Student Publications

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2016
Gross AM, Jaeger PA, Kreisberg JF, et al. "Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA." Mol. Cell. 2016;62(2):157-68.
Rentas S, Holzapfel NT, Belew MS, et al. "Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells." Nature. 2016;532(7600):508-11.
2015
Gross AM, Ideker T. "Molecular networks in context." Nat. Biotechnol.. 2015;33(7):720-1.
2014
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.
Hauff SJ, Raju SC, Orosco RK, et al. "Matrix-metalloproteinases in head and neck carcinoma-cancer genome atlas analysis and fluorescence imaging in mice." Otolaryngol Head Neck Surg. 2014;151(4):612-8.
Gross AM, Orosco RK, Shen JP, et al. "Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss." Nat. Genet.. 2014;46(9):939-43.
2013
Nakatsuji T, Chiang H-I, Jiang SB, Nagarajan H, Zengler K, Gallo RL. "The microbiome extends to subepidermal compartments of normal skin." Nat Commun. 2013;4:1431.
Nguyen D D, Wu C-H, Moree WJ, et al. "MS/MS networking guided analysis of molecule and gene cluster families." Proc. Natl. Acad. Sci. U.S.A.. 2013;110(28):E2611-20.
2010
Lerman J, Palsson BO. "Microbiology. Topping off a multiscale balancing act." Science. 2010;330(6007):1058-9.
Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BØ. "Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli." Metab. Eng.. 2010;12(3):173-86.
2009
Sears DD, Hsiao G, Hsiao A, et al. "Mechanisms of human insulin resistance and thiazolidinedione-mediated insulin sensitization." Proc. Natl. Acad. Sci. U.S.A.. 2009;106(44):18745-50.
Manichaikul A, Ghamsari L, Hom EFY, et al. "Metabolic network analysis integrated with transcript verification for sequenced genomes." Nat. Methods. 2009;6(8):589-92.
2008
Chen CY-C, Chen G-W, Chen WY-C. "Molecular Simulation of HER2/neu Degradation by HSP90 Inhibitors." Journal of the Chinese Chemical Society. 2008;55:297-302.
Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H. "A multidimensional chromatography technology for in-depth phosphoproteome analysis." Mol. Cell Proteomics. 2008;7(7):1389-96.
2007
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.
Zhang H, Liu AY, Loriaux P, et al. "Mass spectrometric detection of tissue proteins in plasma." Mol. Cell Proteomics. 2007;6(1):64-71.
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.
Cho B-K, Charusanti P, Herrgård MJ, Palsson BO. "Microbial regulatory and metabolic networks." Curr. Opin. Biotechnol.. 2007;18(4):360-4.
2006
Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO. "Matrix formalism to describe functional states of transcriptional regulatory systems." PLoS Comput. Biol.. 2006;2(8):e101.

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