Publications

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K
Kurkulos M, Weinberg JM, Pepling ME, Mount SM.  1991.  Polyadenylylation in copia requires unusually distant upstream sequences.. Proc Natl Acad Sci U S A. 88(8):3038-42.
Kurkulos M, Weinberg JM, Roy D, Mount SM.  1994.  P element-mediated in vivo deletion analysis of white-apricot: deletions between direct repeats are strongly favored.. Genetics. 136(3):1001-11.
Khan Z, Ford MJ, Cusanovich DA, Mitrano A, Pritchard JK, Gilad Y.  2013.  Primate transcript and protein expression levels evolve under compensatory selection pressures.. Science. 342(6162):1100-4.
Khan Z., Bloom J.S, Kruglyak L., Singh M..  2009.  A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays. Bioinformatics. 25(13):1609-1616.
Khan Z, Bloom JS, Kruglyak L, Singh M.  2009.  A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays.. Bioinformatics. 25(13):1609-16.
Khan Z., Bloom J.S, Garcia B.A, Singh M., Kruglyak L..  2009.  Protein quantification across hundreds of experimental conditions. Proceedings of the National Academy of Sciences. 106(37):15544-15548.
Khan Z, Bloom JS, Garcia BA, Singh M, Kruglyak L.  2009.  Protein quantification across hundreds of experimental conditions.. Proc Natl Acad Sci U S A. 106(37):15544-8.
Khan Z., Ford M.J, Cusanovich D.A, Mitrano A., Pritchard J.K, Gilad Y..  2013.  Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures. Science. 342(6162):1100-1104.
Karathia H, Kingsford C, Girvan M, Hannenhalli S.  2016.  A pathway-centric view of spatial proximity in the 3D nucleome across cell lines. Scientific Reports. 6:39279.
J
Jerby-Arnon L, Pfetzer N, Waldman YY, McGarry L, James D, Shanks E, Seashore-Ludlow B, Weinstock A, Geiger T, Clemons PA et al..  2014.  Predicting cancer-specific vulnerability via data-driven detection of synthetic lethality.. Cell. 158(5):1199-209.
I
Islam M.S, Tasmin R, Khan SI s l a m, Bakht HBM, Mahmood ZH a y a t, Rahman M.Z i a u r, Bhuiyan NA m i n, Nishibuchi M, Nair G.B a l a k, e y Sack R.B r a d l et al..  2004.  Pandemic strains of O3:K6 Vibrio parahaemolyticus in the aquatic environment of Bangladesh. Canadian Journal of MicrobiologyCanadian Journal of Microbiology. 50
H
Hua K.A, Hannenhalli S.  1991.  Parallel transitive closure computations using topological sort. Proceedings of the First International Conference on Parallel and Distributed Information Systems, 1991.
Hannenhalli S.  1996.  Polynomial-time algorithm for computing translocation distance between genomes. Discrete Applied MathematicsDiscrete Applied Mathematics. 71
Hannenhalli S.  1995.  Polynomial-time algorithm for computing translocation distance between genomes. Combinatorial Pattern MatchingCombinatorial Pattern Matching.
Hannenhalli S, Levy S.  2002.  Predicting Transcription Factor Synergism. Nucleic Acids ResearchNucl. Acids Res.Nucleic Acids ResearchNucl. Acids Res.. 30
Hannenhalli S, Feldman W, Lewis HF, Skiena SS, Pevzner PA.  1996.  Positional sequencing by hybridization. Computer applications in the biosciences : CABIOSComputer applications in the biosciences : CABIOS. 12
Hannenhalli S, Levy S..  2001.  Promoter prediction in the human genome. BioinformaticsBioinformatics. 17
Haley BJ, Grim CJ, Hasan NA, Taviani E, Jongsik C, Brettin TS, Bruce DC, Challacombe JF, J. Detter C, Han CS et al..  2010.  The pre‐seventh pandemic Vibrio cholerae BX 330286 El Tor genome: evidence for the environment as a genome reservoir. Environmental Microbiology ReportsEnvironmental Microbiology Reports. 2
Hadley D., Murphy T., Valladares O., Hannenhalli S, Ungar L., Kim J., Bucan M.,.  2006.  Patterns of sequence conservation in presynaptic neural genes. Genome BiolGenome Biol. 7
G
García-Varela M., Cummings MP, G. de León P-P, Gardner S.L, Laclette J.P.  2002.  Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class Polyacanthocephala (Acanthocephala). Mol Phylogenet EvolMol Phylogenet Evol. 23
García-Varela M., G. de León P-P, de la Torre P., Cummings MP, Sarma S.S, Laclette J.P.  2000.  Phylogenetic relationships of Acanthocephala based on analysis of 18S ribosomal RNA gene sequences. J Mol EvolJ Mol Evol. 50
F
Förster H., Cummings MP, Coffey M.D.  2000.  Phylogenetic relationships of ıt Phytophthora species based on ribosomal ITS I DNA sequence analysis with emphasis on Waterhouse groups V and VI. Mycol ResMycol Res. 104
Folger O, Jerby L, Frezza C, Gottlieb E, Ruppin E, Shlomi T.  2011.  Predicting selective drug targets in cancer through metabolic networks.. Mol Syst Biol. 7:501.
Faruque SM, Kamruzzaman M., Meraj IM, Chowdhury N, G. Nair B, R. Sack B, Colwell RR, Sack DA.  2003.  Pathogenic Potential of Environmental Vibrio Cholerae Strains Carrying Genetic Variants of the Toxin-Coregulated Pilus Pathogenicity Island. Infection and ImmunityInfect. Immun.Infection and ImmunityInfect. Immun.. 71

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