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Hannenhalli S.  2007.  Eukaryotic Transcriptional Regulation: Signals, Interactions, and Modules. Computational Genomics: Current MethodsComputational Genomics: Current Methods.
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, 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.  Eukaryotic Transcription Factor Binding Sites—modeling and Integrative Search Methods. BioinformaticsBioinformaticsBioinformaticsBioinformatics. 24
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.  1996.  Polynomial-time algorithm for computing translocation distance between genomes. Discrete Applied MathematicsDiscrete Applied Mathematics. 71
Hannenhalli S, Hubbell E, Lipshutz R, Pevzner P.  2002.  Combinatorial Algorithms for Design of DNA Arrays. Chip TechnologyChip Technology. 77
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 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.  2009.  Mimosa: mixture model of co-expression to detect modulators of regulatory interaction. Algorithms in BioinformaticsAlgorithms in Bioinformatics.
Harrington R, Ondov BD, Radune D, Friss MBeth, Klubnik J, Diviak L, Hnath J, Cendrowski SR, Blank TE, Karaolis D et al..  2013.  Genome sequence of the attenuated Carbosap vaccine strain of Bacillus anthracis. Genome announcements. 1:e00067–12.
Hasan NA, Grim CJ, Haley BJ, Jongsik C, Alam M, Taviani E, Mozammel H, A. Munk C, Colwell RR.  2010.  Comparative Genomics of Clinical and Environmental Vibrio Mimicus. Proceedings of the National Academy of SciencesPNASProceedings of the National Academy of SciencesPNAS. 107
Hasan NA, W. Chowdhury B, Rahim N, Sultana M, S. Shabnam A, Mai V, Ali A, Morris GJ, R. Sack B, Huq A et al..  2011.  Metagenomic 16S rDNA Targeted PCR-DGGE in Determining Bacterial Diversity in Aquatic Ecosystem. Bangladesh Journal of MicrobiologyBangladesh Journal of Microbiology. 27
Hashmi N., Lee S., Cummings MP.  2004.  Abstracting workflows: unifying bioinformatics task conceptualization and specification through Semantic Web services. W3C Workshop on Semantic Web for Life Sciences.
He X, Chatterjee R, John S, Bravo H, Sathyanarayana BK, Biddie SC, FitzGerald PC, Stamatoyannopoulos JA, Hager GL, Vinson C.  2013.  Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding. BMC Genomics. 14(1):428.
Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM et al..  2004.  The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nature biotechnologyNature biotechnology. 22
Pop M.  2015.  Encyclopedia of MetagenomicsHuman Microbiome, Assembly and Analysis Software, Project. :243-246.
Hill CM, Astrovskaya I, Huang H, Koren S, Memon A, Treangen T, Pop M.  2013.  De novo likelihood-based measures for comparing metagenomic assemblies. 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
Hill CM, Albach CH, Angel S, Pop M..  2013.  K-mulus: Strategies for BLAST in the cloud. 10th International Conference on Parallel Processing and Applied Mathematics (PPAM).
Hinsch H, Hannenhalli S.  2006.  Recurring genomic breaks in independent lineages support genomic fragility. BMC Evolutionary BiologyBMC Evolutionary Biology. 6
Hochheiser H, Baehrecke EH, Mount SM, Shneiderman B.  2005.  Dynamic Querying for Pattern Identification in Microarray and Genomic Data (2003). Institute for Systems Research Technical ReportsInstitute for Systems Research Technical Reports.
Hochheiser H., Baehrecke E.H, Mount SM, Shneiderman B.  2003.  Dynamic querying for pattern identification in microarray and genomic data. 2003 International Conference on Multimedia and Expo, 2003. ICME '03. Proceedings. 3
Hotopp JCDunning, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Eisen J, Seshadri R, Ren Q, Wu M et al..  2006.  Comparative genomics of emerging human ehrlichiosis agents. PLoS geneticsPLoS genetics. 2

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