Publications
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2015. Algorithms in Bioinformatics: 15th International Workshop, WABI 2015. Lecture Notes in Bioinformatics. :328.
2004. Whole-genome shotgun assembly and comparison of human genome assemblies. Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America. 101
2011. Warming Oceans, Phytoplankton, and River Discharge: Implications for Cholera Outbreaks. The American Journal of Tropical Medicine and HygieneAm J Trop Med HygThe American Journal of Tropical Medicine and HygieneAm J Trop Med Hyg. 85
2012. Vibrio Cholerae Classical Biotype Strains Reveal Distinct Signatures in Mexico. Journal of Clinical MicrobiologyJ. Clin. Microbiol.Journal of Clinical MicrobiologyJ. Clin. Microbiol..
2004. Variation of toxigenic Vibrio cholerae O1 in the aquatic environment of Bangladesh and its correlation with the clinical strains. Microbiology and immunologyMicrobiology and Immunology. 48
2010. Tackling the widespread and critical impact of batch effects in high-throughput data. Nature reviews. GeneticsNature reviews. Genetics. 11
2013. Somatic alterations contributing to metastasis of a castration-resistant prostate cancer. Human mutationHuman mutation. 34
2011. Social Snapshot: A System for Temporally Coupled Social Photography. Computer Graphics and Applications, IEEEComputer Graphics and Applications, IEEE. 31
2009. Serogroup, Virulence, and Genetic Traits of Vibrio Parahaemolyticus in the Estuarine Ecosystem of Bangladesh. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 75
2010. Saliency Guided Summarization of Molecular Dynamics Simulations. Scientific Visualization: Advanced ConceptsScientific Visualization: Advanced Concepts. 1
2009. RNA Colony Blot Hybridization Method for Enumeration of Culturable Vibrio Cholerae and Vibrio Mimicus Bacteria. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 75
2003. Reduction of Cholera in Bangladeshi Villages by Simple Filtration. Proceedings of the National Academy of SciencesPNASProceedings of the National Academy of SciencesPNAS. 100
2013. Quantitative PCR for Detection of Shigella Improves Ascertainment of Shigella Burden in Children with Moderate-to-Severe Diarrhea in Low-Income Countries. Journal of Clinical MicrobiologyJournal of Clinical Microbiology. 51
2012. The partitioned LASSO-patternsearch algorithm with application to gene expression data. BMC bioinformaticsBMC Bioinformatics. 13
2004. Pandemic strains of O3:K6 Vibrio parahaemolyticus in the aquatic environment of Bangladesh. Canadian Journal of MicrobiologyCanadian Journal of Microbiology. 50
2010. Overcoming bias and systematic errors in next generation sequencing data. Genome medicineGenome medicine. 2
2009. Model-based quality assessment and base-calling for second-generation sequencing data. Johns Hopkins University, Dept. of Biostatistics Working PapersJohns Hopkins University, Dept. of Biostatistics Working Papers.
2010. Model-Based Quality Assessment and Base-Calling for Second-Generation Sequencing Data. Biometrics. 66(3):665-674.
2015. Microbiota that affect risk for shigellosis in children in low-income countries. Emerg Infect DisEmerg Infect Dis. 21:242-50.
2010. Intensity normalization improves color calling in SOLiD sequencing. Nat MethNat MethNat MethNat Meth. 7
2011. Influence of Host Gene Transcription Level and Orientation on HIV-1 Latency in a Primary-Cell Model. Journal of Virology. 85(11):5384-5393.
2011. Influence of host gene transcription level and orientation on HIV-1 latency in a primary-cell model. Journal of virologyJournal of virology. 85
2015. Independent Emergence of Artemisinin Resistance Mutations Among Plasmodium falciparum in Southeast Asia. Journal of Infectious Diseases. 211:670-679.
2011. Increased methylation variation in epigenetic domains across cancer types. Nature Genetics. 43(8):768-775.