Nicolas Rodrigue

I am a professor in the Department of Biology, with cross-appointments in the Institute of Biochemistry and the School of Mathematics and Statistics, at Carleton University, in Ottawa, Canada.


Room 4610, CTTC
Department of Biology
Carleton University
1125 Colonel By Drive
Ottawa, Ontario, Canada, K1S 5B6

Tel: +1 613.520.2600 ext. 4194


I obtained a Ph.D. in Bioinformatics from the Université de Montréal in 2008. I then did post-doctoral work (University of Ottawa, Jan. 2008 - Dec. 2010; McGill University, Jan. 2011 - March 2011), followed by an appointment as Research Scientist at Agriculture and Agri-Food Canada (April 2011 - Aug. 2013). I spent a year as an Assistant Professor in the Department of Mathematics and Statistics at the University of Calgary (Sept. 2013 - Aug. 2014) before joining the Faculty at Carleton. Prior to all of this, I completed an M.Sc. (Information Technology, École de technologie supérieure, 2004), a B.Sc. (Biochemistry, McGill University, 2002), and a B.A. (Music, Bishop's University, 1999).


My main area of research deals with Bayesian modeling of molecular evolution, primarily focused on protein-coding genes and the various forces (e.g., mutation, selection, drift) that have shaped extant sequences. In this line, I am also interested in Markov chain Monte Carlo methods and high-performance statistical computing. Other areas that interest me include protein structure modeling, statistical protein design, and modern sequencing approaches for studying viral and microbial evolution.


Bujaki, T., Van Looyen, K. and Rodrigue, N. (2023). Measuring the relative contribution to predictive power of modern nucleotide substitution modeling approaches. Bioinform. Adv., 3:vbad091.

Latrille, T., Rodrigue, N. and Lartillot, N. (2023). Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale. Proc. Natl. Acad. Sci. U. S. A., 120:e2214977120.

Bujaki, T. and Rodrigue, N. (2022). Bayesian cross-validation comparison of amino acid replacement models: comparing profile mixtures, pairwise exchangeabilities, and gamma-distributed rates across sites. J. Mol. Evol., 90:468-475.

Rodrigue, N. (2022). Le paradigme bayésien en phylogénie moléculaire. In Modèles et méthodes pour l'évolution moléculaire. Ed. G. Didier and S. Guindon. ISTE Science Publishing LTD, London, UK.

Laurin-Lemay, S., Dickson, K. and Rodrigue, N. (2022). Jump-chain simulation of Markov substitution processes over phylogenies. J. Mol. Evol., 90:239-243.

Rodrigue, N., Latrille, T. and Lartillot, N. (2021). A Bayesian mutation-selection framework for detecting site-specific adaptive evolution in protein-coding genes. Mol. Biol. Evol., 38:1199-1208.

Lowe, C. and Rodrigue, N. (2020). Detecting adaptation from multi-species protein-coding DNA sequence alignments. In Phylogenetics in the Genomic Era. Ed. Scornavacca, C., Delsuc, F. and Galtier, N., No commercial publisher. Authors' open access book.

Shafiei-Koij, F., Ravichandran, S., Barthet, V. J., Rodrigue, N., Mirlohi, A., Majidi, M. M., and Cloutier, S. (2020). Evolution of Carthamus species revealed through sequence analyses of the fad2 gene family. Physiol. Mol. Biol. Plants, 26:419-432.

Kazmi, S. O. and Rodrigue, N. (2019). Detecting amino acid preference shifts with codon-level mutation-selection mixture models. BMC Evol. Biol., 19:62.

Aris-Brosou, S. and Rodrigue, N. (2019). A not-so-long introduction to computational molecular evolution. In Evolutionary Genomics. Ed. Anisimona, M., Methods in Molecular Biology, Vol. 1910, Humana - Springer, New York, NY.

