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Conference Proceedings
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.
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.
Conference Papers
Wang H, Duggal G, Patro R, Girvan M, Hannenhalli S, Kingsford C.  2013.  Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin. Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics. :306-315.
Wang K, Das A, Xiong Z-M, Cao K, Hannenhalli S.  2013.  Identification of gene clusters with phenotype-dependent expression with application to normal and premature ageing. Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics. :377-383.
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, 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).
Wang K, Cao K, Hannenhalli S.  2015.  Chromatin and genomic determinants of alternative splicing. BCB '15 Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics .
Books
Hannenhalli S, Pevzner P.A.  1995.  Reversals do not cut long strips.
Pop M.  2015.  Encyclopedia of MetagenomicsHuman Microbiome, Assembly and Analysis Software, Project. :243-246.
Giancarlo R., Hannenhalli S.  2007.  Algorithms in Bioinformatics: 7th International Workshop, WABI 2007, Philadelphia, PA, USA, September 8-9, 2007, Proceedings. 4645
Book Chapters
Hannenhalli S, Pevzner P.  1995.  Towards a computational theory of genome rearrangements. Computer Science TodayComputer Science Today. 1000
Kim Y, Patro R, Ip CYiu, O'Leary DP, Anishkin A, Sukharev S, Varshney A.  2009.  Salient Frame Detection for Molecular Dynamics Simulations. Scientific VisualizationScientific Visualization.
Cummings MP.  2004.  PHYLIP (Phylogeny Inference Package).
Donelson J.E., Hill K.L., El-Sayed N.M.A..  1999.  Multiple mechanisms of immune evasion by African trypanosomes. The Trypanosome Surface . :71-91.
Otto S.P, Cummings MP, Wakeley J..  1996.  Inferring phylogenies from DNA sequence data: The effects of sampling. New Uses for New PhylogeniesNew Uses for New Phylogenies.
Berman P, Hannenhalli S.  1996.  Fast sorting by reversal. Combinatorial Pattern MatchingCombinatorial Pattern Matching. 1075
Berman P, Hannenhalli S.  1996.  Fast sorting by reversal. Combinatorial Pattern MatchingCombinatorial Pattern Matching. 1075
Roe A., Weller S., Baixeras J., Brown J.W, Cummings MP, Davis D.R, Horak M., Kawahara A.Y, Mitter C., Parr C.S et al..  2010.  Evolutionary framework for Lepidoptera model systems. Genetics and Molecular Biology of LepidopteraGenetics and Molecular Biology of Lepidoptera.
Huq A, Grim C, Colwell RR, G. Nair B.  2006.  Detection, Isolation, and Identification of Vibrio cholerae from the Environment. Current Protocols in MicrobiologyCurrent Protocols in Microbiology.
S. Kosaraju R, Pop M..  1998.  De-amortization of Algorithms. Computing and CombinatoricsComputing and Combinatorics. 1449
Evans P, Donahue G, Hannenhalli S.  2006.  Conservation Patterns in cis-Elements Reveal Compensatory Mutations. Comparative GenomicsComparative Genomics. 4205
Hannenhalli S, Hubbell E, Lipshutz R, Pevzner P.  2002.  Combinatorial Algorithms for Design of DNA Arrays. Chip TechnologyChip Technology. 77
Hannenhalli S, Hubbell E, Lipshutz R, Pevzner P.  2002.  Combinatorial Algorithms for Design of DNA Arrays. Chip TechnologyChip Technology. 77
Hannenhalli S, Hubbell E, Lipshutz R, Pevzner P.  2002.  Combinatorial Algorithms for Design of DNA Arrays. Chip TechnologyChip Technology. 77
Hannenhalli S, Hubbell E, Lipshutz R, Pevzner P.  2002.  Combinatorial Algorithms for Design of DNA Arrays. Chip TechnologyChip Technology. 77

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