Publications
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2007. Eukaryotic Transcriptional Regulation: Signals, Interactions, and Modules. Computational Genomics: Current MethodsComputational Genomics: Current Methods.
2006. Transcriptional Genomics Associates FOX Transcription Factors With Human Heart Failure. CirculationCirculation. 114
1999. Bacterial Start Site Prediction. Nucleic Acids ResearchNucl. Acids Res.Nucleic Acids ResearchNucl. Acids Res.. 27
1995. Polynomial-time algorithm for computing translocation distance between genomes. Combinatorial Pattern MatchingCombinatorial Pattern Matching.
1993. A distributed algorithm for ear decomposition. Fifth International Conference on Computing and Information, 1993. Proceedings ICCI '93.
1995. Genome Sequence Comparison and Scenarios for Gene Rearrangements: A Test Case. GenomicsGenomics. 30
2008. Eukaryotic Transcription Factor Binding Sites—modeling and Integrative Search Methods. BioinformaticsBioinformaticsBioinformaticsBioinformatics. 24
1995. Towards a computational theory of genome rearrangements. Computer Science TodayComputer Science Today. 1000
2006. Identification and cross-species comparison of canine osteoarthritic gene regulatory cis-elements. Osteoarthritis and cartilage/OARS, Osteoarthritis Research SocietyOsteoarthritis and cartilage/OARS, Osteoarthritis Research Society. 14
1999. Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. J. ACMJ. ACM. 46
2002. Predicting Transcription Factor Synergism. Nucleic Acids ResearchNucl. Acids Res.Nucleic Acids ResearchNucl. Acids Res.. 30
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.
2011. Increased methylation variation in epigenetic domains across cancer types. Nature Genetics. 43(8):768-775.
2010. Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction. Algorithms for Molecular BiologyAlgorithms for Molecular Biology. 5
2009. Mimosa: mixture model of co-expression to detect modulators of regulatory interaction. Algorithms in BioinformaticsAlgorithms in Bioinformatics.
2013. Genome sequence of the attenuated Carbosap vaccine strain of Bacillus anthracis. Genome announcements. 1:e00067–12.
2010. Comparative Genomics of Clinical and Environmental Vibrio Mimicus. Proceedings of the National Academy of SciencesPNASProceedings of the National Academy of SciencesPNAS. 107
2011. Metagenomic 16S rDNA Targeted PCR-DGGE in Determining Bacterial Diversity in Aquatic Ecosystem. Bangladesh Journal of MicrobiologyBangladesh Journal of Microbiology. 27
2004. Abstracting workflows: unifying bioinformatics task conceptualization and specification through Semantic Web services. W3C Workshop on Semantic Web for Life Sciences.
2013. Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding. BMC Genomics. 14(1):428.
2004. The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nature biotechnologyNature biotechnology. 22