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Haft DH, Selengut J., Mongodin EF, Nelson KE.  2005.  A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS computational biologyPLOS Computational Biology. 1
Haft DH, Selengut J., White O.  2003.  The TIGRFAMs database of protein families. Nucleic acids researchNucleic Acids Research. 31
Haft DH, Paulsen IT, Ward N, Selengut J..  2006.  Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic. BMC biologyBMC biology. 4
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.
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
Hammel M, Sfyroera G, Pyrpassopoulos S, Ricklin D, Ramyar KX, Pop M., Jin Z, Lambris JD, Geisbrecht BV.  2007.  Characterization of Ehp, a Secreted Complement Inhibitory Protein from Staphylococcus aureus. Journal of Biological ChemistryJournal of Biological Chemistry. 282
Hannenhalli S, Wang L.S.  2005.  Enhanced position weight matrices using mixture models. BioinformaticsBioinformatics. 21
Hannenhalli S.  1995.  Transforming men into mice (a computational theory of genome rearrangements).
Hannenhalli S.  1995.  Polynomial-time algorithm for computing translocation distance between genomes. Combinatorial Pattern MatchingCombinatorial Pattern Matching.
Hannenhalli S.  2008.  Eukaryotic Transcription Factor Binding Sites—modeling and Integrative Search Methods. BioinformaticsBioinformaticsBioinformaticsBioinformatics. 24
Hannenhalli S, Levy S.  2003.  Transcriptional regulation of protein complexes and biological pathways. Mammalian GenomeMammalian Genome. 14
Hannenhalli S, Levy S.  2002.  Predicting Transcription Factor Synergism. Nucleic Acids ResearchNucl. Acids Res.Nucleic Acids ResearchNucl. Acids Res.. 30
Hannenhalli S, Hayes WS, Hatzigeorgiou AG, Fickett JW.  1999.  Bacterial Start Site Prediction. Nucleic Acids ResearchNucl. Acids Res.Nucleic Acids ResearchNucl. Acids Res.. 27
Hannenhalli S, Pevzner P.  1995.  Towards a computational theory of genome rearrangements. Computer Science TodayComputer Science Today. 1000
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, Kaestner KH.  2009.  The evolution of Fox genes and their role in development and disease. Nature reviews. GeneticsNat Rev GenetNature reviews. GeneticsNat Rev Genet. 10
Hannenhalli S, Pevzner PA.  1999.  Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. J. ACMJ. ACM. 46
Hannenhalli S, Levy S..  2001.  Promoter prediction in the human genome. BioinformaticsBioinformatics. 17
Hannenhalli S.  2006.  Invited Talk: Deciphering Gene Regulatory Networks by in silico approaches. 6th International Workshop on Data Mining in Bioinformatics (BIOKDD06)6th International Workshop on Data Mining in Bioinformatics (BIOKDD06).
Hannenhalli S, Middleton R.P, Levy S., Perroud B., Holzwarth J.A, McDonald K., Hannah S.S,.  2006.  Identification and cross-species comparison of canine osteoarthritic gene regulatory cis-elements. Osteoarthritis and cartilage/OARS, Osteoarthritis Research SocietyOsteoarthritis and cartilage/OARS, Osteoarthritis Research Society. 14
Hannenhalli S.  2008.  BIOINFORMATICS REVIEW. BIOINFORMATICSBioinformatics. 24
Hannenhalli S, Russell R.B.  2001.  Analysis and prediction of protein functional sub-types from protein sequence alignments.
Hannenhalli S, Hubbell E, Lipshutz R, Pevzner P.  2002.  Combinatorial Algorithms for Design of DNA Arrays. Chip TechnologyChip Technology. 77
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, Chappey C., Koonin E.V, Pevzner P.A,.  1995.  Genome sequence comparison and scenarios for gene rearrangements: A test case. GenomicsGenomics. 30

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