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Authors: Nicolas Rodrigue
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Journal Article

Measuring the relative contribution to predictive power of modern nucleotide substitution modeling approaches Open Access

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Thomas Bujaki and others
Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad091, https://doi.org/10.1093/bioadv/vbad091
Published: 14 July 2023
Journal Article

Erratum to: A Bayesian mutation-selection framework for detecting site-specific adaptive evolution in protein-coding genes Open Access

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Nicolas Rodrigue and others
Molecular Biology and Evolution, Volume 38, Issue 7, July 2021, Page 3032, https://doi.org/10.1093/molbev/msab135
Published: 19 May 2021
Journal Article

A Bayesian Mutation–Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes Open Access

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Nicolas Rodrigue and others
Molecular Biology and Evolution, Volume 38, Issue 3, March 2021, Pages 1199–1208, https://doi.org/10.1093/molbev/msaa265
Published: 12 October 2020
Journal Article

Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation–Selection Models Free

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Simon Laurin-Lemay and others
Molecular Biology and Evolution, Volume 35, Issue 11, November 2018, Pages 2819–2834, https://doi.org/10.1093/molbev/msy173
Published: 07 September 2018
Journal Article

Multiple Factors Confounding Phylogenetic Detection of Selection on Codon Usage Free

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Simon Laurin-Lemay and others
Molecular Biology and Evolution, Volume 35, Issue 6, June 2018, Pages 1463–1472, https://doi.org/10.1093/molbev/msy047
Published: 27 March 2018
Journal Article

COMPASS: the COMPletely Arbitrary Sequence Simulator Free

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Andrew Low and others
Bioinformatics, Volume 33, Issue 19, October 2017, Pages 3101–3103, https://doi.org/10.1093/bioinformatics/btx347
Published: 05 June 2017
Journal Article

Genomics of Compensatory Adaptation in Experimental Populations of Aspergillus nidulans Open Access

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Jeremy R Dettman and others
G3 Genes|Genomes|Genetics, Volume 7, Issue 2, 1 February 2017, Pages 427–436, https://doi.org/10.1534/g3.116.036152
Published: 01 February 2017
Journal Article

Detecting Adaptation in Protein-Coding Genes Using a Bayesian Site-Heterogeneous Mutation-Selection Codon Substitution Model Open Access

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Nicolas Rodrigue and Nicolas Lartillot
Molecular Biology and Evolution, Volume 34, Issue 1, January 2017, Pages 204–214, https://doi.org/10.1093/molbev/msw220
Published: 15 October 2016
Journal Article

Relaxing the Molecular Clock to Different Degrees for Different Substitution Types Free

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Hui-Jie Lee and others
Molecular Biology and Evolution, Volume 32, Issue 8, August 2015, Pages 1948–1961, https://doi.org/10.1093/molbev/msv099
Published: 29 April 2015
Journal Article

The Effect of Selection Environment on the Probability of Parallel Evolution Free

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Susan F. Bailey and others
Molecular Biology and Evolution, Volume 32, Issue 6, June 2015, Pages 1436–1448, https://doi.org/10.1093/molbev/msv033
Published: 11 March 2015
Journal Article

Genome-Wide Patterns of Recombination in the Opportunistic Human Pathogen Pseudomonas aeruginosa Open Access

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Jeremy R. Dettman and others
Genome Biology and Evolution, Volume 7, Issue 1, January 2015, Pages 18–34, https://doi.org/10.1093/gbe/evu260
Published: 04 December 2014
Journal Article

Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package Open Access

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Nicolas Rodrigue and Nicolas Lartillot
Bioinformatics, Volume 30, Issue 7, April 2014, Pages 1020–1021, https://doi.org/10.1093/bioinformatics/btt729
Published: 18 December 2013
Journal Article

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment Get access

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Nicolas Lartillot and others
Systematic Biology, Volume 62, Issue 4, July 2013, Pages 611–615, https://doi.org/10.1093/sysbio/syt022
Published: 05 April 2013
Journal Article

On the Statistical Interpretation of Site-Specific Variables in Phylogeny-Based Substitution Models Free

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Nicolas Rodrigue
Genetics, Volume 193, Issue 2, 1 February 2013, Pages 557–564, https://doi.org/10.1534/genetics.112.145722
Published: 01 February 2013
Journal Article

Fast Bayesian Choice of Phylogenetic Models: Prospecting Data Augmentation–Based Thermodynamic Integration Get access

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Nicolas Rodrigue and Stéphane Aris-Brosou
Systematic Biology, Volume 60, Issue 6, December 2011, Pages 881–887, https://doi.org/10.1093/sysbio/syr065
Published: 29 July 2011
Journal Article

Statistical Potentials for Improved Structurally Constrained Evolutionary Models Free

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Claudia L. Kleinman and others
Molecular Biology and Evolution, Volume 27, Issue 7, July 2010, Pages 1546–1560, https://doi.org/10.1093/molbev/msq047
Published: 16 February 2010
Journal Article

A Dirichlet Process Covarion Mixture Model and Its Assessments Using Posterior Predictive Discrepancy Tests Free

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Yan Zhou and others
Molecular Biology and Evolution, Volume 27, Issue 2, February 2010, Pages 371–384, https://doi.org/10.1093/molbev/msp248
Published: 12 October 2009
Journal Article

Computational Methods for Evaluating Phylogenetic Models of Coding Sequence Evolution with Dependence between Codons Free

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Nicolas Rodrigue and others
Molecular Biology and Evolution, Volume 26, Issue 7, July 2009, Pages 1663–1676, https://doi.org/10.1093/molbev/msp078
Published: 21 April 2009
Journal Article

Bayesian Comparisons of Codon Substitution Models Get access

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Nicolas Rodrigue and others
Genetics, Volume 180, Issue 3, 1 November 2008, Pages 1579–1591, https://doi.org/10.1534/genetics.108.092254
Published: 01 November 2008
Journal Article

Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models Free

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Nicolas Rodrigue and others
Bioinformatics, Volume 24, Issue 1, January 2008, Pages 56–62, https://doi.org/10.1093/bioinformatics/btm532
Published: 14 November 2007