Rui Borges

Publications

MY orcid: 0000-0002-5905-3778

• Borges, R., and Hughes, J. (2026). Phylogenetic inference with not-so-rare mutations and tiny organisms. Systematic Biology, syag065.

• Hooshyar, L., Godin, R., Khastan, A., Borges, R., and Tahiri, N. (2026). New integrative approach to lung cancer risk prediction using fuzzy logic, Bayesian networks, and fuzzy c-means clustering. Conference of the International Federation of Classification Societies, 194–201.

• Braichenko, S., Borges, R., and Kosiol, C. (2025). Phylogenetic methods meet deep learning. Genome Biology and Evolution, 17(10), evaf177.

• Borges, R. (2025). The rarity of mutations and the inflation of bacterial effective population sizes. Methods in Ecology and Evolution, 16(4), 722–732.

• Braichenko, S., Borges, R., and Kosiol, C. (2024). Polymorphism-aware models in RevBayes: Species trees, disentangling balancing selection, and GC-biased gene conversion. Molecular Biology and Evolution, 41(7), msae138.

• Kotari, I., Kosiol, C., and Borges, R. (2024). The patterns of codon usage between chordates and arthropods are different but co-evolving with mutational biases. Molecular Biology and Evolution, 41(5), msae080.

• Ribeiro, D., Borges, R., Rocha, A. P., and Antunes, A. (2023). Testing phylogenetic signal with categorical traits and tree uncertainty. Bioinformatics, 39(7), btad433.

• Borges, R., Boussau, B., Höhna, S., Pereira, R. J., and Kosiol, C. (2022). Polymorphism-aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes. Methods in Ecology and Evolution, 00:1-8

• Borges, R., Boussau, B., Szöllősi, G. J., and Kosiol, C. (2022). Nucleotide usage biases distort inferences of the species tree. Genome Biology and Evolution, 14:1

• Barido-Sottani, J., Justison, J. A., Borges, R., Brown, J. M., Dismukes, W., Petrucci, B. D. R., Fabreti, L. G., Höhna, S., Landis, M. J., Lewis, P. O., May, M. R., Mendes, F. K., Pett, W., Redelings, B. D., Tribble, C. M., Wright, A. M., Zenil-Ferguson, R., and Heath, T. A. (2022). Lessons learned from organizing and teaching virtual phylogenetics workshops. Bulletin of the Society of Systematic Biologists, 1

• Borges, R., Barata, C., and Kosiol, C. (2020). Bait-er: a Bayesian method to detect targets of selection in evolve-and-resequence experiments. BioRxiv

• Borges, R. and Kosiol, C. (2020). Consistency and identifiability of the polymorphism-aware phylogenetic models. Journal of Theoretical Biology, 486:110074

• Gomes, C., Mendes, T., Borges, R., Guarneri, I., Marchi, I., Guilhermino, L., Vasconcelos, V., Riccardi, N., and Antunes, A. (2020). The genetic diversity of two invasive sympatric bivalves (Corbicula fluminea and Dreissena polymorpha) from lakes garda and maggiore, northern Italy. Journal of Great Lakes Research, 46:225–229

• Turakhia, Y., Maio, N. D., Thornlow, B., Gozashti, L., Lanfear, R., Walker, C. R., Hinrichs, A. S., Fernandes, J. D., Borges, R., Slodkowicz, G., Weilguny, L., Haussler, D., Goldman, N., and Corbett-Detig, R. (2020). Stability of sars-cov-2 phylogenies. PloS Genetics, 16:e1009175

• Maio, N. D., Walker, C., Borges, R., Weilguny, L., Slodkowicz, G., and Goldman, N. (2020). Issues with sars-cov-2 sequencing data. virological.org

• De Maio, N., Walker, C., Borges, R., Weilguny, L., Slodkowicz, G., and Goldman, N. (2020). Masking strategies for sars-cov-2 alignments. virological.org

• Borges, R., Szöllősi, G., and Kosiol, C. (2019). Quantifying GC-biased gene conversion in great ape genomes using polymorphism-aware models. Genetics, 212(4):1321-1336

• Borges, R., Machado, J. P., Gomes, C., Rocha, A. P., and Antunes, A. (2019). Measuring phylogenetic signal between categorical traits and phylogenies. Bioinformatics, 35:1862–1869

