamics of Transcription Factor Binding Site Evolution. PLoS Genet, 11(11), e1005639. https://doi.org/10.1371/journal.pgen.1005639

Barton, N. H., Novak, S., & Paixão, T. (2014). Diverse forms of selection in evolution and computer science. Proceedings of the National Academy of Sciences, 111(29), 10398–10399. https://doi.org/10.1073/pnas.1410107111

Phadke, S. S., Paixão, T., Pham, T., Pham, S., & Zufall, R. A. (2014). Genetic Background Alters Dominance Relationships between mat Alleles in the Ciliate Tetrahymena thermophila. Journal of Heredity, 105(1), 130–135. https://doi.org/10.1093/jhered/est063

Barton, N., & Paixão, T. (2013). Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation? Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation Conference (GECCO 2013), 1573–1580. https://doi.org/10.1145/2463372.2463568

Long, H.-A., Paixão, T., Azevedo, R. B. R., & Zufall, R. A. (2013). Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena thermophila. Genetics, 195(2), 527–540. https://doi.org/10.1534/genetics.113.153536

Paixão, T., & Barton, N. (2013). A Variance Decomposition Approach to the Analysis of Genetic Algorithms. Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation Conference (GECCO 2013), 845–852. https://doi.org/10.1145/2463372.2463470

Paixão, T., Phadke, S. S., Azevedo, R. B. R., & Zufall, R. A. (2011). Sex ratio evolution under probabilistic sex determination. Evolution, 65(7), 2050–2060. https://doi.org/10.1111/j.1558-5646.2011.01266.x

Cooper, T. F., Paixão, T., & Heinemann, J. A. (2010). Within-host competition selects for plasmid-encoded toxin–antitoxin systems. Proceedings of the Royal Society B: Biological Sciences, 277(1697), 3149–3155. https://doi.org/10.1098/rspb.2010.0831

Paixão, T., & Azevedo, R. B. R. (2010). Redundancy and the Evolution of Cis-Regulatory Element Multiplicity. PLoS Comput Biol, 6(7), e1000848. https://doi.org/10.1371/journal.pcbi.1000848

Azevedo, R. B. R., Lohaus, R., & Paixão, T. (2008). Networking networks. Evolution & Development, 10(5), 514–515. https://doi.org/10.1111/j.1525-142X.2008.00265.x

Carneiro, J., Leon, K., Caramalho, Í., Van Den Dool, C., Gardner, R., Oliveira, V., Bergman, M.-L., Sepúlveda, N., Paixão, T., Faro, J., & Demengeot, J. (2007). When three is not a crowd: A Crossregulation Model of the dynamics and repertoire selection of regulatory CD4+ T cells. Immunological Reviews, 216(1), 48–68. https://doi.org/10.1111/j.1600-065X.2007.00487.x

Paixão, T., Carvalho, T. P., Calado, D. P., & Carneiro, J. (2007). Quantitative insights into stochastic monoallelic expression of cytokine genes. Immunology and Cell Biology, 85(4), 315–322. https://doi.org/7100057

Calado, D. P., Paixão, T., Holmberg, D., & Haury, M. (2006). Stochastic Monoallelic Expression of IL-10 in T Cells. The Journal of Immunology, 177(8), 5358–5364. http://www.jimmunol.org/content/177/8/5358

Carneiro, J., Paixão, T., Milutinovic, D., Sousa, J., Leon, K., Gardner, R., & Faro, J. (2005). Immunological self-tolerance: Lessons from mathematical modeling. Journal of Computational and Applied Mathematics, 184(1), 77–100. https://doi.org/10.1016/j.cam.2004.10.025