Student Publications

Export 400 results:
2004
Hsiao A, Worrall DS, Olefsky JM, Subramaniam S. "Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes." Bioinformatics. 2004;20(17):3108-27.
Crooks GE, Hon G, Chandonia J-M, Brenner SE. "WebLogo: a sequence logo generator." Genome Res.. 2004;14(6):1188-90.
2003
Price ND, Reed JL, Papin JA, Famili I, Palsson BO. "Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices." Biophys. J.. 2003;84(2 Pt 1):794-804.
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.
Famili I, Palsson BO. "The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools." Biophys. J.. 2003;85(1):16-26.
Palsson BO, Price ND, Papin JA. "Development of network-based pathway definitions: the need to analyze real metabolic networks." Trends Biotechnol.. 2003;21(5):195-8.
Allen TE, Herrgård MJ, Liu M, et al. "Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets." J. Bacteriol.. 2003;185(21):6392-9.
Price ND, Papin JA, Schilling CH, Palsson BO. "Genome-scale microbial in silico models: the constraints-based approach." Trends Biotechnol.. 2003;21(4):162-9.
Förster J, Famili I, Fu P, Palsson BØ, Nielsen J. "Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network." Genome Res.. 2003;13(2):244-53.
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.
Förster J, Famili I, Palsson BO, Nielsen J. "Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae." OMICS. 2003;7(2):193-202.
Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BO. "Metabolic pathways in the post-genome era." Trends Biochem. Sci.. 2003;28(5):250-8.
Price ND, Reed JL, Papin JA, Wiback SJ, Palsson BO. "Network-based analysis of metabolic regulation in the human red blood cell." J. Theor. Biol.. 2003;225(2):185-94.
Herrgård MJ, Covert MW, Palsson BØ. "Reconciling gene expression data with known genome-scale regulatory network structures." Genome Res.. 2003;13(11):2423-34.
Famili I, Forster J, Nielsen J, Palsson BO. "Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network." Proc. Natl. Acad. Sci. U.S.A.. 2003;100(23):13134-9.
Famili I, Palsson BO. "Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices." J. Theor. Biol.. 2003;224(1):87-96.
2002
Price ND, Papin JA, Palsson BØ. "Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis." Genome Res.. 2002;12(5):760-9.
Papin JA, Price ND, Palsson BØ. "Extreme pathway lengths and reaction participation in genome-scale metabolic networks." Genome Res.. 2002;12(12):1889-900.
Price ND, Famili I, Beard DA, Palsson BØ. "Extreme pathways and Kirchhoff's second law." Biophys. J.. 2002;83(5):2879-82.
Papin JA, Price ND, Edwards JS, Palsson B BØ. "The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy." J. Theor. Biol.. 2002;215(1):67-82.
Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO. "Genome-scale metabolic model of Helicobacter pylori 26695." J. Bacteriol.. 2002;184(16):4582-93.
Edwards JS, Covert M, Palsson B. "Metabolic modelling of microbes: the flux-balance approach." Environ. Microbiol.. 2002;4(3):133-40.
Covert MW, Palsson BØ. "Transcriptional regulation in constraints-based metabolic models of Escherichia coli." J. Biol. Chem.. 2002;277(31):28058-64.
2001
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, Schilling CH, Palsson B. "Regulation of gene expression in flux balance models of metabolism." J. Theor. Biol.. 2001;213(1):73-88.

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