Welcome to the Computational Paleogenomics group of Cedric Chauve, Department of Mathematics and Interdisciplinary Research in the Mathematical and Computational Sciences (IRMACS) Centre at Simon Fraser University.

The research of our group focuses primarily on computational approaches to understand the evolution of the architecture of genomes through genome rearrangements. Currently, our main interest considers the problem of inferring the architecture of ancestral genomes (of extinct species) through the comparison of related extant genomes (of descendants species and close outgroups). We also work on connected topics, namely phylogenomics, gene family evolution, in order to infer the ancestral gene content of extinct species, and genome rearrangements that aim at understanding large-scale evolutionary events between related species, both extant and extinct.

See our Research page for more details.

News and announcements

• September 2017: Congratulations to Fang Zhang who defended successfuly his MSc thesis "Computational exploration of transmission and acquisition of drug-resistant tuberculosis".
• September 2017: Two new students join our group. Baraa Orabi (co-supervised with Faraz Hach) and Hooman Zabeti (co-supervised with leonid Chindelevitch and Tamon Stephen)
• August 2017: Congratulations to ALice Yue who defended successfuly her MSc thesis "Feature-based Comparison of Flow Cytometry Data".
• August 2017: Our preprint "MentaLiST - A fast MLST caller for large MLST schemes" is available on biorXiv.
• July 2017: Our paper "LRCstats, a tool for evaluating long reads correction methods" has been accepted in Bioinformatics
• July 2017: Our paper "Constructing a Consensus Phylogeny from a Leaf-Removal Distance" has been accepted in SPIRE 2017.
• July 2017: The final version of our paper on scaffolding ancient Yersini pestis genomes has been published in Microbial Genomics.
• May 2017: The full length version of our paper "The gene family-free median of three" has been published in Algorithms for Molecular Biology
• May 2017: Hugo Menet (ENS Lyon), Laura Gutierrez Funderburk (SFU) and Mark Forteza (SFU USRA) join our team for the summer. Welcome
• April 2017: The papers "MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers" (biorXiv) and "DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies" (Genome Biolgy and Evolution) are now available.
• April 2017: Hua-Ting Yao (Polytechnique) and Etienne Lassale (ENS Cachan) join our PathoGiST project. Welcome.
• February 2017: Cedric and Pedro give talks at the workshop Mathematical Approaches to Evolutionary Trees and Networks
• January 2017: Pedro Feijao joins the lab as a post-doctoral fellow, co-supervised with Leonid Chindelevitch and Will Hsiao, to work on computational epidemiology (Genome Canada project).