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Journal Article

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HCorrada, Davis S, Gatto L, Girke T et al.. 2015. Orchestrating high-throughput genomic analysis with Bioconductor.. Nat Methods. 12(2):115-21.

Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA. 2014. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.. Bioinformatics. 30(10):1363-9.

Zarecki R, Oberhardt MA, Yizhak K, Wagner A, Segal EShtifman, Freilich S, Henry CS, Gophna U, Ruppin E. 2014. Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms. PLoS ONE. 9(5):e98372.

Seaver SMD, Bradbury LMT, Frelin O, Zarecki R, Ruppin E, Hanson AD, Henry CS. 2015. Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm.. Front Plant Sci. 6:142.

Seaver SMD, Bradbury LMT, Frelin O, Zarecki R, Ruppin E, Hanson AD, Henry CS. 2015. Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm.. Front Plant Sci. 6:142.

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.

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.

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.

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.

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.

Alemu E.Y, Carl J.W, H. Bravo C, Hannenhalli S.. 2014. Determinants of expression variability. Nucleic Acids Research. 42(6):3503-3514.

Mukherjee R., Singh L.NS, Evans P., Hannenhalli S. 2013. Correlated evolution of positions within mammalian cis elements . Plos One. 8:e55521.

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.

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.

Conference Proceedings

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, 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. 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.

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.

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.

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.

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.

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

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