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 comparative 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 (genotyping, epidemiologic clustering) 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

• February 2020: our paper "HASLR: Fast Hybrid Assembly of Long Reads" has been accepted at RECOMB-Seq 2020
• January 2020: our paper "The Distance and Median Problems in the Single-Cut-or-Join model with Single-Gene Duplications" has been accepted for publication in Algorithms for Molecular Biology.
• January 2020: Cedric joins the Editorial Board of Bioinformaics.
• January 2020: our paper on the improving Anopheles genomes assemblies has been published in BMC Biology.
• December 2019: our paper "Deconvoluting the Diversity of Within-host Pathogen Strains in a Multi-Locus Sequence Typing Framework" is now available in BMC Bioinformatics.
• December 2019: our paper "Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models" has been accepted for publication in Journal of Mathematical Biology.
• December 2019: our recent works on RNA design and the assembly of linked reads are presented at SeqBIM 2019.
• November 2019: our paper "Identifying differential cell populations in flow cytometry data accounting for marker frequency" has been accepted for spotlight presentation at MLCB 2019.
• September 2019: Cedric travels to Bielefeld to teach a block seminar Applied Comparative Genomics.
• July 2019: our paper "Deconvoluting the Diversity of Within-host Pathogen Strains in a Multi-Locus Sequence Typing Framework" has been accepted at RECOMBCG 2019.
• June 2019: our paper "Exponentially few RNA structures are designable" has been accepted at ACM BCB 2019.