Aligning sequences with non-Affine Gap penalty: Plains Algorithm, a Practical Implementation, and its biological Applications in Comparative genomics. - Ofer H. Gill; Yi Zhou; Bud Mishra (Advances in Bioinformatics and Its Applications, 2005)

SEPA: Approximate Non-subjective Empirical p-Value Estimation for Nucleotide Sequence Alignment. - Ofer H. Gill; Bud Mishra (International Conference on Computational Science (2), 2006)

COMBAT: Search Rapidly for Highly Similar Protein-Coding Sequences Using Bipartite Graph Matching. - Bing Sun; Jacob T. Schwartz; Ofer H. Gill; Bud Mishra (International Conference on Computational Science (2), 2006)

Finding Your Match: Techniques for Improving Sequence Alignment in DNA and RNA. - Ofer H. Gill (2006)