Publications

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Journal Articles
Banerjee A G, Gupta SK.  2007.  Geometrical algorithms for automated design of side actions in injection moulding of complex parts. Computer-Aided Design. 39(10):882-897.
Arkin EM, Khuller S, Mitchell JSB.  1993.  Geometric knapsack problems. Algorithmica. 10(5):399-427.
Karnik M, Gupta SK, Magrab EB.  2005.  Geometric algorithms for containment analysis of rotational parts. Computer-Aided Design. 37(2):213-230.
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.
Li X, Gupta SK.  2004.  Geometric algorithms for automated design of rotary-platen multi-shot molds. Computer-Aided Design. 36(12):1171-1187.
Priyadarshi AK, Gupta SK.  2004.  Geometric algorithms for automated design of multi-piece permanent molds. Computer-Aided Design. 36(3):241-260.
Mount SM.  2000.  Genomic Sequence, Splicing, and Gene Annotation. American Journal of Human GeneticsAm J Hum Genet. 67(4):788-792.
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.
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.
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.
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.
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)
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.
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.
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.
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.
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.
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.
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.
El-Sayed NM, Myler PJ, Bartholomeu DC, Nilsson D, Aggarwal G, Tran A-N, Ghedin E, Worthey EA, Delcher AL, Blandin G et al..  2005.  The Genome Sequence of Trypanosoma cruzi, Etiologic Agent of Chagas Disease. Science. 309(5733):409-415.
El-Sayed NM, Myler PJ, Bartholomeu DC, Nilsson D, Aggarwal G, Tran A-N, Ghedin E, Worthey EA, Delcher AL, Blandin G et al..  2005.  The Genome Sequence of Trypanosoma Cruzi, Etiologic Agent of Chagas Disease. ScienceScience. 309(5733):409-415.
El-Sayed NM, Myler PJ, Bartholomeu DC, Nilsson D, Aggarwal G, Tran AN, Ghedin E, Worthey EA, Delcher AL, Blandin G et al..  2005.  The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science. 309(5733)
Grim CJ, Hasan NA, Taviani E, Haley B, Chun J, Brettin TS, Bruce DC, Detter CJ, Han CS, Chertkov O et al..  2010.  Genome Sequence of Hybrid Vibrio Cholerae O1 MJ-1236, B-33, and CIRS101 and Comparative Genomics with V. Cholerae. Journal of BacteriologyJ. Bacteriol.. 192(13):3524-3533.
Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF et al..  2000.  The genome sequence of Drosophila melanogaster. Science. 287(5461):2185-2185.
Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H|[eacute]|, Fouts DE, Eisen JA, Gill SR et al..  2003.  The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature. 423(6935):81-86.

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