Student Publications

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Duarte NC, Becker SA, Jamshidi N, et al. "Global reconstruction of the human metabolic network based on genomic and bibliomic data." Proc. Natl. Acad. Sci. U.S.A.. 2007;104(6):1777-82.
Cachay ER, Frost SDW, Poon AFY, et al. "Herpes simplex virus type 2 acquisition during recent HIV infection does not influence plasma HIV levels." J. Acquir. Immune Defic. Syndr.. 2008;47(5):592-6.
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.
Papin JA, Reed JL, Palsson BO. "Hierarchical thinking in network biology: the unbiased modularization of biochemical networks." Trends Biochem. Sci.. 2004;29(12):641-7.
Kim T H, Barrera LO, Zheng M, et al. "A high-resolution map of active promoters in the human genome." Nature. 2005;436(7052):876-80.
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.
Hsiao A, Kuo MD. "High-throughput biology in the postgenomic era." J Vasc Interv Radiol. 2009;20(7 Suppl):S488-96.
Garcia-Bassets I, Kwon Y-S, Telese F, et al. "Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors." Cell. 2007;128(3):505-18.
Heintzman ND, Hon GC, Hawkins DR, et al. "Histone modifications at human enhancers reflect global cell-type-specific gene expression." Nature. 2009;459(7243):108-12.
Hightower GK, May SJ, Pérez-Santiago J, et al. "HIV-1 clade B pol evolution following primary infection." PLoS ONE. 2013;8(6):e68188.
O'Dea EL, Barken D, Peralta RQ, et al. "A homeostatic model of IkappaB metabolism to control constitutive NF-kappaB activity." Mol. Syst. Biol.. 2007;3:111.
Bushman FD, Malani N, Fernandes J, et al. "Host cell factors in HIV replication: meta-analysis of genome-wide studies." PLoS Pathog.. 2009;5(5):e1000437.
Schultz MD, He Y, Whitaker JW, et al. "Human body epigenome maps reveal noncanonical DNA methylation variation." Nature. 2015;523(7559):212-6.
Lister R, Pelizzola M, Dowen RH, et al. "Human DNA methylomes at base resolution show widespread epigenomic differences." Nature. 2009;462(7271):315-22.
König R, Stertz S, Zhou Y, et al. "Human host factors required for influenza virus replication." Nature. 2010;463(7282):813-7.
Konopka G, Friedrich T, Davis-Turak J, et al. "Human-specific transcriptional networks in the brain." Neuron. 2012;75(4):601-17.
Birney E, Stamatoyannopoulos JA, Dutta A, et al. "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project." Nature. 2007;447(7146):799-816.
Tan M, Luo H, Lee S, et al. "Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification." Cell. 2011;146(6):1016-28.
Ruiz S, Diep D, Gore A, et al. "Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells." Proc. Natl. Acad. Sci. U.S.A.. 2012;109(40):16196-201.
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.
Yost SE, Smith EN, Schwab RB, et al. "Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens." Nucleic Acids Res.. 2012;40(14):e107.
Roepcke S, Zhi D, Vingron M, Arndt PF. "Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters." Gene. 2006;365:48-56.
Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. "Identification of post-translational modifications by blind search of mass spectra." Nat. Biotechnol.. 2005;23(12):1562-7.
Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. "Identification of post-translational modifications via blind search of mass-spectra." Proc IEEE Comput Syst Bioinform Conf. 2005:157-66.
Li F, Thiele I, Jamshidi N, Palsson BØ. "Identification of potential pathway mediation targets in Toll-like receptor signaling." PLoS Comput. Biol.. 2009;5(2):e1000292.