Student Publications

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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, Palsson BØ, Fong SS. "Metabolic characterization of Escherichia coli strains adapted to growth on lactate." Appl. Environ. Microbiol.. 2007;73(14):4639-47.
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.
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, Ideker T, Olefsky JM, Subramaniam S. "VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data." Nucleic Acids Res.. 2005;33(Web Server issue):W627-32.
Hsiao A, Subramaniam S. "Bivariate microarray analysis: statistical interpretation of two-channel functional genomics data." Syst Synth Biol. 2008;2(3-4):95-104.
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, Kuo MD. "High-throughput biology in the postgenomic era." J Vasc Interv Radiol. 2009;20(7 Suppl):S488-96.
Horler RSP, Butcher A, Papangelopoulos N, Ashton PD, Thomas GH. "EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations." Bioinformatics. 2009;25(2):163-6.
Hon G, Wang W, Ren B. "Discovery and annotation of functional chromatin signatures in the human genome." PLoS Comput. Biol.. 2009;5(11):e1000566.
Hon GC, Hawkins DR, Ren B. "Predictive chromatin signatures in the mammalian genome." Hum. Mol. Genet.. 2009;18(R2):R195-201.
Hon G, Ren B, Wang W. "ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome." PLoS Comput. Biol.. 2008;4(10):e1000201.
Hofree M, Shen JP, Carter H, Gross A, Ideker T. "Network-based stratification of tumor mutations." Nat. Methods. 2013;10(11):1108-15.
Ho Sui SJ, Lo R, Fernandes AR, et al. "Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence." Int. J. Antimicrob. Agents. 2012;40(3):246-51.
Hirose S, Payne SH, Loomis WF. "cis-Acting site controlling bidirectional transcription at the growth-differentiation transition in Dictyostelium discoideum." Eukaryotic Cell. 2006;5(7):1104-10.
Hightower GK, May SJ, Pérez-Santiago J, et al. "HIV-1 clade B pol evolution following primary infection." PLoS ONE. 2013;8(6):e68188.
Hevener AL, Olefsky JM, Reichart D, et al. "Macrophage PPAR gamma is required for normal skeletal muscle and hepatic insulin sensitivity and full antidiabetic effects of thiazolidinediones." J. Clin. Invest.. 2007;117(6):1658-69.
Herring CD, Raghunathan A, Honisch C, et al. "Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale." Nat. Genet.. 2006;38(12):1406-12.
Herrgård MJ, Palsson BØ. "Flagellar biosynthesis in silico: building quantitative models of regulatory networks." Cell. 2004;117(6):689-90.
Herrgård MJ, Fong SS, Palsson BØ. "Identification of genome-scale metabolic network models using experimentally measured flux profiles." PLoS Comput. Biol.. 2006;2(7):e72.