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Journal Articles
Hannenhalli S.  2007.  Eukaryotic Transcriptional Regulation: Signals, Interactions, and Modules. Computational Genomics: Current MethodsComputational Genomics: Current Methods.
Hannenhalli S.  2008.  Eukaryotic Transcription Factor Binding Sites—modeling and Integrative Search Methods. BioinformaticsBioinformaticsBioinformaticsBioinformatics. 24
Bravo HCorrada, Wright S, Eng KH, Keles S, Wahba G.  2009.  Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming. J Mach Learn Res. 5:41-48.
Le Breton Y, Belew AT, Valdes KM, Islam E, Curry P, Tettelin H, Shirtliff ME, El-Sayed NM, McIver KS.  2015.  Essential Genes in the Core Genome of the Human Pathogen Streptococcus pyogenes.. Sci Rep. 5:9838.
D. Avinash S, Aniba R., Chang Y.C, Hannenhalli S.  2012.  Epigenomic model of cardiac enhancers with application to Genome wideassociation studies. Pacific Symposium on BiocomputingPacific Symposium on Biocomputing.
Khaladkar M., Smyda M., Hannenhalli S.  2011.  Epigenomic and RNA structural correlates of polyadenylation. RNA biologyRNA biology. 8
Taviani E, Ceccarelli D, Lazaro N, Bani S, Cappuccinelli P, Colwell RR, Colombo MM.  2008.  Environmental Vibrio spp., isolated in Mozambique, contain a polymorphic group of integrative conjugative elements and class 1 integrons. FEMS Microbiology EcologyFEMS Microbiology Ecology. 64
G. de Magny C, Murtugudde R., Sapiano M.RP, Nizam A., Brown C.W, Busalacchi A.J, Yunus M., Nair G.B, Gil A.I, Lanata C.F et al..  2008.  Environmental signatures associated with cholera epidemics. Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences. 105
Vezzulli L, Pruzzo C, Huq A, Colwell RR.  2010.  Environmental reservoirs of Vibrio cholerae and their role in cholera. Environmental Microbiology ReportsEnvironmental Microbiology Reports. 2
Levy S, Hannenhalli S, Workman C.  2001.  Enrichment of Regulatory Signals in Conserved Non-Coding Genomic Sequence. BioinformaticsBioinformaticsBioinformaticsBioinformatics. 17
Malin J., Aniba M.R, Hannenhalli S.  2013.  Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers. Nucleic Acids ResNucleic Acids ResNucleic Acids Res. 41:6828-38.
Hannenhalli S, Wang L.S.  2005.  Enhanced position weight matrices using mixture models. BioinformaticsBioinformatics. 21
Faruque SM, Sack DA, R. Sack B, Colwell RR, Takeda Y, G. Nair B.  2003.  Emergence and Evolution of Vibrio Cholerae O139. Proceedings of the National Academy of SciencesPNASProceedings of the National Academy of SciencesPNAS. 100
Field D, Garrity G, Morrison N, Selengut J., Sterk P, Tatusova T, Thomson N.  2005.  eGenomics: Cataloguing our Complete Genome Collection. Comparative and functional genomicsComparative and functional genomics. 6
Lipp EK, Huq A, Colwell RR.  2002.  Effects of Global Climate on Infectious Disease: The Cholera Model. Clinical Microbiology ReviewsClin. Microbiol. Rev.Clinical Microbiology ReviewsClin. Microbiol. Rev.. 15
Neel M.C, Cummings MP.  2003.  Effectiveness of conservation targets in capturing genetic diversity. Conserv BiolConserv Biol. 17
Niranjan TS, Adamczyk A, Bravo H, Taub MA, Wheelan SJ, Irizarry R, Wang T.  2011.  Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis. Genome Biology. 12(9):R93.
Caburlotto G, Lleò MM, Hilton T, Huq A, Colwell RR, Kaper JB.  2010.  Effect on Human Cells of Environmental Vibrio Parahaemolyticus Strains Carrying Type III Secretion System 2. Infection and ImmunityInfect. Immun.Infection and ImmunityInfect. Immun.. 78
Alam M., Sadique A., Bhuiyan N.A, Nair G.B, Siddique A.K, Sack D.A, Ahsan S., Huq A., Sack R.B, Colwell RR et al..  2006.  Effect of transport at ambient temperature on detection and isolation of Vibrio cholerae from environmental samples. Applied and environmental microbiologyApplied and environmental microbiology. 72
Asakura H., Selengut J., Orme-Johnson W.H, Dretler S.P.  1998.  The effect of calprotectin on the nucleation and growth of struvite crystals as assayed by light microscopy in real-time. The Journal of urologyThe Journal of urology. 159
Hochheiser H, Baehrecke EH, Mount SM, Shneiderman B.  2005.  Dynamic Querying for Pattern Identification in Microarray and Genomic Data (2003). Institute for Systems Research Technical ReportsInstitute for Systems Research Technical Reports.
Fernandes MCecilia, Dillon LAL, Belew ATrey, Bravo HCorrada, Mosser DM, El-Sayed NM.  2016.  Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures. mBio. 7(3):e00027-16.
Vezzulli L, Guzmán CA, Colwell RR, Pruzzo C.  2008.  Dual role colonization factors connecting Vibrio cholerae's lifestyles in human and aquatic environments open new perspectives for combating infectious diseases. Current Opinion in BiotechnologyCurrent Opinion in Biotechnology. 19
Wagner A, Cohen N, Kelder T, Amit U, Liebman E, Steinberg DM, Radonjic M, Ruppin E.  2015.  Drugs that reverse disease transcriptomic signatures are more effective in a mouse model of dyslipidemia.. Mol Syst Biol. 11(3):791.
Salz HK, S Y Mancebo R, Nagengast AA, Speck O, Psotka M, Mount SM.  2004.  The Drosophila U1-70K protein is required for viability, but its arginine-rich domain is dispensable.. Genetics. 168(4):2059-65.

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