Publications by authors named "Nicolas Rodrigue"

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Stochastic Character Mapping: An Under-Exploited Approach to the Study of Molecular Evolution.
Simon Laurin-Lemay, Nicolas Rodrigue

J Mol Evol· August 2025

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Measuring the relative contribution to predictive power of modern nucleotide substitution modeling approaches.
Thomas Bujaki, Katharine Van Looyen, Nicolas Rodrigue

Bioinform Adv· July 2023

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Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale.
Thibault Latrille, Nicolas Rodrigue, Nicolas Lartillot

Proc Natl Acad Sci U S A· March 2023

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Bayesian Cross-Validation Comparison of Amino Acid Replacement Models: Contrasting Profile Mixtures, Pairwise Exchangeabilities, and Gamma-Distributed Rates-Across-Sites.
Thomas Bujaki, Nicolas Rodrigue

J Mol Evol· December 2022

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Jump-Chain Simulation of Markov Substitution Processes Over Phylogenies.
Simon Laurin-Lemay, Kassandra Dickson, Nicolas Rodrigue

J Mol Evol· August 2022

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Erratum to: A Bayesian mutation-selection framework for detecting site-specific adaptive evolution in protein-coding genes.
Nicolas Rodrigue, Thibault Latrille, Nicolas Lartillot

Mol Biol Evol· June 2021

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A Bayesian Mutation-Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes.
Nicolas Rodrigue, Thibault Latrille, Nicolas Lartillot

Mol Biol Evol· March 2021

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Evolution of species revealed through sequence analyses of the gene family.
Fariba Shafiei-Koij, Sridhar Ravichandran, Véronique J Barthet, Nicolas Rodrigue, Aghafakhr Mirlohi

Physiol Mol Biol Plants· March 2020

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A Not-So-Long Introduction to Computational Molecular Evolution.
Stéphane Aris-Brosou, Nicolas Rodrigue

Methods Mol Biol· January 2020

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Detecting amino acid preference shifts with codon-level mutation-selection mixture models.
S Omar Kazmi, Nicolas Rodrigue

BMC Evol Biol· February 2019

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Clonal evolution and genome stability in a 2500-year-old fungal individual.
James B Anderson, Johann N Bruhn, Dahlia Kasimer, Hao Wang, Nicolas Rodrigue

Proc Biol Sci· December 2018

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Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation-Selection Models.
Simon Laurin-Lemay, Nicolas Rodrigue, Nicolas Lartillot, Hervé Philippe

Mol Biol Evol· November 2018

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Multiple Factors Confounding Phylogenetic Detection of Selection on Codon Usage.
Simon Laurin-Lemay, Hervé Philippe, Nicolas Rodrigue

Mol Biol Evol· June 2018

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COMPASS: the COMPletely Arbitrary Sequence Simulator.
Andrew Low, Nicolas Rodrigue, Alex Wong

Bioinformatics· October 2017

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Genomics of Compensatory Adaptation in Experimental Populations of .
Jeremy R Dettman, Nicolas Rodrigue, Sijmen E Schoustra, Rees Kassen

G3 (Bethesda)· February 2017

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Detecting Adaptation in Protein-Coding Genes Using a Bayesian Site-Heterogeneous Mutation-Selection Codon Substitution Model.
Nicolas Rodrigue, Nicolas Lartillot

Mol Biol Evol· January 2017

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Whole genome sequencing and comparative genomics of closely related Fusarium Head Blight fungi: Fusarium graminearum, F. meridionale and F. asiaticum.
Sean Walkowiak, Owen Rowland, Nicolas Rodrigue, Rajagopal Subramaniam

BMC Genomics· December 2016

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Grouping substitution types into different relaxed molecular clocks.
Hui-Jie Lee, Hirohisa Kishino, Nicolas Rodrigue, Jeffrey L Thorne

Philos Trans R Soc Lond B Biol Sci· July 2016

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Relaxing the Molecular Clock to Different Degrees for Different Substitution Types.
Hui-Jie Lee, Nicolas Rodrigue, Jeffrey L Thorne

Mol Biol Evol· August 2015

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The effect of selection environment on the probability of parallel evolution.
Susan F Bailey, Nicolas Rodrigue, Rees Kassen

Mol Biol Evol· June 2015

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Genome-wide patterns of recombination in the opportunistic human pathogen Pseudomonas aeruginosa.
Jeremy R Dettman, Nicolas Rodrigue, Rees Kassen

Genome Biol Evol· December 2014

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Codon-based phylogenetics introduces novel flagellar gene markers to oomycete systematics.
Gregg P Robideau, Nicolas Rodrigue, C André Lévesque

Mol Phylogenet Evol· October 2014

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Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package.
Nicolas Rodrigue, Nicolas Lartillot

Bioinformatics· April 2014

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Evolutionary genomics of epidemic and nonepidemic strains of Pseudomonas aeruginosa.
Jeremy R Dettman, Nicolas Rodrigue, Shawn D Aaron, Rees Kassen

Proc Natl Acad Sci U S A· December 2013

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PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment.
Nicolas Lartillot, Nicolas Rodrigue, Daniel Stubbs, Jacques Richer

Syst Biol· July 2013

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