Protein interaction verification and functional annotation by integrated analysis of genome-scale data.

[1]  Partha S. Vasisht.  Computational Analysis of Microarray Data , 2003 .

[2]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[3]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[4]  Stefan Hohmann,et al.  Yeast Stress Responses , 1997, Topics in Current Genetics.

[5]  C. Ball,et al.  Saccharomyces Genome Database. , 2002, Methods in enzymology.

[6]  M. Gerstein,et al.  Relating whole-genome expression data with protein-protein interactions. , 2002, Genome research.

[7]  G. Church,et al.  Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae , 2001, Nature Genetics.

[8]  A. Grigoriev.  A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. , 2001, Nucleic acids research.

[9]  T. Gaasterland,et al.  Whole-genome analysis: annotations and updates. , 2001, Current opinion in structural biology.

[10]  Roger E Bumgarner,et al.  Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. , 2001, Science.

[11]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[12]  J. Yates,et al.  Large-scale analysis of the yeast proteome by multidimensional protein identification technology , 2001, Nature Biotechnology.

[13]  A. Brazma,et al.  Gene expression data analysis , 2000, FEBS letters.

[14]  Alex Bateman,et al.  The InterPro database, an integrated documentation resource for protein families, domains and functional sites , 2001, Nucleic Acids Res..

[15]  D. Botstein,et al.  Genomic expression programs in the response of yeast cells to environmental changes. , 2000, Molecular biology of the cell.

[16]  O. Fiehn,et al.  Metabolite profiling for plant functional genomics , 2000, Nature Biotechnology.

[17]  Warren C. Lathe,et al.  Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. , 2000, Genome research.

[18]  R. Young,et al.  Biomedical Discovery with DNA Arrays , 2000, Cell.

[19]  Yudong D. He,et al.  Functional Discovery via a Compendium of Expression Profiles , 2000, Cell.

[20]  E. Winzeler,et al.  Genomics, gene expression and DNA arrays , 2000, Nature.

[21]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[22]  Peter Walter,et al.  Functional and Genomic Analyses Reveal an Essential Coordination between the Unfolded Protein Response and ER-Associated Degradation , 2000, Cell.

[23]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[24]  T. Hughes,et al.  Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. , 2000, Science.

[25]  R. Brent,et al.  Genomic Biology , 2000, Cell.

[26]  Dmitrij Frishman,et al.  MIPS: a database for genomes and protein sequences , 2000, Nucleic Acids Res..

[27]  R. Young,et al.  Transcription of eukaryotic protein-coding genes. , 2000, Annual review of genetics.

[28]  John J. Wyrick,et al.  Genome-wide location and function of DNA binding proteins. , 2000, Science.

[29]  Kei-Hoi Cheung,et al.  Large-scale analysis of the yeast genome by transposon tagging and gene disruption , 1999, Nature.

[30]  S. Fields,et al.  A biochemical genomics approach for identifying genes by the activity of their products. , 1999, Science.

[31]  Anton J. Enright,et al.  Protein interaction maps for complete genomes based on gene fusion events , 1999, Nature.

[32]  D. Eisenberg,et al.  A combined algorithm for genome-wide prediction of protein function , 1999, Nature.

[33]  Ronald W. Davis,et al.  Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. , 1999, Science.

[34]  D. Botstein,et al.  Exploring the new world of the genome with DNA microarrays , 1999, Nature Genetics.

[35]  James I. Garrels,et al.  The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data , 1999, Nucleic Acids Res..

[36]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[37]  Michael Ruogu Zhang,et al.  Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. , 1998, Molecular biology of the cell.

[38]  M. Künzler,et al.  Yeast Los1p Has Properties of an Exportin-Like Nucleocytoplasmic Transport Factor for tRNA , 1998, Molecular and Cellular Biology.

[39]  S. Lindquist,et al.  Thermotolerance in Saccharomyces cerevisiae: the Yin and Yang of trehalose. , 1998, Trends in biotechnology.

[40]  D. Botstein,et al.  The transcriptional program of sporulation in budding yeast. , 1998, Science.

[41]  R. McCartney,et al.  Identification of a calcineurin-independent pathway required for sodium ion stress response in Saccharomyces cerevisiae. , 1998, Genetics.

[42]  G. Fink,et al.  The riddle of MAP kinase signaling specificity. , 1998, Trends in genetics : TIG.

[43]  B. Andrews,et al.  The cyclin family of budding yeast: abundant use of a good idea. , 1998, Trends in genetics : TIG.

[44]  David Botstein,et al.  SGD: Saccharomyces Genome Database , 1998, Nucleic Acids Res..

[45]  André Goffeau,et al.  The yeast genome directory. , 1997, Nature.

[46]  M. Carlson,et al.  Glucose regulates protein interactions within the yeast SNF1 protein kinase complex. , 1996, Genes & development.

[47]  M. Nickas,et al.  BRO1, a novel gene that interacts with components of the Pkc1p-mitogen-activated protein kinase pathway in Saccharomyces cerevisiae , 1996, Molecular and cellular biology.

[48]  Y. Watanabe,et al.  Yeast RLM1 encodes a serum response factor-like protein that may function downstream of the Mpk1 (Slt2) mitogen-activated protein kinase pathway , 1995, Molecular and cellular biology.

[49]  L. Dirick,et al.  Roles and regulation of Cln‐Cdc28 kinases at the start of the cell cycle of Saccharomyces cerevisiae. , 1995, The EMBO journal.

[50]  R. Young,et al.  A kinase–cyclin pair in the RNA polymerase II holoenzyme , 1995, Nature.

[51]  S. Nwaka,et al.  Phenotypic features of trehalase mutants in Saccharomyces cerevisiae , 1995, FEBS letters.

[52]  N. Woychik,et al.  C25, an essential RNA polymerase III subunit related to the RNA polymerase II subunit RPB7 , 1994, Molecular and cellular biology.

[53]  M. Carlson,et al.  Molecular and genetic analysis of the SNF7 gene in Saccharomyces cerevisiae. , 1993, Genetics.