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

• April 2023: our paper "PlasBin-flow: A flow-based MILP algorithm for plasmid contigs binning" has been accepted at ISMB/ECCB 2023.
• October 2022: our paper "Freddie: Annotation-independent Detection and Discovery of Transcriptomic Alternative Splicing Isoforms Using Long-read Sequencing" has been accepted in Nucleic Acids Research.
• June 2022: our paper " Fast and accurate matching of cellular barcodes across short- and long-reads of single-cell RNA-seq experiments" has been published in iScience.
• May 2022: our paper "plASgraph - using graph neural networks to detect plasmid contigs from an assembly graph" is available on biorXiv.
• May 2022: our paper "A Mixed Integer Linear Programming Algorithm for Plasmid Binning" has been presented at RECOMB – Comparative Genomics 2022 and published in Lecture Notes in Bioinformatics.
• May 2022: our paper " Fast and accurate matching of cellular barcodes across short- and long-reads of single-cell RNA-seq experiments" has been presented at RECOMB-Seq 2022.