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Journal Articles
Le Saux MFischer-, Hervio-Heath D, Loaec S, Colwell RR, Pommepuy M.  2002.  Detection of Cytotoxin-Hemolysin mRNA in Nonculturable Populations of Environmental and Clinical Vibrio Vulnificus Strains in Artificial Seawater. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 68
Searle RF, Sellens MH, Elson J, Jenkinson EJ, Billington WD.  1976.  Detection of alloantigens during preimplantation development and early trophoblast differentiation in the mouse by immunoperoxidase labeling.. J Exp Med. 143(2):348-59.
Kim R., Kulkarni P., Hannenhalli S.  2013.  Derepression of Cancer/testis antigens in cancer is associated with distinct patterns of DNA hypomethylation. BMC CancerBMC CancerBMC Cancer. 13:144.
Everett L, San Wang L-, Hannenhalli S.  2006.  Dense Subgraph Computation Via Stochastic Search: Application to Detect Transcriptional Modules. BioinformaticsBioinformaticsBioinformaticsBioinformatics. 22
Liu B., Faller L.L, Klitgord N., Mazumdar V., Ghodsi M., Sommer D.D, Gibbons T.R, Treangen T, Chang Y.C, Li S. et al..  2012.  Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease. PloS onePLoS One. 7
Boca SM, Bravo HCorrada, Caffo B, Leek JT, Parmigiani G.  2013.  A decision-theory approach to interpretable set analysis for high-dimensional data. BiometricsBiometrics. 69
Ghodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M..  2013.  De novo likelihood-based measures for comparing genome assemblies. BMC research notes. 6
Auslander N, Wagner A, Oberhardt M, Ruppin E.  2016.  Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction. PLOS Computational Biology. 12(9):e1005125.
Parr CS, Cummings MP.  2005.  Data sharing in ecology and evolution. Trends in Ecology & EvolutionTrends in Ecology & Evolution. 20
Plasschaert R.N, Vigneau S., Tempera I., Gupta R., Maksimoska J., Everett L., Davuluri R., Mamorstein R., Lieberman P.M, Schultz D. et al..  2014.  CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation. Nucleic Acids ResNucleic Acids ResNucleic Acids Res. 42:774-89.
Essien K, Vigneau S, Apreleva S, Singh LN, Bartolomei MS, Hannenhalli S.  2009.  CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features. Genome BiologyGenome Biology. 10
El‐Sayed NM, Patton C.L, Harkins P.C, Fox R.O, Anderson K..  1995.  Crystallization and preliminary X-ray investigation of the recombinant Trypanosoma brucei rhodesiense calmodulin. Proteins: Structure, Function, and BioinformaticsProteins: Structure, Function, and Bioinformatics. 21
Huq A, R. Sack B, Nizam A, Longini IM, G. Nair B, Ali A, J. Morris G, Khan M.NHuda, A. Siddique K, Yunus M et al..  2005.  Critical Factors Influencing the Occurrence of Vibrio Cholerae in the Environment of Bangladesh. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 71
Colwell RR, Peeters J..  2007.  Creating a nationwide wireless detection sensor network for chemical, biological and radiological threats. Gentag White PaperGentag White Paper.
Zo Y-G, Chokesajjawatee N, Arakawa E, Watanabe H, Huq A, Colwell RR.  2008.  Covariability of Vibrio Cholerae Microdiversity and Environmental Parameters. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 74
Kingsford C, Zaslavsky E, Singh M.  2011.  A cost-aggregating integer linear program for motif finding. Journal of Discrete AlgorithmsJournal of Discrete Algorithms. 9
Ruppin E., Reggia JA.  2001.  Cortical Spreading depression and the pathogenesis of brain disorders: a computational and neural network-based investigation. Neurological researchNeurological research. 23
Singh LN, Hannenhalli S.  2010.  Correlated Changes Between Regulatory Cis Elements and Condition-Specific Expression in Paralogous Gene Families. Nucleic Acids ResearchNucl. Acids Res.Nucleic Acids ResearchNucl. Acids Res.. 38
Cummings MP.  1992.  Copia-like retrotransposons in plants: a brief introduction. The Plant Genetics NewsletterThe Plant Genetics Newsletter. 8
Voytas D.F, Cummings MP, Koniczny A., Ausubel F.M, Rodermel S.R.  1992.  copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USAProc Natl Acad Sci USA. 89
Senoh M, Ghosh‐Banerjee J, Ramamurthy T, Hamabata T, Kurakawa T, Takeda M, Colwell RR, G. Nair B, Takeda Y.  2010.  Conversion of viable but nonculturable Vibrio cholerae to the culturable state by co‐culture with eukaryotic cells. Microbiology and ImmunologyMicrobiology and Immunology. 54
He X, Chatterjee R, John S, Bravo H, Sathyanarayana BK, Biddie SC, FitzGerald PC, Stamatoyannopoulos JA, Hager GL, Vinson C.  2013.  Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding. BMC Genomics. 14(1):428.
Almeida M, Hebert A, Abraham A-L, Rasmussen S, Monnet C, Pons N, Delbes C, Loux V, Batto J-M, Leonard P et al..  2014.  Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products. BMC GenomicsBMC Genomics. 15:1101.
Reggia JA, Ruppin E., Berndt R.S.  1997.  Computer models: A new approach to the investigation of disease. MD ComputingMD Computing. 14
Pertea M, Mount SM, Salzberg SL.  2007.  A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana.. BMC Bioinformatics. 8:159.

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