An overview of bioinformatics methods for modeling biological pathways in yeast.

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Published in Brief Funct Genomics on October 17, 2015

Authors

Jie Hou, Lipi Acharya, Dongxiao Zhu, Jianlin Cheng

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Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A (1998) 192.97

KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res (2000) 117.00

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Life with 6000 genes. Science (1996) 41.51

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WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics (2008) 18.58

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Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res (2003) 7.22

Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet (2001) 7.16

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MINT, the molecular interaction database: 2012 update. Nucleic Acids Res (2011) 5.25

Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc Natl Acad Sci U S A (2000) 5.19

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The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol (2006) 3.69

Inferring cellular networks--a review. BMC Bioinformatics (2007) 3.49

Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature (2012) 3.37

Function and regulation in MAPK signaling pathways: lessons learned from the yeast Saccharomyces cerevisiae. Biochim Biophys Acta (2007) 3.07

A Markov random field model for network-based analysis of genomic data. Bioinformatics (2007) 2.93

Automated modelling of signal transduction networks. BMC Bioinformatics (2002) 2.92

Systematic management and analysis of yeast gene expression data. Genome Res (2000) 2.83

Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst Biol (2009) 2.80

Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res (2005) 2.68

Yeast as a model organism. Science (1997) 2.62

KOBAS server: a web-based platform for automated annotation and pathway identification. Nucleic Acids Res (2006) 2.59

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