Student Publications

Raphael B, Zhi D, Tang H, Pevzner P. "A novel method for multiple alignment of sequences with repeated and shuffled elements." Genome Res. 2004;14(11):2336-46. PubMed PMC DOI

Wiback SJ, Famili I, Greenberg HJ, Palsson BØ. "Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space." J Theor Biol. 2004;228(4):437-47. PubMed DOI

Zhu X, Hart R, Chang MS, Kim JW, Lee SY, Cao YA, Mock D, Ke E, Saunders B, Alexander A, Grossoehme J, Lin KM, Yan Z, Hsueh R, Lee J, Scheuermann RH, Fruman DA, Seaman W, Subramaniam S, Sternweis P, Simon MI, Choi S. "Analysis of the major patterns of B cell gene expression changes in response to short-term stimulation with 33 single ligands." J Immunol. 2004;173(12):7141-9. PubMed DOI

Allen TE, Herrgård MJ, Liu M, Qiu Y, Glasner JD, Blattner FR, Palsson BØ. "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. PubMed PMC DOI

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. PubMed DOI

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. PubMed DOI

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. PubMed PMC DOI

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. PubMed PMC DOI

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. PubMed DOI

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. PubMed PMC DOI

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. PubMed DOI

Herrgård MJ, Covert MW, Palsson BØ. "Reconciling gene expression data with known genome-scale regulatory network structures." Genome Res. 2003;13(11):2423-34. PubMed PMC DOI

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. PubMed DOI

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. PubMed DOI

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. PubMed DOI

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. PubMed PMC DOI

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. PubMed DOI

Covert MW, Palsson BØ. "Transcriptional regulation in constraints-based metabolic models of Escherichia coli." J Biol Chem. 2002;277(31):28058-64. PubMed DOI

Edwards JS, Covert M, Palsson B. "Metabolic modelling of microbes: the flux-balance approach." Environ Microbiol. 2002;4(3):133-40. PubMed

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. PubMed DOI

Papin JA, Price ND, Palsson BØ. "Extreme pathway lengths and reaction participation in genome-scale metabolic networks." Genome Res. 2002;12(12):1889-900. PubMed PMC DOI

Price ND, Famili I, Beard DA, Palsson BØ. "Extreme pathways and Kirchhoff's second law." Biophys J. 2002;83(5):2879-82. PubMed PMC DOI

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. PubMed PMC DOI

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. PubMed PMC DOI

Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BO. "Metabolic modeling of microbial strains in silico." Trends Biochem Sci. 2001;26(3):179-86. PubMed