Student Publications

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Crooks GE, Hon G, Chandonia J-M, Brenner SE. "WebLogo: a sequence logo generator." Genome Res.. 2004;14(6):1188-90.
Covert MW, Famili I, Palsson BO. "Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?" Biotechnol. Bioeng.. 2003;84(7):763-72.
Covert MW, Schilling CH, Famili I, et al. "Metabolic modeling of microbial strains in silico." Trends Biochem. Sci.. 2001;26(3):179-86.
Covert MW, Palsson BØ. "Transcriptional regulation in constraints-based metabolic models of Escherichia coli." J. Biol. Chem.. 2002;277(31):28058-64.
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.
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. "Integrating high-throughput and computational data elucidates bacterial networks." Nature. 2004;429(6987):92-6.
Covert MW, Schilling CH, Palsson B. "Regulation of gene expression in flux balance models of metabolism." J. Theor. Biol.. 2001;213(1):73-88.
Covert MW, Palsson BO. "Constraints-based models: regulation of gene expression reduces the steady-state solution space." J. Theor. Biol.. 2003;221(3):309-25.
Covert MW, Leung TH, Gaston JE, Baltimore D. "Achieving stability of lipopolysaccharide-induced NF-kappaB activation." Science. 2005;309(5742):1854-7.
Conway AE, Van Nostrand EL, Pratt GA, et al. "Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival." Cell Rep. 2016;15(3):666-79.
Cohen T, G Whitfield K, Schvaneveldt RW, Mukund K, Rindflesch T. "EpiphaNet: An Interactive Tool to Support Biomedical Discoveries." J Biomed Discov Collab. 2010;5:21-49.
Cline MS, Smoot M, Cerami E, et al. "Integration of biological networks and gene expression data using Cytoscape." Nat Protoc. 2007;2(10):2366-82.
Chuang H-Y, Lee E, Liu Y-T, Lee D, Ideker T. "Network-based classification of breast cancer metastasis." Mol. Syst. Biol.. 2007;3:140.
Choueiri MB, Shen JPaul, Gross AM, Huang JK, Ideker T, Fanta P. "ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer." PLoS ONE. 2015;10(6):e0126898.
Cho B-K, Charusanti P, Herrgård MJ, Palsson BO. "Microbial regulatory and metabolic networks." Curr. Opin. Biotechnol.. 2007;18(4):360-4.
Cho B-K, Federowicz SA, Embree M, Park Y-S, Kim D, Palsson BØ. "The PurR regulon in Escherichia coli K-12 MG1655." Nucleic Acids Res.. 2011;39(15):6456-64.
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.
Cheng CS, Johnson TL, Hoffmann A. "Epigenetic control: slow and global, nimble and local." Genes Dev.. 2008;22(9):1110-4.
Chen OY-C, Chen G-W, Chen WY-C. "A novel strategy for the structure-based drug design of heat shock protein 90 inhibitors.". In: Neural Networks, 2008. IJCNN 2008. (IEEE World Congress on Computational Intelligence). IEEE International Joint Conference on.; 2008.
Chen Y, Rao F, Rodriguez-Flores JL, et al. "Naturally occurring human genetic variation in the 3'-untranslated region of the secretory protein chromogranin A is associated with autonomic blood pressure regulation and hypertension in a sex-dependent fashion." J. Am. Coll. Cardiol.. 2008;52(18):1468-81.
Chen WY-C, Chen P-Y, Chen CY-C, Chung J-G. "Exploring 3D-QSAR pharmacophore mapping of azaphenanthrenone derivatives for mPGES-1 inhibition Using HypoGen technique.". In: Computational Intelligence in Bioinformatics and Computational Biology, 2008. CIBCB '08. IEEE Symposium on.; 2008.
Chen J, Swamidass JS, Dou Y, Bruand J, Baldi P. "ChemDB: a public database of small molecules and related chemoinformatics resources." Bioinformatics. 2005;21(22):4133-9.
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.
Chen Y, Rao F, Rodriguez-Flores JL, et al. "Common genetic variants in the chromogranin A promoter alter autonomic activity and blood pressure." Kidney Int.. 2008;74(1):115-25.
Charusanti P, Chauhan S, McAteer K, et al. "An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92." BMC Syst Biol. 2011;5:163.