Anderson, J. B., Bruhn, J. N., Kasimer, D., Wang. H., Rodrigue, N., and Smith, M. L. (2018). Clonal evolution and genome stability in a 2500-year-old fungal individual. Proc. R. Soc. B., 285:20182233.

Laurin-Lemay, S., Rodrigue, N., Lartillot, N. and Philippe, H. (2018). Conditional Approximate Bayesian Computation, a new approach for across-site dependency in high-dimensional mutation-selection models. Mol. Biol. Evol., 35:2819-2834.

Laurin-Lemay, S., Philippe, H. and Rodrigue, N. (2018). Multiple factors confounding phylogenetic detection of selection on codon usage. Mol. Biol. Evol., 35:1463-1472.

Low, A., Rodrigue, N. and Wong, A. (2017). COMPASS: the COMPletely Arbitrary Sequence Simulator. Bioinformatics, 33:3101-3103.

Rodrigue, N. and Lartillot, N. (2017). Detecting adaptation in protein-coding genes using a Bayesian site-heterogeneous mutation-selection model. Mol. Biol. Evol., 34:204-214.

Dettman, J. R., Rodrigue, N., Schoustra, S. and Kassen, R. (2017). Genomics of compensatory adaptation in experimental populations of Aspergillus nidulans. G3 (Bethesda), 7:427-436.

Walkowiak, S., Rowland, O., Rodrigue, N. and Subramaniam, R. (2016). Whole genome sequencing and comparative genomics of closely related Fusarium Head Blight fungi: Fusarium graminearum, F. meridionale and F. asiaticum. BMC Genomics, 17:1014.

Lee, H. J., Kishino, H., Rodrigue, N. and Thorne, J. L. (2016). Grouping substitution types into different relaxed molecular clocks. Phil. Trans. R. Soc. B, 371:20150141.

Lee, H. J., Rodrigue, N. and Thorne, J. (2015). Relaxing the molecular clock to different degrees for different substitution types. Mol. Biol. Evol., 32:1948-1961.

Bailey, S. F., Rodrigue, N. and Kassen, R. (2015). The effect of selection environment on the probability of parallel evolution. Mol. Biol. Evol., 32:1436-1448.

Dettman, J. R., Rodrigue, N. and Kassen, R. (2015). Genome-wide patterns of recombination in the opportunistic human pathogen Pseudomonas aeruginosa. Genome Biol. Evol., 7:18-34.

Robideau, G. P., Rodrigue, N. and Lévesque, C. A. (2014). Codon-based phylogenetics introduces novel flagellar gene markers to oomycete systematics. Mol. Phylogenet. Evol., 79:279-291.

Rodrigue, N. and Lartillot, N. (2014). Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package. Bioinformatics, 30:1020-1021.

Liu, M., Rodrigue, N. and Kolmer, J. (2014). Population divergence in the wheat leaf rust fungus Puccinia triticina is correlated with wheat evolution. Heredity, 122:443-453.

Dettman, J. R., Rodrigue, N., Aaron, S. D. and Kassen, R. (2013). Evolutionary genomics of epidemic and nonepidemic strains of Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. U. S. A., 110:21065-21070.

Lartillot, N., Rodrigue, N., Stubbs, D. and Richer, J. (2013). PhyloBayes-MPI: Phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst. Biol., 62:611-615.

Rodrigue, N. (2013). On the statistical interpretation of site-specific variables in phylogeny-based substitution models. Genetics, 193:557-564.

Wong, A., Rodrigue, N. and Kassen, R. (2012). Genomics of adaptation during experimental evolution of the opportunistic pathogen Pseudomonas aeruginosa. PLoS Genet., 8:e1002928.

Dettman, J. R., Rodrigue, N., Melnyk, A. H., Wong, A., Bailey, S. F. and Kassen, R. (2012). Evolutionary insights from whole-genome sequencing of experimentally evolved microbes. Mol. Ecol. 20:2058-2077.

