Publications
2000. Analysis and prediction of functional sub-types from protein sequence alignments. Journal of Molecular Biology. 303(1):61-76.
1995. Towards a computational theory of genome rearrangements. Computer Science TodayComputer Science Today. 1000:184-202.
1999. Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. J. ACM. 46(1):1-27.
2006. Invited Talk: Deciphering Gene Regulatory Networks by in silico approaches. 6th International Workshop on Data Mining in Bioinformatics (BIOKDD06). :31-31.
2002. Predicting Transcription Factor Synergism. Nucleic Acids ResearchNucl. Acids Res.. 30(19):4278-4284.
1996. Positional sequencing by hybridization. Computer applications in the biosciences : CABIOS. 12(1):19-24.
1996. To cut… or not to cut (applications of comparative physical maps in molecular evolution). Proceedings of the seventh annual ACM-SIAM symposium on Discrete algorithms. :304-313.
2009. The evolution of Fox genes and their role in development and disease. Nature reviews. GeneticsNat Rev Genet. 10(4):233-240.
2005. Enhanced position weight matrices using mixture models. Bioinformatics. 21(Suppl 1):i204-i212-i204-i212.
1995. Genome Sequence Comparison and Scenarios for Gene Rearrangements: A Test Case. Genomics. 30(2):299-311.
1995. Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. Proceedings of the twenty-seventh annual ACM symposium on Theory of computing. :178-189.
1996. Polynomial-time algorithm for computing translocation distance between genomes. Discrete Applied Mathematics. 71(1–3):137-151.
1993. A distributed algorithm for ear decomposition. , Fifth International Conference on Computing and Information, 1993. Proceedings ICCI '93. :180-184.
2006. Transcriptional Genomics Associates FOX Transcription Factors With Human Heart Failure. Circulation. 114(12):1269-1276.
2006. Identification and cross-species comparison of canine osteoarthritic gene regulatory cis-elements. Osteoarthritis and Cartilage. 14(8):830-838.
1995. Polynomial-time algorithm for computing translocation distance between genomes. Combinatorial Pattern MatchingCombinatorial Pattern Matching. 937:162-176.
2008. Eukaryotic Transcription Factor Binding Sites—modeling and Integrative Search Methods. BioinformaticsBioinformatics. 24(11):1325-1331.
2001. Analysis and prediction of protein functional sub-types from protein sequence alignments. EP20000203764(EP1096411)
2007. Eukaryotic Transcriptional Regulation: Signals, Interactions, and Modules. Computational genomics: current methods. :21-21.
2003. Transcriptional regulation of protein complexes and biological pathways. Mammalian Genome. 14(9):611-619.
1995. Transforming men into mice (polynomial algorithm for genomic distance problem). Foundations of Computer Science, Annual IEEE Symposium on. :581-581.