RODRIGUE, NICOLAS - University of Calgary - Department of Biochemistry & Molecular Biology

研究领域

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 next-generation-sequencing approaches for studying viral and microbial evolution in clinical and experimental settings.

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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.

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