• Vlachos, C., Burny, C., Pelizzola, M., Borges, R., Futschik, A., Kofler, R., and Schlötterer, C. (2019). Benchmarking software tools for detecting and quantifying selection in evolve and resequencing studies. Genome Biology, 20:169

• Borges, R., Fonseca, J., Gomes, C., Johnson, W. E., O’Brien, S. J., Zhang, G., Gilbert, M. T. P., Jarvis, E. D., and Antunes, A. (2019). Avian binocularity and adaptation to nocturnal environments: Genomic insights from a highly derived visual phenotype. Genome Biology and Evolution, 11:2244–2255

• Borges, R., Johnson, W. E., O’Brien, S. J., Gomes, C., Heesy, C. P., and Antunes, A. (2018). Adaptive genomic evolution of opsins reveals that early mammals flourished in nocturnal environments. BMC Genomics, 19:121

• Gomes, C., Sousa, R., Mendes, T., Borges, R., Vilares, P., Vasconcelos, V., Guilhermino, L., and Antunes, A. (2016). Low genetic diversity and high invasion success of corbicula fluminea (bivalvia, corbiculidae) (Müller, 1774) in portugal. PloS One, 11:e0158108

• Borges, R., Khan, I., Johnson, W. E. W., Gilbert, M. T. P., Zhang, G., Jarvis, E. E. D., O’Brien, S. J., and Antunes, A. (2015). Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds. BMC genomics, 16:1–13

• Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., Storz, J. F., Antunes, A., Greenwold, M. J., Meredith, R. W., Odeen, A., Cui, J., Zhou, Q., Xu, L., Pan, H., Wang, Z., Jin, L., Zhang, P., Hu, H., Yang, W., Hu, J., Xiao, J., Yang, Z., Liu, Y., Xie, Q., Yu, H., Lian, J., Wen, P., Zhang, F., Li, H., Zeng, Y., Xiong, Z., Liu, S., Zhou, L., Huang, Z., An, N., Wang, J., Zheng, Q., Xiong, Y., Wang, G., Wang, B., Wang, J., Fan, Y., da Fonseca, R. R., Alfaro-Nunez, A., Schubert, M., Orlando, L., Mourier, T., Howard, J. T., Ganapathy, G., Pfenning, A., Whitney, O., Rivas, M. V., Hara, E., Smith, J., Farre, M., Narayan, J., Slavov, G., Romanov, M. N., Borges, R., Machado, J. P., Khan, I., Springer, M. S., Gatesy, J., Hoffmann, F. G., Opazo, J. C., Hastad, O., Sawyer, R. H., Kim, H., Kim, K.-W., Kim, H. J., Cho, S., Li, N., Huang, Y., Bruford, M. W., Zhan, X., Dixon, A., Bertelsen, M. F., Derryberry, E., Warren, W., Wilson, R. K., Li, S., Ray, D. A., Green, R. E., O’Brien, S. J., Griffin, D., Johnson, W. E., Haussler, D., Ryder, O. A., Willerslev, E., Graves, G. R., Alstrom, P., Fjeldsa, J., Mindell, D. P., Edwards, S. V., Braun, E. L., Rahbek, C., Burt, D. W., Houde, P., Zhang, Y., Yang, H., Wang, J., Jarvis, E. D., Gilbert, M. T. P., Wang, J., Ye, C., Liang, S., Yan, Z., Zepeda, M. L., Campos, P. F., Velazquez, A. M. V., Samaniego, J. A., Avila-Arcos, M., Martin, M. D., Barnett, R., Ribeiro, A. M., Mello, C. V., Lovell, P. V., Almeida, D., Maldonado, E., Pereira, J., Sunagar, K., Philip, S., Dominguez-Bello, M. G., Bunce, M., Lambert, D., Brumfield, R. T., Sheldon, F. H., Holmes, E. C., Gardner, P. P., Steeves, T. E., Stadler, P. F., Burge, S. W., Lyons, E., Smith, J., McCarthy, F., Pitel, F., Rhoads, D., and Froman, D. P. (2014). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346:1311–1320

1. Borges, R., Johnson, W. E., O’Brien, S. J., Vasconcelos, V., and Antunes, A. (2012). The role of gene duplication and unconstrained selective pressures in the melanopsin gene family evolution and vertebrate circadian rhythm regulation. PloS One, 7:e52413