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Journal Articles
Haft DH, Selengut J., White O.  2003.  The TIGRFAMs database of protein families. Nucleic acids researchNucleic Acids Research. 31
Selengut J., Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, R. Richter A, White O.  2007.  TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic acids researchNucleic Acids Research. 35
Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E.  2013.  TIGRFAMs and Genome Properties in 2013.. Nucleic Acids Res. 41(Database issue):D387-95.
Haft DH, Selengut J., Richter RA, Harkins D, Basu MK, Beck E.  2013.  TIGRFAMs and Genome Properties in 2013. Nucleic acids researchNucleic Acids Research. 41
Choi S.S, Hannenhalli S.  2013.  Three independent determinants of protein evolutionary rate. J Mol EvolJ Mol EvolJ Mol Evol. 76:98-111.
Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J et al..  2009.  Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Applied and environmental microbiologyApplied and environmental microbiology. 75
Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J et al..  2009.  Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.. Appl Environ Microbiol. 75(7):2046-56.
Cunningham CE, Li S, Vizeacoumar FS, Bhanumathy KKalyanasun, Lee JSang, Parameswaran S, Furber L, Abuhussein O, Paul JM, McDonald M et al..  2016.  Therapeutic relevance of the protein phosphatase 2A in cancer. Oncotarget.com.
Simpson J.T, Pop M..  2015.  The Theory and Practice of Genome Sequence Assembly. Annu Rev Genomics Hum GenetAnnu Rev Genomics Hum Genet. 16:153-72.
Arkin EM, Belleville P, Mitchell JSB, Mount D, Romanik K, Salzberg S, Souvaine D.  1997.  Testing simple polygons. Computational GeometryComputational Geometry. 8
Banakar V., G. de Magny C, Jacobs J., Murtugudde R., Huq A., Wood R.J, Colwell RR.  2012.  Temporal and Spatial Variability in the Distribution of Vibrio vulnificus in the Chesapeake Bay: A Hindcast Study. EcoHealthEcoHealth.
Louis VR, Gillespie IA, O'Brien SJ, Russek-Cohen E, Pearson AD, Colwell RR.  2005.  Temperature-Driven Campylobacter Seasonality in England and Wales. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 71
Kimes NE, Grim CJ, Johnson WR, Hasan NA, Tall BD, Kothary MH, Kiss H, A. Munk C, Tapia R, Green L et al..  2011.  Temperature regulation of virulence factors in the pathogen Vibrio coralliilyticus. The ISME JournalThe ISME journal. 6
Kim D, Chiurillo MAngel, El-Sayed N, Jones K, Santos MRM, Porcile PE, Andersson B, Myler P, da Silveira JFranco, Ramírez JLuis.  2005.  Telomere and subtelomere of Trypanosoma cruzi chromosomes are enriched in (pseudo)genes of retrotransposon hot spot and trans-sialidase-like gene families: the origins of T. cruzi telomeres.. Gene. 346:153-61.
Leek JT, Scharpf RB, Bravo HCorrada, Simcha D, Langmead B, W. Johnson E, Geman D, Baggerly K, Irizarry RA.  2010.  Tackling the widespread and critical impact of batch effects in high-throughput data. Nature reviews. GeneticsNature reviews. Genetics. 11
Journal Article
Dillon LAL, Okrah K, V Hughitt K, Suresh R, Li Y, Fernandes MCecilia, A Belew T, Bravo HCorrada, Mosser DM, El-Sayed NM.  2015.  Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation.. Nucleic Acids Res. 43(14):6799-813.
Savage AF, Cerqueira GC, Regmi S, Wu Y, Sayed NMEl, Aksoy S.  2012.  Transcript expression analysis of putative Trypanosoma brucei GPI-anchored surface proteins during development in the tsetse and mammalian hosts.. PLoS Negl Trop Dis. 6(6):e1708.
Conference Proceedings
Hannenhalli S, Pevzner P.A.  1995.  Transforming men into mice (polynomial algorithm for genomic distance problem). Foundations of Computer Science, Annual IEEE Symposium on.
Hannenhalli S, Pevzner P.  1995.  Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. Proceedings of the twenty-seventh annual ACM symposium on Theory of computing.
Hannenhalli S, Pevzner P.  1996.  To cut… or not to cut (applications of comparative physical maps in molecular evolution). Proceedings of the seventh annual ACM-SIAM symposium on Discrete algorithms.
Conference Papers
Wang H, Duggal G, Patro R, Girvan M, Hannenhalli S, Kingsford C.  2013.  Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin. Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics. :306-315.
Book Chapters
Hannenhalli S, Pevzner P.  1995.  Towards a computational theory of genome rearrangements. Computer Science TodayComputer Science Today. 1000
Colwell RR.  2004.  A Tangled Bank: Reflections on the Tree of Life and Human Health. Assembling the Tree of LifeAssembling the Tree of Life.

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