Publications

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Lewinski MK, Bisgrove D, Shinn P, Chen H, Hoffmann C, Hannenhalli S, Verdin E, Berry CC, Ecker JR, Bushman FD.  2005.  Genome-Wide Analysis of Chromosomal Features Repressing Human Immunodeficiency Virus Transcription. Journal of VirologyJ. Virol.. 79(11):6610-6619.
Sethupathy P, Giang H, Plotkin JB, Hannenhalli S.  2008.  Genome-Wide Analysis of Natural Selection on Human Cis-Elements. PLoS ONEPLoS ONE. 3(9):e3137-e3137.
Nagarajan N, Navajas-Pérez R, Pop M, Alam M, Ming R, Paterson A, Salzberg S.  2008.  Genome-Wide Analysis of Repetitive Elements in Papaya. Tropical Plant Biology. 1(3):191-201.
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 Micro. 3(11):848-858.
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 Biology. 8(11):R247-R247.
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 Evol. 28(9):2615-2627.
Taviani E, Spagnoletti M, Ceccarelli D, Haley BJ, Hasan NA, Chen A, Colombo MM, Huq A, Colwell RR.  2012.  Genomic analysis of ICE Vch Ban8: An atypical genetic element in Vibrio cholerae. FEBS Letters. (11):1617-1621.
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 biology. 11(1)
Hasan N.A, Choi S.Y, Eppinger M., Clark P.W, Chen A., Alam M., Haley B.J, Taviani E., Hine E., Su Q. et al..  2012.  Genomic diversity of 2010 Haitian cholera outbreak strains. Proceedings of the National Academy of Sciences. :E2010-E2017.
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.
Tighe S, Afshinnekoo E, Rock TM, McGrath K, Alexander N, McIntyre A, Ahsanuddin S, Bezdan D, Green SJ, Joye S et al..  2017.  Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP). Journal of Biomolecular Techniques : JBT. 28(1):31-39.
Zo YG, Rivera ING, Russek-Cohen E, Islam MS, Siddique AK, Yunus M, Sack RB, 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 Sciences. 99(19):12409-12409.
Mount SM.  2000.  Genomic Sequence, Splicing, and Gene Annotation. American Journal of Human GeneticsAm J Hum Genet. 67(4):788-792.
Colwell RR, Chun J.  2009.  The Genus Vibrio and Related Genera. Practical handbook of microbiologyPractical handbook of microbiology. :267-267.
Kang H, Sehgal V, Getoor L.  2007.  GeoDDupe: A Novel Interface for Interactive Entity Resolution in Geospatial Data. Information Visualization, 2007. IV '07. 11th International Conference. :489-496.
Freedman MJ, Vutukuru M, Feamster N, Balakrishnan H.  2005.  Geographic locality of IP prefixes. Proceedings of the 5th ACM SIGCOMM conference on Internet Measurement. :13-13.
Kumar M, Gupta SK.  2001.  A geometric algorithm for automated design of multi-stage molds for manufacturing multi-material objects. :278-288.
Yao Z, Gupta SK, Nau DS.  2000.  A Geometric Algorithm for Finding the Largest Milling Cutter. ISR; TR 2000-40
Yao Z, Gupta SK, Nau DS.  2000.  A geometric algorithm for finding the maximal cutter for 2-D milling operations. :26-28.
Yao Z, Gupta SK, Nau DS.  2000.  A Geometric Algorithm for Multi-Part Milling Cutter Selection. ISR; TR 2000-42
Yao Z, Gupta SK, Nau DS.  2001.  A geometric algorithm for selecting optimal set of cutters for multi-part milling. :130-139.
Priyadarshi AK, Gupta SK.  2004.  Geometric algorithms for automated design of multi-piece permanent molds. Computer-Aided Design. 36(3):241-260.
Li X, Gupta SK.  2004.  Geometric algorithms for automated design of rotary-platen multi-shot molds. Computer-Aided Design. 36(12):1171-1187.
Gupta SK, Saini SK, Spranklin BW, Yao Z.  2005.  Geometric algorithms for computing cutter engagement functions in 2.5D milling operations. Computer-Aided Design. 37(14):1469-1480.
Karnik M, Gupta SK, Magrab EB.  2005.  Geometric algorithms for containment analysis of rotational parts. Computer-Aided Design. 37(2):213-230.

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