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Hansen KDaniel, Timp W, Bravo HCorrada, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D et al..  2011.  Increased methylation variation in epigenetic domains across cancer types. Nature Genetics. 43(8):768-775.
Hansen M, Everett L, Singh L, Hannenhalli S.  2010.  Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction. Algorithms for Molecular BiologyAlgorithms for Molecular Biology. 5
Hansen M., Everett L., Singh L., Hannenhalli S.  2009.  Mimosa: mixture model of co-expression to detect modulators of regulatory interaction. Algorithms in BioinformaticsAlgorithms in Bioinformatics.
Hannenhalli S, Pevzner P.A.  1995.  Reversals do not cut long strips.
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, 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, 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.A.  1995.  Transforming men into mice (polynomial algorithm for genomic distance problem). Foundations of Computer Science, Annual IEEE Symposium on.
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
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.  1995.  Polynomial-time algorithm for computing translocation distance between genomes. Combinatorial Pattern MatchingCombinatorial Pattern Matching.
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, 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, Chappey C, Koonin EV, Pevzner PA.  1995.  Genome Sequence Comparison and Scenarios for Gene Rearrangements: A Test Case. GenomicsGenomics. 30
Hannenhalli S.  1995.  Transforming men into mice (a computational theory of genome rearrangements).
Hannenhalli S, Hubbell E, Lipshutz R, Pevzner P.  2002.  Combinatorial Algorithms for Design of DNA Arrays. Chip TechnologyChip Technology. 77
Hannenhalli S.  2008.  Eukaryotic Transcription Factor Binding Sites—modeling and Integrative Search Methods. BioinformaticsBioinformaticsBioinformaticsBioinformatics. 24

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