Student Publications

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Filters: Keyword is Saccharomyces cerevisiae  [Clear All Filters]
2009
Wang H, Kakaradov B, Collins SR, et al. "A complex-based reconstruction of the Saccharomyces cerevisiae interactome." Mol. Cell Proteomics. 2009;8(6):1361-81.
Mo ML, Palsson BO, Herrgård MJ. "Connecting extracellular metabolomic measurements to intracellular flux states in yeast." BMC Syst Biol. 2009;3:37.
2008
Herrgård MJ, Swainston N, Dobson P, et al. "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat. Biotechnol.. 2008;26(10):1155-60.
Roguev A, Bandyopadhyay S, Zofall M, et al. "Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast." Science. 2008;322(5900):405-10.
Wilmes GM, Bergkessel M, Bandyopadhyay S, et al. "A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing." Mol. Cell. 2008;32(5):735-46.
Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H. "A multidimensional chromatography technology for in-depth phosphoproteome analysis." Mol. Cell Proteomics. 2008;7(7):1389-96.
Payne SH, Yau M, Smolka MB, Tanner S, Zhou H, Bafna V. "Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis." J. Proteome Res.. 2008;7(8):3373-81.
2007
Shlomi T, Herrgard M, Portnoy V, et al. "Systematic condition-dependent annotation of metabolic genes." Genome Res.. 2007;17(11):1626-33.
2006
Reguly T, Breitkreutz A, Boucher L, et al. "Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae." J. Biol.. 2006;5(4):11.
Herrgård MJ, Lee B-S, Portnoy V, Palsson BØ. "Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae." Genome Res.. 2006;16(5):627-35.
Bandyopadhyay S, Sharan R, Ideker T. "Systematic identification of functional orthologs based on protein network comparison." Genome Res.. 2006;16(3):428-35.
2005
Famili I, Mahadevan R, Palsson BO. "k-Cone analysis: determining all candidate values for kinetic parameters on a network scale." Biophys. J.. 2005;88(3):1616-25.
Suthram S, Sittler T, Ideker T. "The Plasmodium protein network diverges from those of other eukaryotes." Nature. 2005;438(7064):108-12.
Kelley R, Ideker T. "Systematic interpretation of genetic interactions using protein networks." Nat. Biotechnol.. 2005;23(5):561-6.
Herrgård MJ, Palsson BØ. "Untangling the web of functional and physical interactions in yeast." J. Biol.. 2005;4(2):5.
2004
Haugen AC, Kelley R, Collins JB, et al. "Integrating phenotypic and expression profiles to map arsenic-response networks." Genome Biol.. 2004;5(12):R95.
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.
2003
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.
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.
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.