Publications
2006. Invited Talk: Deciphering Gene Regulatory Networks by in silico approaches. 6th International Workshop on Data Mining in Bioinformatics (BIOKDD06)6th International Workshop on Data Mining in Bioinformatics (BIOKDD06).
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
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.
2006. Transcriptional Genomics Associates FOX Transcription Factors With Human Heart Failure. CirculationCirculation. 114
1995. Genome sequence comparison and scenarios for gene rearrangements: A test case. GenomicsGenomics. 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.
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.
2011. Increased methylation variation in epigenetic domains across cancer types. Nature Genetics. 43(8):768-775.
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
2015. Encyclopedia of MetagenomicsHuman Microbiome, Assembly and Analysis Software, Project. :243-246.
2013. K-mulus: Strategies for BLAST in the cloud. 10th International Conference on Parallel Processing and Applied Mathematics (PPAM).
2013. De novo likelihood-based measures for comparing metagenomic assemblies. 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
2006. Recurring genomic breaks in independent lineages support genomic fragility. BMC Evolutionary BiologyBMC Evolutionary Biology. 6
2005. Dynamic Querying for Pattern Identification in Microarray and Genomic Data (2003). Institute for Systems Research Technical ReportsInstitute for Systems Research Technical Reports.
2003. Dynamic querying for pattern identification in microarray and genomic data. 2003 International Conference on Multimedia and Expo, 2003. ICME '03. Proceedings. 3