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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

Haft DH, Selengut J., Brinkac LM, Zafar N, White O. 2005. Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics. Bioinformatics (Oxford, England)Bioinformatics (Oxford, England). 21

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, 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

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. 2008. Eukaryotic Transcription Factor Binding Sites—modeling and Integrative Search Methods. BioinformaticsBioinformaticsBioinformaticsBioinformatics. 24

Hannenhalli S. 2008. BIOINFORMATICS REVIEW. BIOINFORMATICSBioinformatics. 24

Hannenhalli S. 1995. Transforming men into mice (a computational theory of genome rearrangements).

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, 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, Levy S. 2003. Transcriptional regulation of protein complexes and biological pathways. Mammalian GenomeMammalian Genome. 14

Hannenhalli S. 1996. Polynomial-time algorithm for computing translocation distance between genomes. Discrete Applied MathematicsDiscrete Applied Mathematics. 71

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, Pevzner P. 1995. Towards a computational theory of genome rearrangements. Computer Science TodayComputer Science Today. 1000

Hannenhalli S, Pevzner P.A. 1995. Reversals do not cut long strips.

Hannenhalli S, Pevzner PA. 1999. Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. J. ACMJ. ACM. 46

Hannenhalli S, Perumalla K., Chandrasekharan N., Sridhar R.. 1993. A distributed algorithm for ear decomposition. Fifth International Conference on Computing and Information, 1993. Proceedings ICCI '93.

Hannenhalli S, Russell RB. 2000. Analysis and prediction of functional sub-types from protein sequence alignments. Journal of Molecular BiologyJournal of Molecular Biology. 303

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, Chappey C., Koonin E.V, Pevzner P.A,. 1995. Genome sequence comparison and scenarios for gene rearrangements: A test case. GenomicsGenomics. 30

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.

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