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),
School of Computing Science, SFU (associate member),
SFU Discrete Mathematics Group,
Centre for Experimental and Constructive Mathematics (CECM),
Centre for Operations Research and Decision Sciences (CORDS),
Bioinformatics Training Program for Health Research (associate faculty),
PIMS International Graduate Training Centre (IGTC) in Mathematical Biology,
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 Spring 2015 term, I will
teach MATH 343: Applied Discrete Mathematics.
I am part of the VanBUG seminar series organizing team, and admission chair for the MADD-GEN graduate program.
News and links.
Recent and upcoming conferences and workshops.
Open positions. If you are interested in
the application of mathematical and computational methods in genomics,
I plan to supervise at least one new graduate students (PhD or MSc), starting
in september 2015
(see the Computational
Paleogenomics lab page for more information on my current research).
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 January 15th, 2015) or
the MADD-GEN graduate
program (Computational Methods for the Analysis of the Dynamics and
Diversity of Genomes).
Alternatively, you can apply to
of Computing Sciences, SFU (deadline February 1st, 2015) or
bioinformatics training program. If you plan to apply in any of
the last two programs, please let me know in advance as I will need to
explore co-supervision options with other faculty.
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.