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Conference Papers
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, 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.
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.
Conference Proceedings
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.
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.
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
Chandrasekharan N., Hannenhalli S.  1992.  Efficient algorithms for computing matching and chromatic polynomials on series-parallel graphs. Fourth International Conference on Computing and Information, 1992. Proceedings. ICCI '92.
Pop M., Duncan C, Barequet G, Goodrich M, Huang W, Kumar S.  2001.  Efficient perspective-accurate silhouette computation and applications. Proceedings of the seventeenth annual symposium on Computational geometry.
Hua K.A, Hannenhalli S.  1991.  Parallel transitive closure computations using topological sort. Proceedings of the First International Conference on Parallel and Distributed Information Systems, 1991.
Hua K.A, Hannenhalli S.  1991.  Parallel transitive closure computations using topological sort. Proceedings of the First International Conference on Parallel and Distributed Information Systems, 1991.
Borah M., Bajwa R.S, Hannenhalli S, Irwin M.J.  1994.  A SIMD solution to the sequence comparison problem on the MGAP. International Conference on Application Specific Array Processors, 1994. Proceedings.
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.  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, Pevzner P.A.  1995.  Transforming men into mice (polynomial algorithm for genomic distance problem). Foundations of Computer Science, Annual IEEE Symposium on.
Journal Article
Ye C, Hsiao C, Bravo HCorrada.  2014.  BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution.. Bioinformatics. 30(9):1214-9.
Park S, Hannenhalli S, Choi S.  2014.  Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals. BMC Genomics. 15(1):526.
Mukherjee R., Singh L.NS, Evans P., Hannenhalli S.  2013.  Correlated evolution of positions within mammalian cis elements . Plos One. 8:e55521.
Alemu E.Y, Carl J.W, H. Bravo C, Hannenhalli S..  2014.  Determinants of expression variability. Nucleic Acids Research. 42(6):3503-3514.
Darnell DK, Zhang LS, Hannenhalli S, Yaklichkin SY.  2014.  Developmental expression of chicken FOXN1 and putative target genes during feather development.. Int J Dev Biol. 58(1):57-64.
Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, M Hossain A, Oundo J, Tamboura B, Mai V, Astrovskaya I et al..  2014.  Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition.. Genome Biol. 15(6):R76.
Korpal M, Ell BJ, Buffa FM, Ibrahim T, Blanco MA, Terrassa Tà-, Mercatali L, Khan Z, Goodarzi H, Hua Y et al..  2011.  Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization. Nature Medicine. 17(9):1101-1108.
Korpal M, Ell BJ, Buffa FM, Ibrahim T, Blanco MA, Terrassa Tà-, Mercatali L, Khan Z, Goodarzi H, Hua Y et al..  2011.  Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization. Nature Medicine. 17(9):1101-1108.
Korpal M, Ell BJ, Buffa FM, Ibrahim T, Blanco MA, Terrassa Tà-, Mercatali L, Khan Z, Goodarzi H, Hua Y et al..  2011.  Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization. Nature Medicine. 17(9):1101-1108.
Lu Y, Hannenhalli S, Cappola T, Putt M.  2014.  An evaluation of Monte-Carlo logic and logicFS motivated by a study of the regulation of gene expression in heart failure. Journal of Applied Statistics. 41(9):1956-1975.
Zheng L, Cardaci S, Jerby L, MacKenzie ED, Sciacovelli M, T Johnson I, Gaude E, King A, Leach JDG, Edrada-Ebel RA et al..  2015.  Fumarate induces redox-dependent senescence by modifying glutathione metabolism.. Nat Commun. 6:6001.

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