I am interested in the algorithmic, modeling, and combinatorial problems related
In particular, I develop novel methods for finding evolutionary distances
between whole genomes, reconstructing evolutionary histories, and comparing
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.
Here is My Publication List.
- 2012: Best Paper award at RECOMB 2012 in Barcelona.
- 2010: Finalist for the dissertation award at EPFL.
- 2005: Winner of the UNM CS outstanding graduate student award.
- WABI (Workshop on Algorithms in Bioinformatics)
- RECOMB-CG (RECOMB Satellite Workshop on Comparative Genomics)
- ISMB (International Conference on Intelligent Systems for Molecular Biology)
- ACM-BCB (ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics)
- APBC (Asian Pacific Biocomputing Conference)
- Journal of Computational Biology
- IEEE/ACM Transactions on Computation Biology and Bioinformatics
- Algorithms for Molecular Biology
- BMC Bioinformatics
- Journal of Theoretical Biology
- Bulletin of Mathematical Biology
- PLoS Computational Biology
- SIAM Journal on Discrete Mathematics
- ACM Journal of Experimental Algorithmics
- Information Processing Letters
- Discrete Applied Mathematics
- Theoretical Computer Science
- Algorithms (MDPI)
Alpha -- ALignment of PHAges
Alpha is a tool designed for detailed comparative
study of bacteriophage genomes. Go here for more
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...
My dissertation is here
(the version with links is here)
My current CV is here.
Pilar de la Torre, the person who sparked my interest in
algorithms died from lung cancer November 1st, 2012.