Lower Bounds for Maximum Parsimony with Gene Order Data (2005)
Abraham Bachrach, Kevin Chen, Chris Harrelson, Radu Mihaescu, Satish Rao, Apurva Shah
Abstract. In this paper, we study lower bound techniques for branchand-bound algorithms for maximum parsimony, with a focus on gene order data. We give a simple O(n 3) time dynamic programming...
Simple sequence repeats in prokaryotic genomes
Mrázek, Jan, Guo, Xiangxue, Shah, Apurva
Simple sequence repeats (SSRs) in DNA sequences are composed of tandem iterations of short oligonucleotides and may have functional and/or structural properties that distinguish them from general DNA...