Student Publications

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Filters: Keyword is Gene Expression Regulation  [Clear All Filters]
2015
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.
2013
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.
2012
Cho B-K, Federowicz S, Park Y-S, Zengler K, Palsson BØ. "Deciphering the transcriptional regulatory logic of amino acid metabolism." Nat. Chem. Biol.. 2012;8(1):65-71.
Lagier-Tourenne C, Polymenidou M, Hutt KR, et al. "Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs." Nat. Neurosci.. 2012;15(11):1488-97.
Loriaux PM, Hoffmann A. "A framework for modeling the relationship between cellular steady-state and stimulus-responsiveness." Methods Cell Biol.. 2012;110:81-109.
Panopoulos AD, Yanes O, Ruiz S, et al. "The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming." Cell Res.. 2012;22(1):168-77.
Yamaguchi S, Hong K, Liu R, et al. "Tet1 controls meiosis by regulating meiotic gene expression." Nature. 2012;492(7429):443-7.
2008
Barrera LO, Li Z, Smith AD, et al. "Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs." Genome Res.. 2008;18(1):46-59.
Shlomi T, Cabili MN, Herrgård MJ, Palsson BØ, Ruppin E. "Network-based prediction of human tissue-specific metabolism." Nat. Biotechnol.. 2008;26(9):1003-10.
2007
Ye C, Eskin E. "Discovering tightly regulated and differentially expressed gene sets in whole genome expression data." Bioinformatics. 2007;23(2):e84-90.
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.
Sears DD, Hsiao A, Ofrecio JM, Chapman J, He W, Olefsky JM. "Selective modulation of promoter recruitment and transcriptional activity of PPARgamma." Biochem. Biophys. Res. Commun.. 2007;364(3):515-21.
2005
Covert MW, Leung TH, Gaston JE, Baltimore D. "Achieving stability of lipopolysaccharide-induced NF-kappaB activation." Science. 2005;309(5742):1854-7.
Barken D, Wang C J, Kearns J, Cheong R, Hoffmann A, Levchenko A. "Comment on "Oscillations in NF-kappaB signaling control the dynamics of gene expression"." Science. 2005;308(5718):52; author reply 52.
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.
Famili I, Mahadevan R, Palsson BO. "k-Cone analysis: determining all candidate values for kinetic parameters on a network scale." Biophys. J.. 2005;88(3):1616-25.
Werner SL, Barken D, Hoffmann A. "Stimulus specificity of gene expression programs determined by temporal control of IKK activity." Science. 2005;309(5742):1857-61.

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