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2003
Cummings MP, Nugent J.M, Olmstead R.G, Palmer J.D.  2003.  Phylogenetic analysis reveals five independent transfers of the chloroplast gene ıt rbcL to the mitochondrial genome in angiosperms. Curr GenetCurr Genet. 43
Louis VR, Russek-Cohen E, Choopun N, Rivera ING, Gangle B, Jiang SC, Rubin A, Patz JA, Huq A, Colwell RR.  2003.  Predictability of Vibrio Cholerae in Chesapeake Bay. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 69
2004
Islam M.S, Tasmin R, Khan SI s l a m, Bakht HBM, Mahmood ZH a y a t, Rahman M.Z i a u r, Bhuiyan NA m i n, Nishibuchi M, Nair G.B a l a k, e y Sack R.B r a d l et al..  2004.  Pandemic strains of O3:K6 Vibrio parahaemolyticus in the aquatic environment of Bangladesh. Canadian Journal of MicrobiologyCanadian Journal of Microbiology. 50
Cummings MP.  2004.  PHYLIP (Phylogeny Inference Package).
Espeland EM, Lipp EK, Huq A, Colwell RR.  2004.  Polylysogeny and prophage induction by secondary infection in Vibrio cholerae. Environmental MicrobiologyEnvironmental Microbiology. 6
2005
Pruzzo C., Huq A., Colwell RR, Donelli G..  2005.  Pathogenic Vibrio species in the marine and estuarine environment. Oceans and health: pathogens in the marine environmentOceans and health: pathogens in the marine environment.
Simola D.F, Dalva M., Hannenhalli S, Liebhaber S., Bucan M., Ungar L..  2005.  Post-transcriptional Control in Mammalian Dendrites.
Ouhammouch M, Langham GE, Hausner W, Simpson AJ, El‐Sayed NM, E. Geiduschek P.  2005.  Promoter architecture and response to a positive regulator of archaeal transcription. Molecular MicrobiologyMolecular Microbiology. 56
2006
Hadley D., Murphy T., Valladares O., Hannenhalli S, Ungar L., Kim J., Bucan M.,.  2006.  Patterns of sequence conservation in presynaptic neural genes. Genome BiolGenome Biol. 7
Darling AE, Treangen T, Zhang L, Kuiken C, Messeguer X, Perna NT.  2006.  Procrastination leads to efficient filtration for local multiple alignment. International Workshop on Algorithms in Bioinformatics.
Darling AE, Treangen T, Zhang L, Kuiken C, Messeguer X, Perna NT.  2006.  Procrastination Leads to Efficient Filtration for Local Multiple Alignment. 4175:126-137.
2007
Vardhanabhuti S, Wang J, Hannenhalli S.  2007.  Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. Nucleic Acids ResearchNucleic Acids Research. 35
2009
Nagarajan N, Pop M..  2009.  Parametric Complexity of Sequence Assembly: Theory and Applications to Next Generation Sequencing. Journal of Computational BiologyJournal of Computational Biology. 16
Eng K.H, Bravo HCorrada, Keles S..  2009.  A phylogenetic mixture model for the evolution of gene expression. Molecular biology and evolutionMolecular biology and evolution. 26
Khan Z., Bloom J.S, Kruglyak L., Singh M..  2009.  A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays. Bioinformatics. 25(13):1609-1616.
Khan Z, Bloom JS, Kruglyak L, Singh M.  2009.  A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays.. Bioinformatics. 25(13):1609-16.
G. de Magny C, Long W., Brown C.W, Hood R.R, Huq A., Murtugudde R., Colwell RR.  2009.  Predicting the distribution of Vibrio spp. in the Chesapeake Bay: a Vibrio cholerae case study. EcoHealthEcoHealth. 6
Khan Z., Bloom J.S, Garcia B.A, Singh M., Kruglyak L..  2009.  Protein quantification across hundreds of experimental conditions. Proceedings of the National Academy of Sciences. 106(37):15544-15548.
Khan Z, Bloom JS, Garcia BA, Singh M, Kruglyak L.  2009.  Protein quantification across hundreds of experimental conditions.. Proc Natl Acad Sci U S A. 106(37):15544-8.
Everett L., Vo A., Hannenhalli S.  2009.  PTM-Switchboard—a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. Nucleic acids researchNucleic Acids Research. 37
2010
Navlakha S., Kingsford C.  2010.  The power of protein interaction networks for associating genes with diseases. BioinformaticsBioinformatics. 26
Haley BJ, Grim CJ, Hasan NA, Taviani E, Jongsik C, Brettin TS, Bruce DC, Challacombe JF, J. Detter C, Han CS et al..  2010.  The pre‐seventh pandemic Vibrio cholerae BX 330286 El Tor genome: evidence for the environment as a genome reservoir. Environmental Microbiology ReportsEnvironmental Microbiology Reports. 2
2011
De Magny GConstantin, Mozumder PK, Grim CJ, Hasan NA, M. Naser N, Alam M, Sack B, Huq A, Colwell RR.  2011.  Population Dynamics of Vibrio Cholerae and Cholera in the Bangladesh Sundarbans: Role of Zooplankton Diversity. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol..
Folger O, Jerby L, Frezza C, Gottlieb E, Ruppin E, Shlomi T.  2011.  Predicting selective drug targets in cancer through metabolic networks.. Mol Syst Biol. 7:501.
Basu MK, Selengut J., Haft DH.  2011.  ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. BMC bioinformaticsBMC Bioinformatics. 12

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