Tang, J., Bromfield, E. S. P., Rodrigue, N., Cloutier, S. and Tambong, J. T. (2012). Microevolution of symbiotic Bradyrhizobium populations associated with soybeans in eastern North America. Ecol. Evol., 2:2943-2961.

Rodrigue, N. and Lartillot, N. (2012). Monte Carlo computational approaches in Bayesian codon substitution modeling. In Codon Evolution, Eds. Schneider, A. and Cannarozzi, G. Oxford University Press, UK, Chapter 4.

Thorne, J. L., Lartillot, N., Rodrigue, N. and Sang Chul Choi (2012). Codon models as a vehicle for reconciling population genetics with interspecific sequence data. In Codon Evolution, Eds. Schneider, A. and Cannarozzi, G., Oxford University Press, UK, Chapter 7.

Aris-Brosou, S. and Rodrigue, N. (2012). The Essentials of Computational Molecular Evolution. In Evolutionary Genomics: statistical and computational methods, Ed. Anisimona, M. - Evolutionary Genomics: Statistical and Computational Methods, Vol. 1, Series, Methods in Molecular Biology, Vol. 855, Humana - Springer.

Rodrigue, N. and Aris-Brosou, S. (2011). Fast Bayesian choice of phylogenetic models: prospecting data-augmentation-based thermodynamic integration. Syst. Biol., 60:881-887.

Rodrigue, N. and Philippe, H. (2010). Mechanistic revisions of phenomenological modeling strategies in molecular evolution. Trends in Genetics, 26:248-252.

Kleinman, C. L., Rodrigue, N., Lartillot, N. and Philippe, H. (2010). Statistical potentials for improved structurally constrained evolutionary models. Mol. Biol. Evol., 27:1546-1560.

Rodrigue, N., Philippe, H. and Lartillot, N. (2010). Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles. Proc. Natl. Acad. Sci. U. S. A., 107:4629-4634.

Zhou, Y., Brinkmann, H., Rodrigue, N., Lartillot, N. and Philippe, H. (2010). A Dirichlet process covarion mixture model and its assessments using posterior predictive discrepancy tests. Mol. Biol. Evol., 27:371-384

Bonnard, C., Kleinman, C. L., Rodrigue, N. and Lartillot, N. (2009). Fast optimization of statistical potentials for structurally constrained models. BMC Evol. Biol., 9:227.

Rodrigue, N., Kleinman, C. L., Philippe, H. and Lartillot, N. (2009). Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codons. Mol. Biol. Evol., 26:1663-1676.

Rodrigue, N., Lartillot, N. and Philippe, H. (2008). Bayesian comparisons of codon substitution models. Genetics, 180:1579-1591.

Rodrigue, N., Philippe, H. and Lartillot, N. (2008). Uniformization for sampling realizations of Markov processes: Applications to Bayesian implementations of codon substitution models. Bioinformatics, 24:56-62.

Zhou, Y., Rodrigue, N., Lartillot, N. and Philippe, H. (2007). Evaluation of the models handling heterotachy in phylogenetic inference. BMC Evol. Biol., 7:206.

Rodrigue, N., Philippe, H. and Lartillot, N. (2007). Exploring fast computational strategies for probabilistic phylogenetic analysis. Syst. Biol., 56, 711-726.

Rodrigue, N., Philippe, H. and Lartillot, N. (2006). Assessing site-interdependent phylogenetic models of sequence evolution. Mol. Biol. Evol., 23:1762-1775.

Kleinman, C. L., Rodrigue, N., Bonnard, C., Philippe, H. and Lartillot, N. (2006). A maximum likelihood framework for protein design. BMC Bioinformatics, 7:326.

Rodrigue, N., Lartillot, N., Bryant, D. and Philippe, H. (2005). Site interdependence attributed to tertiary structure in amino acid sequence evolution. Gene, 347:207-217.

Philippe, H., Zhou, Y., Brinkmann, H., Rodrigue, N. and Delsuc, F. (2005). Heterotachy and long-branch attraction in phylogenetics. BMC Evol. Biol., 5:50.