Research Interests
I am interested in the algorithmic, modeling, and combinatorial problems related
to evolution.
In particular, I develop novel methods for finding evolutionary distances
between whole genomes, reconstructing evolutionary histories, and comparing
phylogenetic trees.
Development of this area requires new algorithms and data structures for string
matching, sorting permutations, graph and tree comparison, as well
as heuristics and rigorous methods to evaluate those heuristics.
My Publication List is here.
Experience
Program Committees
- WABI 2012 (Workshop on Algorithms in Bioinformatics)
- RECOMB-CG 2012 (RECOMB Satellite Workshop on Comparative Genomics)
- RECOMB-CG 2011
- RECOMB-CG 2010
- ISMB 2009 (International Conference on Intelligent Systems for Molecular Biology)
Journal Referee
- Journal of Computational Biology
- Transactions on Computation Biology and Bioinformatics
- Algorithms for Molecular Biology
- BMC Bioinformatics
- SIAM Journal on Discrete Mathematics
Honors
- 2010: Finalist for the dissertation award at EPFL.
- 2005: Winner of the UNM CS outstanding graduate student award.
Software
My colleagues and I have written open source code useful
for research on whole genome evolution through reversals (inversions).
Among other things the code:
- computes a minimum reversal (inversion) scenario faster than any existing code,
- computes an evolutionary scenario using reversals, insertions, and deletions,
- displays all minimum reversals scenarios between two genomes as a DAG,
- draws the Hannenhalli-Pevzner graph,
- and much more...
Links
My dissertation is here
(the version with links is here)
My current CV is here.
