Student Publications

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. PubMed DOI

Crooks GE, Hon G, Chandonia JM, Brenner SE. "WebLogo: a sequence logo generator." Genome Res. 2004;14(6):1188-90. PubMed PMC DOI

Duarte NC, Herrgård MJ, Palsson BØ. "Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model." Genome Res. 2004;14(7):1298-309. PubMed PMC DOI

Haugen AC, Kelley R, Collins JB, Tucker CJ, Deng C, Afshari CA, Brown JM, Ideker T, Van Houten B. "Integrating phenotypic and expression profiles to map arsenic-response networks." Genome Biol. 2004;5(12):R95. PubMed PMC DOI

Herrgård MJ, Covert MW, Palsson BØ. "Reconstruction of microbial transcriptional regulatory networks." Curr Opin Biotechnol. 2004;15(1):70-7. PubMed DOI

Herrgård MJ, Palsson BØ. "Flagellar biosynthesis in silico: building quantitative models of regulatory networks." Cell. 2004;117(6):689-90. PubMed DOI

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. PubMed DOI

Papin JA, Palsson BO. "The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis." Biophys J. 2004;87(1):37-46. PubMed PMC DOI

Papin JA, Palsson BO. "Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk." J Theor Biol. 2004;227(2):283-97. PubMed DOI

Papin JA, Reed JL, Palsson BO. "Hierarchical thinking in network biology: the unbiased modularization of biochemical networks." Trends Biochem Sci. 2004;29(12):641-7. PubMed DOI

Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BO. "Comparison of network-based pathway analysis methods." Trends Biotechnol. 2004;22(8):400-5. PubMed DOI

Price ND, Schellenberger J, Palsson BO. "Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies." Biophys J. 2004;87(4):2172-86. PubMed PMC DOI

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