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Journal Article
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.
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.
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.
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.
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.
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.
Khan Z, Herman RA, Wallen K, Balch T.  2005.  An outdoor 3-D visual tracking system for the study of spatial navigation and memory in rhesus monkeys.. Behav Res Methods. 37(3):453-63.
Wang K, Das A, Xiong Z-M, Cao K, Hannenhalli S.  2015.  Phenotype-Dependent Coexpression Gene Clusters: Application to Normal and Premature Ageing. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 12(1):30-39.
Patella F, Schug ZT, Persi E, Neilson LJ, Erami Z, Avanzato D, Maione F, Hernandez-Fernaud JR, Mackay G, Zheng L et al..  2015.  Proteomics-based metabolic modeling reveals that fatty acid oxidation (FAO) controls endothelial cell (EC) permeability.. Mol Cell Proteomics. 14(3):621-34.
Liu Y, Morley M, Brandimarto J, Hannenhalli S, Hu Y, Ashley EA, Tang WHWilson, Moravec CS, Margulies KB, Cappola TP et al..  2015.  RNA-Seq identifies novel myocardial gene expression signatures of heart failure.. Genomics. 105(2):83-9.
Liu Y, Morley M, Brandimarto J, Hannenhalli S, Hu Y, Ashley EA, Tang WHWilson, Moravec CS, Margulies KB, Cappola TP et al..  2015.  RNA-Seq identifies novel myocardial gene expression signatures of heart failure.. Genomics. 105(2):83-9.
Akula N, Barb J, Jiang X, Wendland JR, Choi KH, Sen SK, Hou L, Chen DTW, Laje G, Johnson K et al..  2014.  RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder.. Mol Psychiatry. 19(11):1179-85.
Dillon LAL, Okrah K, V Hughitt K, Suresh R, Li Y, Fernandes MCecilia, A Belew T, Bravo HCorrada, Mosser DM, El-Sayed NM.  2015.  Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation.. Nucleic Acids Res. 43(14):6799-813.
Journal Articles
Berman P., Hannenhalli S, Karpinski M..  2002.  1.375-approximation algorithm for sorting by reversals. Algorithms—ESA 2002Algorithms—ESA 2002.
R. Sack B, A. Siddique K, Longini IM, Nizam A, Yunus M, M. Islam S, Morris, Ali A, Huq A, G. Nair B et al..  2003.  A 4-Year Study of the Epidemiology of Vibrio Cholerae in Four Rural Areas of Bangladesh. Journal of Infectious DiseasesJ Infect Dis.Journal of Infectious DiseasesJ Infect Dis.. 187
Yaklichkin SYu, Darnell DK, Pier MV, Antin PB, Hannenhalli S.  2011.  Accelerated evolution of 3'avian FOXE1 genes, and thyroid and feather specific expression of chicken FoxE1. BMC Evolutionary BiologyBMC Evolutionary Biology. 11
El‐Sayed NM, Hegde P, Quackenbush J, Melville SE, Donelson JE.  2000.  The African trypanosome genome. International Journal for ParasitologyInternational Journal for Parasitology. 30
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, Russell R.B.  2001.  Analysis and prediction of protein functional sub-types from protein sequence alignments.
Diehl S, Diehl F, El-Sayed NM, Clayton C, Hoheisel JD.  2002.  Analysis of stage-specific gene expression in the bloodstream and the procyclic form of Trypanosoma brucei using a genomic DNA-microarray.. Mol Biochem Parasitol. 123(2):115-23.
Diehl S, Diehl F, El‐Sayed NM, Clayton C, Hoheisel JD.  2002.  Analysis of stage-specific gene expression in the bloodstream and the procyclic form of Trypanosoma brucei using a genomic DNA-microarray. Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology. 123
Huq A., Grim C.J, Colwell RR.  2011.  Aquatic Realm and Cholera. Epidemiological and Molecular Aspects on CholeraEpidemiological and Molecular Aspects on Cholera.
Haft DH, Payne SH, Selengut J..  2012.  Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification. Journal of bacteriologyJournal of bacteriology. 194
Haft DH, Payne SH, Selengut JD.  2012.  Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification.. J Bacteriol. 194(1):36-48.

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