Student Publications

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Kim J, Levy E, Ferbrache A, et al. "MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure." Bioinformatics. 2014;30(19):2826-7.
Kelley R, Ideker T. "Systematic interpretation of genetic interactions using protein networks." Nat. Biotechnol.. 2005;23(5):561-6.
Kelley R, Feizi H, Ideker T. "Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood." Bioinformatics. 2008;24(1):71-7.
Kang H M, Zaitlen NA, Wade CM, et al. "Efficient control of population structure in model organism association mapping." Genetics. 2008;178(3):1709-23.
Kaikkonen MU, Spann NJ, Heinz S, et al. "Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription." Mol. Cell. 2013;51(3):310-25.
Jung H, Bleazard T, Lee J, Hong D. "Systematic investigation of cancer-associated somatic point mutations in SNP databases." Nat. Biotechnol.. 2013;31(9):787-9.
Joyce AR, Palsson BØ. "The model organism as a system: integrating 'omics' data sets." Nat. Rev. Mol. Cell Biol.. 2006;7(3):198-210.
Joyce AR, Palsson BØ. "Predicting gene essentiality using genome-scale in silico models." Methods Mol. Biol.. 2008;416:433-57.
Joyce AR, Palsson BO. "Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach." Prog Drug Res. 2007;64:265, 267-309.
Joyce AR, Reed JL, White A, et al. "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J. Bacteriol.. 2006;188(23):8259-71.
Jones NC, Zhi D, Raphael BJ. "AliWABA: alignment on the web through an A-Bruijn approach." Nucleic Acids Res.. 2006;34(Web Server issue):W613-6.
Johnson DBF, Xu J, Shen Z, et al. "RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites." Nat. Chem. Biol.. 2011;7(11):779-86.
Johnson DBF, Wang C, Xu J, et al. "Release factor one is nonessential in Escherichia coli." ACS Chem. Biol.. 2012;7(8):1337-44.
Jin F, Li Y, Dixon JR, et al. "A high-resolution map of the three-dimensional chromatin interactome in human cells." Nature. 2013;503(7475):290-4.
Hung T, Pratt GA, Sundararaman B, et al. "The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression." Science. 2015;350(6259):455-9.
Hughey JJ, Lee TK, Covert MW. "Computational modeling of mammalian signaling networks." Wiley Interdiscip Rev Syst Biol Med. 2010;2(2):194-209.
Huelga SC, Vu AQ, Arnold JD, et al. "Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins." Cell Rep. 2012;1(2):167-178.
Huelga SC, Yeo GW. "Genomics of Alternative Splicing in Stem Cells.". In: Computational Biology of Embryonic Stem Cells (Ming Zhan, Ed.), pp. 147-160. Oak Park, IL: Bentham Science Publishers; 2012.
Hua Z, Pool JE, Schmitz RJ, et al. "Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis." Proc. Natl. Acad. Sci. U.S.A.. 2013;110(42):16927-32.
Hua Q, Joyce AR, Fong SS, Palsson BØ. "Metabolic analysis of adaptive evolution for in silico-designed lactate-producing strains." Biotechnol. Bioeng.. 2006;95(5):992-1002.
Hua Q, Joyce AR, Palsson BØ, Fong SS. "Metabolic characterization of Escherichia coli strains adapted to growth on lactate." Appl. Environ. Microbiol.. 2007;73(14):4639-47.
Hu M, Deng K, Qin Z, et al. "Bayesian inference of spatial organizations of chromosomes." PLoS Comput. Biol.. 2013;9(1):e1002893.
Hu M, Deng K, Selvaraj S, Qin Z, Ren B, Liu JS. "HiCNorm: removing biases in Hi-C data via Poisson regression." Bioinformatics. 2012;28(23):3131-3.
Hsiao A, Worrall DS, Olefsky JM, Subramaniam S. "Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes." Bioinformatics. 2004;20(17):3108-27.
Hsiao A, Subramaniam S. "Bivariate microarray analysis: statistical interpretation of two-channel functional genomics data." Syst Synth Biol. 2008;2(3-4):95-104.