|
|
|
|
| Regular expression constrained sequence alignment. Journal of Discrete
Algorithms, Elsevier, 5(4), pp. 647-661, (available online:
http://dx.doi.org/10.1016/j.jda.2007.01.003 ) (RE-MuSiC alignment tool by Chung et al uses my formulation (Nucleic Acids Research, 2007, link to this article) ) A largest common d-dimensional subsequence of two d-dimensional strings, FCT 2007, Lecture Notes in Computer Science (LNCS) 4639, Springer, Erzsebet Csuhaj-Varju, Zoltan Esik (Eds.), pp. 40-51 (with Omer Egecioglu)
(with Omer Egecioglu and Pavel A. Pevzner)
Click here for more |
A fast algorithm for finding a longest common subsequence of two given similar strings (submitted to SODA 2009) (please e-mail me at aarslan@cs.uvm.edu I would be happy to send you a copy of my submission) The following are other on-going papers: - processing suffix trees to accelarate approximate look-up - a new computational problem for cost optmization for a buyer of multiple items from multiple vendors - improved algorithms for sequence alignment using inversions - new algorithms for a constrained pattern matching problem -improved algorithms for several constrained sequence alignment problems -revising and extending a paper on approximate dictionary look-up (written with Johannes Nowak) |
- new formulations for d-dimensional common subsequences of d-dimensional strings and algorithms for their computations - approximation algorithms, and heuristics for maximum clique, constrained maximal bipartite matching, and quadratic integer programming problems -algorithms to create generalized suffix trees with certain properties |