Computational genetics: finding protein function by nonhomology methods.

[1]  J. Monod,et al.  Genetic regulatory mechanisms in the synthesis of proteins. , 1961, Journal of molecular biology.

[2]  I. G. Young,et al.  Tn5 mutagenesis of the enterochelin gene cluster of Escherichia coli. , 1980, Gene.

[3]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[4]  A. Kerlavage,et al.  Complementary DNA sequencing: expressed sequence tags and human genome project , 1991, Science.

[5]  D. Eisenberg,et al.  A method to identify protein sequences that fold into a known three-dimensional structure. , 1991, Science.

[6]  C S McLaughlin,et al.  Protein identifications for a Saccharomyces cerevisiae protein database , 1994, Electrophoresis.

[7]  F. Cohen,et al.  An evolutionary trace method defines binding surfaces common to protein families. , 1996, Journal of molecular biology.

[8]  Gapped BLAST and PSI-BLAST: A new , 1997 .

[9]  C. Chothia,et al.  Intermediate sequences increase the detection of homology between sequences. , 1997, Journal of molecular biology.

[10]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.

[11]  P. Brown,et al.  Yeast microarrays for genome wide parallel genetic and gene expression analysis. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[12]  A. Valencia,et al.  Conserved Clusters of Functionally Related Genes in Two Bacterial Genomes , 1997, Journal of Molecular Evolution.

[13]  J Skolnick,et al.  Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity. , 1998, Journal of molecular biology.

[14]  Temple F. Smith,et al.  Comparison of the complete protein sets of worm and yeast: orthology and divergence. , 1998, Science.

[15]  Juri Rappsilber,et al.  Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex , 1998, Nature Genetics.

[16]  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.

[17]  Martin Vingron,et al.  Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning , 1998, Mechanisms of Development.

[18]  Ruedi Aebersold,et al.  High throughput protein characterization by automated reverse‐phase chromatography/electrospray tandem mass spectrometry , 1998, Protein science : a publication of the Protein Society.

[19]  J A Eisen,et al.  A phylogenomic study of the MutS family of proteins. , 1998, Nucleic acids research.

[20]  B. Snel,et al.  Conservation of gene order: a fingerprint of proteins that physically interact. , 1998, Trends in biochemical sciences.

[21]  P. Bork,et al.  Differential genome analysis applied to the species‐specific features of Helicobacter pylori , 1998, FEBS letters.

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

[23]  A. Bairoch,et al.  The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999 , 1999, Nucleic Acids Res..

[24]  D. Eisenberg,et al.  Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.

[25]  Dmitrij Frishman,et al.  MIPS: a database for genomes and protein sequences , 1999, Nucleic Acids Res..

[26]  M. Q. Zhang.  Large-scale gene expression data analysis: a new challenge to computational biologists. , 1999, Genome research.

[27]  R. Overbeek,et al.  The use of gene clusters to infer functional coupling. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[28]  T. Maniatis,et al.  A Striking Organization of a Large Family of Human Neural Cadherin-like Cell Adhesion Genes , 1999, Cell.

[29]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[30]  R. Sauer,et al.  SmpB, a unique RNA‐binding protein essential for the peptide‐tagging activity of SsrA (tmRNA) , 1999, The EMBO journal.

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

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

[33]  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.

[34]  S. Gygi,et al.  Quantitative analysis of complex protein mixtures using isotope-coded affinity tags , 1999, Nature Biotechnology.

[35]  P. Schulze-Lefert,et al.  A Novel Class of Eukaryotic Zinc-Binding Proteins Is Required for Disease Resistance Signaling in Barley and Development in C. elegans , 1999, Cell.

[36]  Christian A. Rees,et al.  Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[37]  Michael G. Walker,et al.  Pharmaceutical Target Discovery Using Guilt-by-Association: Schizophrenia and Parkinson's Disease Genes , 1999, ISMB.

[38]  S. Gygi,et al.  Correlation between Protein and mRNA Abundance in Yeast , 1999, Molecular and Cellular Biology.

[39]  D. Eisenberg,et al.  Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[40]  Y. Pekarsky,et al.  Genomic analysis of human and mouse TCL1 loci reveals a complex of tightly clustered genes. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

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

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

[43]  Miguel A. Andrade-Navarro,et al.  Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions , 1999, ISMB.

[44]  A. Godzik,et al.  Functional insights from structural predictions: Analysis of the Escherichia coli genome , 2008, Protein science : a publication of the Protein Society.

[45]  B J Stapley,et al.  Biobibliometrics: information retrieval and visualization from co-occurrences of gene names in Medline abstracts. , 1999, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[46]  Peter D. Karp,et al.  The EcoCyc and MetaCyc databases , 2000, Nucleic Acids Res..

[47]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 , 2000, Nucleic Acids Res..

[48]  Michael E. Cusick,et al.  The Yeast Proteome Database (YPD) and Caenorhabditis elegans Proteome Database (WormPD): comprehensive resources for the organization and comparison of model organism protein information , 2000, Nucleic Acids Res..

[49]  Ioannis Xenarios,et al.  DIP: the Database of Interacting Proteins , 2000, Nucleic Acids Res..

[50]  Ji Huang,et al.  [Serial analysis of gene expression]. , 2002, Yi chuan = Hereditas.