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Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD et al..  2003.  Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.. Nucleic Acids Res. 31(19):5654-66.
Haas BJ, Berriman M, Hirai H, Cerqueira GG, LoVerde PT, El‐Sayed NM.  2007.  Schistosoma mansoni genome: Closing in on a final gene set. Experimental ParasitologyExperimental Parasitology. 117
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
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.
Haft DH, Selengut J., White O.  2003.  The TIGRFAMs database of protein families. Nucleic acids researchNucleic Acids Research. 31
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, 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, 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, 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
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, 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.  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, 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.  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, Levy S.  2003.  Transcriptional regulation of protein complexes and biological pathways. Mammalian GenomeMammalian Genome. 14
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.  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, Chappey C., Koonin E.V, Pevzner P.A,.  1995.  Genome sequence comparison and scenarios for gene rearrangements: A test case. GenomicsGenomics. 30
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, Levy S..  2001.  Promoter prediction in the human genome. BioinformaticsBioinformatics. 17

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