I am currently a professor in the
Department of Mathematics of
Simon Fraser University.
I was previously with the
Computer Science Department
Université du Québec à Montréal.
I am a member of the following labs, groups and programs:
Computational Methods for the Analysis of the Dynamics and Diversity of Genomes (MADD-GEN) Program (faculty),
Graduate Studies in Bioinformatics at UBC and SFU,
Centre for Operations Research and Decision Sciences (CORDS),
School of Computing Science, SFU (associate member),
SFU Discrete Mathematics Group,
Centre for Experimental and Constructive Mathematics (CECM),
Laboratoire de Combinatoire et Informatique Mathématiques (LaCIM, UQAM).
Research interests and funding. (See
My current research
deals primarily with mathematical and computational questions arising
from comparative genomics. This includes problems on genome
rearrangements, gene families evolution, and computational analysis of
RNA, with a strong focus on algorithmic and mathematical aspects.
Depending on the sessions, I am teaching courses in discrete
mathematics, programming, theoretical computer science and
bioinformatics. In the Fall 2015 term, I am
teaching MATH 345: Graph Theory I and MATH 154: Calculus for Life Sciences I.
I am part of the VanBUG seminar series organizing team, and admission chair for the MADD-GEN graduate program.
News and links.
Open positions. If you are interested in
the application of mathematical and computational methods to life sciences, I will likely recruit one graduate student to start in the Fall 2016. Please refer to the Computational
Paleogenomics lab page for more information about research projects.
Candidates with a BSc in mathematics or computer science and a serious
interest in computational biology are welcome to apply either through
the Department of
Mathematics, SFU (deadline February 1st, 2016),
the MADD-GEN graduate
program (Computational Methods for the Analysis of the Dynamics and
Diversity of Genomes, deadline February 1st, 2016), or the
Graduate Studies in Bioinformatics at UBC and SFU program (again, deadline February 1st, 2016).
Finally, I welcome at any time applications from motivated
undergraduate students to work with us, either as coop interns or as
Students and post-doctoral fellows.
List of current and past students including their projects and publications.
FPSAC: Fast Phylogenetic Scaffolding of Ancient Contigs.
ANGES: reconstructing ANcestral GEnomeS maps.
BRASERO: Benchmarking RNA secondary structure comparison algorithms. Paper.
RNA StrAT, our
RNA Structure Analysis Toolkit. ISMB 2008 poster.
a machine-learning tool for the prediction of GPI-anchored protein
Selected recent papers.