Student Publications

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Gendron JM, Pruneda-Paz JL, Doherty CJ, Gross AM, S Kang E, Kay SA. "Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor." Proc. Natl. Acad. Sci. U.S.A.. 2012;109(8):3167-72.
Tompa M, Li N, Bailey TL, et al. "Assessing computational tools for the discovery of transcription factor binding sites." Nat. Biotechnol.. 2005;23(1):137-44.
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.
Lunyak VV, Prefontaine GG, Núñez E, et al. "Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis." Science. 2007;317(5835):248-51.
Kim T H, Barrera LO, Qu C, et al. "Direct isolation and identification of promoters in the human genome." Genome Res.. 2005;15(6):830-9.
Hawkins DR, Hon GC, Yang C, et al. "Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency." Cell Res.. 2011;21(10):1393-409.
Seok J, Xiao W, Moldawer LL, Davis RW, Covert MW. "A dynamic network of transcription in LPS-treated human subjects." BMC Syst Biol. 2009;3:78.
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.
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.
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.
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.
Covert MW, Xiao N, Chen TJ, Karr JR. "Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli." Bioinformatics. 2008;24(18):2044-50.
Haugen AC, Kelley R, Collins JB, et al. "Integrating phenotypic and expression profiles to map arsenic-response networks." Genome Biol.. 2004;5(12):R95.
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.
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.
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.
Joyce AR, Palsson BØ. "The model organism as a system: integrating 'omics' data sets." Nat. Rev. Mol. Cell Biol.. 2006;7(3):198-210.
Herrgård MJ, Covert MW, Palsson BØ. "Reconciling gene expression data with known genome-scale regulatory network structures." Genome Res.. 2003;13(11):2423-34.
Herrgård MJ, Covert MW, Palsson BØ. "Reconstruction of microbial transcriptional regulatory networks." Curr. Opin. Biotechnol.. 2004;15(1):70-7.
Covert MW, Schilling CH, Palsson B. "Regulation of gene expression in flux balance models of metabolism." J. Theor. Biol.. 2001;213(1):73-88.