Welcome to the "Computational Methods for Paleogenomics and Comparative Genomics" group of Cedric Chauve, Department of Mathematics at Simon Fraser University.

The research of our group focuses currently on various problems in computational biology, with a strong focus on comparative genomics and cancer genomics. We are working on various problems related to phylogenomics (the construction and analysis of gene families and gene trees), genome rearrangements and the reconstruction of ancestral gene orders, pathogen genomics and cancer genomics. We are also working on machine-learning algorithms for the analysis of large-scale flow cytometry data.

See our Research page for more details.

News and announcements

• January 2024: our paper "TKSM: Highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator" has been accepted in Bioinformatics.
• January 2024: Cedric starts a 3-year term as Chair of the SFU Department of Mathematics.
• September 2023: our paper "plASgraph2: Using Graph Neural Networks to Detect Plasmid Contigs from an Assembly Graph" is available on Frontiers Microbiology.
• Summer 2023: we welcome several visitors, Tomas Vinar, Brona Berjova, Daniel Doerr, Paola Bonizzoni and Mattia Sgro.
• June 2023: our preprint "TKSM: Highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator" is available on bioRxiv.
• April 2023: our paper "PlasBin-flow: A flow-based MILP algorithm for plasmid contigs binning" has been accepted at ISMB/ECCB 2023.