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

• November 2018: Cedric gives a talk on genome rearrangements at the Dagstuhl workshop on Genomics, pattern avoidance and statistical mechanics.
• November 2018: Our paper "Alignment-free Clustering of UMI Tagged DNA Molecules" is available in advance access in Bioinformatics.
• October 2018: Our collaborative work on improving Anopheles genomes assembly is now available on biorxiv: Leveraging evolutionary relationships to improve Anopheles genome assemblies
• September 2018: Stanley (Guo Liang) Gan successfuly defends his MSc thesis "Resolving Complexity of Within-host Pathogen Strain Diversity and Antimicrobial Resistance using Optimization and Machine Learning". Congrats Stanley.
• September 2018: Fatih Karaoglanoglu joins our lab as a PhD student, co-supervised with Faraz Hach.
• August 2018: Our paper "Counting, Generating, Analyzing and Sampling Tree Alignments" has been published in Int. J. Foundations Comput. Sci..
• August 2018: Aniket Mane successfuly defends his MSc thesis Genome rearrangement problems accounting for duplicate genes, and continues in the lab as a PhD candidate. Congrats Aniket.
• July 2018: the papers "Detecting introgression in Anopheles mosquito genomes using a reconciliation-based approach" and "The rooted SCJ median with single gene duplications" have been accepted at RECOMB-CG 2018.
• June 2018: The paper "PRINCE: Accurate Approximation of the Copy Number of Tandem Repeats" has been accepted at WABI 2018.
• May 2018: The paper "Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes" has been published in BMC Genomics.
• May 2018: Robert Mueller, from Bielefeld, joins the lab for 6 months to work on plasmids assembly.