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Journal Articles
Harrington R, Ondov BD, Radune D, Friss MBeth, Klubnik J, Diviak L, Hnath J, Cendrowski SR, Blank TE, Karaolis D et al..  2013.  Genome sequence of the attenuated Carbosap vaccine strain of Bacillus anthracis. Genome announcements. 1:e00067–12.
Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S et al..  2002.  Genome sequence of the human malaria parasite Plasmodium falciparum. NatureNature. 419
El‐Sayed NM, Myler P.J, Bartholomeu D.C, Nilsson D., Aggarwal G., Tran A.N, Ghedin E., Worthey E.A, Delcher A.L, Blandin G. et al..  2005.  The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. ScienceScience. 309
Bishop-Lilly KA, Ge H, Butani A, Osborne B, Verratti K, Mokashi V, Nagarajan N, Pop M., Read TD, Richards AL.  2013.  Genome sequencing of four strains of Rickettsia prowazekii, the causative agent of epidemic typhus, including one flying squirrel isolate. Genome announcementsGenome announcements. 1
Hyötyläinen T, Jerby L, Petäjä EM, Mattila I, Jäntti S, Auvinen P, Gastaldelli A, Yki-Järvinen H, Ruppin E, Orešič M.  2016.  Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease.. Nat Commun. 7:8994.
tyläinen Tö, Jerby L, jä EM ä, Mattila I, ntti Sä, Auvinen P, Gastaldelli A, rvinen Hä, Ruppin E, ič Mš.  2016.  Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease. Nature Communications. 7:8994.
Lewinski M.K, Bisgrove D., Shinn P., Chen H., Hoffmann C., Hannenhalli S, Verdin E., Berry C.C, Ecker J.R, Bushman F.D.  2005.  Genome-Wide Analysis of Chromosomal Features Repressing Human Immunodeficiency Virus Transcription. Journal of VirologyJ. Virol.Journal of VirologyJ. Virol.. 79
Sethupathy P, Giang H, Plotkin JB, Hannenhalli S.  2008.  Genome-Wide Analysis of Natural Selection on Human Cis-Elements. PLoS ONEPLoS ONEPLoS ONEPLoS ONE. 3
Nagarajan N., Navajas-Pérez R., Pop M., Alam M., Ming R., Paterson A.H, Salzberg S.L.  2008.  Genome-wide analysis of repetitive elements in papaya. Tropical Plant BiologyTropical Plant Biology. 1
Bushman F, Lewinski M, Ciuffi A, Barr S, Leipzig J, Hannenhalli S, Hoffmann C.  2005.  Genome-wide analysis of retroviral DNA integration. Nat Rev MicroNat Rev MicroNat Rev MicroNat Rev Micro. 3
Severance S, Rajagopal A, Rao AU, Cerqueira GC, Mitreva M, El-Sayed NM, Krause M, Hamza I.  2010.  Genome-wide analysis reveals novel genes essential for heme homeostasis in Caenorhabditis elegans.. PLoS Genet. 6(7):e1001044.
Yang S., Wang K., Valladares O., Hannenhalli S, Bucan M.,.  2007.  Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex. Genome BiolGenome Biol. 8
Vishnoi A, Sethupathy P, Simola D, Plotkin JB, Hannenhalli S.  2011.  Genome-Wide Survey of Natural Selection on Functional, Structural, and Network Properties of Polymorphic Sites in Saccharomyces Paradoxus. Molecular Biology and EvolutionMol Biol EvolMolecular Biology and EvolutionMol Biol Evol. 28
Taviani E, Spagnoletti M, Ceccarelli D, Haley BJ, Hasan NA, Chen A, Colombo MM, Huq A, Colwell RR.  2012.  Genomic analysis of ICEVchBan8: An atypical genetic element in Vibrio cholerae. FEBS LettersFEBS Letters.
G. Christopher V, Lucia P, Jennifer H.KChoi, Mathieu W, Devan J, J. Pepe H, Jennifer B, Karuna M, J. Alan P, Hannenhalli S et al..  2012.  Genomic analysis of sleep deprivation reveals translational regulation in the hippocampus. Physiological GenomicsPhysiological Genomics.
Chen PE, Cook C, Stewart AC, Nagarajan N, Sommer DD, Pop M., Thomason B, Thomason MPK, Lentz S, Nolan N et al..  2010.  Genomic characterization of the Yersinia genus. Genome BiologyGenome Biology. 11
Dupont CL, Rusch DB, Yooseph S, Lombardo M-J, R. Richter A, Valas R, Novotny M, Yee-Greenbaum J, Selengut J., Haft DH et al..  2012.  Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. The ISME journalThe ISME journal. 6
Dupont CL, Rusch DB, Yooseph S, Lombardo M-J, R Richter A, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH et al..  2012.  Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage.. ISME J. 6(6):1186-99.
Bartholomeu DC, Cerqueira GC, Leão ACarolina A, daRocha WD, Pais FS, Macedo C, Djikeng A, Teixeira SMR, El-Sayed NM.  2009.  Genomic organization and expression profile of the mucin-associated surface protein (masp) family of the human pathogen Trypanosoma cruzi.. Nucleic Acids Res. 37(10):3407-17.
Zo Y.G, Rivera I.NG, Russek-Cohen E., Islam M.S, Siddique A.K, Yunus M., Sack R.B, Huq A., Colwell RR.  2002.  Genomic profiles of clinical and environmental isolates of Vibrio cholerae O1 in cholera-endemic areas of Bangladesh. Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences. 99
Mount SM.  2000.  Genomic sequence, splicing, and gene annotation.. Am J Hum Genet. 67(4):788-92.
Battle A, Khan Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, Gilad Y.  2015.  Genomic variation. Impact of regulatory variation from RNA to protein.. Science. 347(6222):664-7.
Pruzzo C, Vezzulli L, Colwell RR.  2008.  Global impact of Vibrio cholerae interactions with chitin. Environmental MicrobiologyEnvironmental Microbiology. 10
Colwell RR.  2005.  Global microbial ecology of Vibrio cholerae. Oceans and health: pathogens in the marine environmentOceans and health: pathogens in the marine environment.
Blanco MAndres, LeRoy G, Khan Z, Alečković M, Zee BM, Garcia BA, Kang Y.  2012.  Global secretome analysis identifies novel mediators of bone metastasis.. Cell Res. 22(9):1339-55.

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