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Hannenhalli S, Pevzner PA.  1999.  Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. J. ACMJ. ACM. 46
Hannenhalli S, Chappey C, Koonin EV, Pevzner PA.  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.
Hannenhalli S, Wang L.S.  2005.  Enhanced position weight matrices using mixture models. BioinformaticsBioinformatics. 21
Hannenhalli S.  2007.  Eukaryotic Transcriptional Regulation: Signals, Interactions, and Modules. Computational Genomics: Current MethodsComputational Genomics: Current Methods.
Hannenhalli S, Putt ME, Gilmore JM, Wang J, Parmacek MS, Epstein JA, Morrisey EE, Margulies KB, Cappola TP.  2006.  Transcriptional Genomics Associates FOX Transcription Factors With Human Heart Failure. CirculationCirculation. 114
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.  1996.  To cut… or not to cut (applications of comparative physical maps in molecular evolution). Proceedings of the seventh annual ACM-SIAM symposium on Discrete algorithms.
Hannenhalli S.  2008.  Eukaryotic Transcription Factor Binding Sites—modeling and Integrative Search Methods. BioinformaticsBioinformaticsBioinformaticsBioinformatics. 24
Hannenhalli S.  1996.  Polynomial-time algorithm for computing translocation distance between genomes. Discrete Applied MathematicsDiscrete Applied Mathematics. 71
Hannenhalli S, Pevzner P.A.  1995.  Transforming men into mice (polynomial algorithm for genomic distance problem). Foundations of Computer Science, Annual IEEE Symposium on.
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, 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 P.A.  1995.  Reversals do not cut long strips.
Hannenhalli S, Hubbell E, Lipshutz R, Pevzner P.  2002.  Combinatorial Algorithms for Design of DNA Arrays. Chip TechnologyChip Technology. 77
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.  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
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
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
Haft DH, Payne SH, Selengut J..  2012.  Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification. Journal of bacteriologyJournal of bacteriology. 194
Haft DH, Payne SH, Selengut JD.  2012.  Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification.. J Bacteriol. 194(1):36-48.
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

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