Rui Borges

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Publications

MY orcid: 0000-0002-5905-3778

  1. Borges, R., Kotari, I., Chase, M., Bergman, J., Mugal, C., and Kosiol, C. (2022). Traditional phylogenetic models are insensitive to variations in the effective population size. BioRxiv

  2. 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

  3. 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

  4. 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

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

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

  7. 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

  8. 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

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

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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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