Publications by authors named "Rui Borges"

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Phylogenetic Methods Meet Deep Learning.
Svitlana Braichenko, Rui Borges, Carolin Kosiol

Genome Biol Evol· September 2025

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Polymorphism-Aware Models in RevBayes: Species Trees, Disentangling Balancing Selection, and GC-Biased Gene Conversion.
Svitlana Braichenko, Rui Borges, Carolin Kosiol

Mol Biol Evol· July 2024

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The Patterns of Codon Usage between Chordates and Arthropods are Different but Co-evolving with Mutational Biases.
Ioanna Kotari, Carolin Kosiol, Rui Borges

Mol Biol Evol· May 2024

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Testing phylogenetic signal with categorical traits and tree uncertainty.
Diogo Ribeiro, Rui Borges, Ana Paula Rocha, Agostinho Antunes

Bioinformatics· July 2023

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Bait-ER: A Bayesian method to detect targets of selection in Evolve-and-Resequence experiments.
Carolina Barata, Rui Borges, Carolin Kosiol

J Evol Biol· January 2023

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Nucleotide Usage Biases Distort Inferences of the Species Tree.
Rui Borges, Bastien Boussau, Gergely J Szöllősi, Carolin Kosiol

Genome Biol Evol· January 2022

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Stability of SARS-CoV-2 phylogenies.
Yatish Turakhia, Nicola De Maio, Bryan Thornlow, Landen Gozashti, Robert Lanfear, Rui Borges

PLoS Genet· November 2020

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Consistency and identifiability of the polymorphism-aware phylogenetic models.
Rui Borges, Carolin Kosiol

J Theor Biol· February 2020

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Quantifying GC-Biased Gene Conversion in Great Ape Genomes Using Polymorphism-Aware Models.
Rui Borges, Gergely J Szöllősi, Carolin Kosiol

Genetics· August 2019

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Avian Binocularity and Adaptation to Nocturnal Environments: Genomic Insights from a Highly Derived Visual Phenotype.
Rui Borges, João Fonseca, Cidália Gomes, Warren E Johnson, Stephen J O'Brien

Genome Biol Evol· August 2019

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Benchmarking software tools for detecting and quantifying selection in evolve and resequencing studies.
Christos Vlachos, Claire Burny, Marta Pelizzola, Rui Borges, Andreas Futschik

Genome Biol· August 2019

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Measuring phylogenetic signal between categorical traits and phylogenies.
Rui Borges, João Paulo Machado, Cidália Gomes, Ana Paula Rocha, Agostinho Antunes

Bioinformatics· June 2019

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Adaptive genomic evolution of opsins reveals that early mammals flourished in nocturnal environments.
Rui Borges, Warren E Johnson, Stephen J O'Brien, Cidália Gomes, Christopher P Heesy

BMC Genomics· February 2018

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Low Genetic Diversity and High Invasion Success of Corbicula fluminea (Bivalvia, Corbiculidae) (Müller, 1774) in Portugal.
Cidália Gomes, Ronaldo Sousa, Tito Mendes, Rui Borges, Pedro Vilares

PLoS One· July 2017

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Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds.
Rui Borges, Imran Khan, Warren E Johnson, M Thomas P Gilbert, Guojie Zhang

BMC Genomics· October 2015

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Comparative genomics reveals insights into avian genome evolution and adaptation.
Guojie Zhang, Cai Li, Qiye Li, Bo Li, Denis M Larkin, Rui Borges

Science· December 2014

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The role of gene duplication and unconstrained selective pressures in the melanopsin gene family evolution and vertebrate circadian rhythm regulation.
Rui Borges, Warren E Johnson, Stephen J O'Brien, Vitor Vasconcelos, Agostinho Antunes

PLoS One· June 2013

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