On the Complexity of Protein Similarity Search under mRNA Structure Constraints. - Rolf Backofen; N. S. Narayanaswamy; Firas Swidan (STACS, 2002)

Protein similarity search under mRNA structural constraints: application to selenocysteine incorporation. - Rolf Backofen; N. S. Narayanaswamy; Firas Swidan (Silico Biol., 2002)

Sorting by Length-Weighted Reversals: Dealing with Signs and Circularity. - Firas Swidan; Michael A. Bender; Dongdong Ge; Simai He; Haodong Hu; Ron Y. Pinter (CPM, 2004)

Improved bounds on sorting with length-weighted reversals. - Michael A. Bender; Dongdong Ge; Simai He; Haodong Hu; Ron Y. Pinter; Steven Skiena; Firas Swidan (SODA, 2004)

On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem. - Firas Swidan; Michal Ziv-Ukelson; Ron Y. Pinter (J. Comput. Biol., 2006)

An Integrative Method for Accurate Comparative Genome Mapping. - Firas Swidan; Eduardo P. C. Rocha; Michael Shmoish; Ron Y. Pinter (PLoS Comput. Biol., 2006)

Comparative genomics: from accurate mapping to sorting by weighted reversals and repeat-annotated phylogenies. - Firas Swidan (2006)

Improved bounds on sorting by length-weighted reversals. - Michael A. Bender; Dongdong Ge; Simai He; Haodong Hu; Ron Y. Pinter; Steven Skiena; Firas Swidan (J. Comput. Syst. Sci., 2008)

Assessing the Quality of Whole Genome Alignments in Bacteria. - Firas Swidan; Ron Shamir (Adv. Bioinformatics, 2009)