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Original Articles

Biology Databases for the New Life Sciences

Pages 139-170 | Published online: 10 Oct 2008

References

  • Bernardi , L. , Ratsche , E. , Kania , R. , Saric , J. and Rojas , I. 2002 . Interdisciplinary work: The key to functional genomics . IEEE Intelligent Systems , 17 ( 3 ) : 66 – 68 .
  • Birney , E. , Clamp , M. and Hubbard , T. 2002 . Databases and tools for browsing genomes . Annual Review of Genomics and Human Genetics , 3 : 293 – 310 .
  • Blaschke , C. and Valencia , A. 2002 . Molecular biology nomenclature thwarts information-extraction progress . IEEE Intelligent Systems , 17 ( 3 ) : 73 – 76 .
  • Branca , M. 2003 . Putting gene arrays to the test . Science , 300 April 11 : 238
  • Brenner , S. E. 1999 . Errors in genome annotation . TIG , 15 ( 4 ) : 132 – 133 .
  • Celera Genomics. 2000 . Celera Genomics: Groups Deny They are Racing . Biotech Week , 5 July : 18 – 19 .
  • Dicks , J. 2000 . Plant genome databases: From references to inference tools . Briefings in Bioinformatics , 1 ( 2 ) : 138 – 150 .
  • Fields , S. 2001 . Proteomics in genomeland . Science , 291 ( 5507 ) : 1221 – 1224 .
  • Frazier , M. E. , Johnson , G. M. , Thomassen , D. G. , Oliver , C. E. and Patrinos , A. 2003 . Realizing the potential of the genome revolution: The Genomes to Life Program . Science , 300 ( 5617 ) : 290 – 293 .
  • Gabriel , J. 2002 . Sensing trouble . Cornell Engineering Magazine , 8 ( 1 ) : 1
  • Gardiner-Garden , M. and Littlejohn , T. G. 2001 . A comparison of microarray databases . Briefings in Bioinformatics , 2 ( 2 ) : 143 – 158 .
  • Genbank. 2003 . ftp://ftp.ncbi.nih.gov/genbank/gbrel.txtNCBI-GenBank Flat File Release 138.0
  • Geschwind , D. H. 2001 . Sharing gene expression data: An array of options . Nature Reviews Neuroscience , 2 ( 6 ) : 435 – 438 .
  • Hung , L. W. and Kim , S. H. 2000 . “ Genome, proteome, and the quest for a full structure-function description of an organism ” . In Nature Encyclopedia of Life Sciences , London : Nature Publishing Group . http://www.els.net/doi:10.1038/npg.els.0003024
  • Jenssen , T. K. , Laegried , A. , Kmorowski , J. and Hovig , E. 2001 . A literature network of human genes for high-throughput analysis of gene expression . Nature Genetics , 28 ( 1 ) : 21 – 28 .
  • Johnson , S. 1773 . “ Preface to the English Dictionary ” . In Johnson Prose and Poetry , 302 – 323 . Cambridge, MA : Harvard University Press .
  • Karp , P. D. , Paley , S. and Zhu , J. 2001 . Database verification studies of SWISS-PROT and GenBank . Bioinformatics , 17 ( 6 ) : 526 – 532 .
  • Law , A. S. and Archibald , A. L. 2000 . Farm animal genome databases . Briefings in Bioinformatics , 1 ( 2 ) : 151 – 160 .
  • Lin , D. 2003 . Various Stuff About Microarrays , Ithaca, NY : Cornell Computational Biology Service Unit .
  • Marcotte , E. M. and Date , S. V. 2001 . Exploiting big biology: Integrating large-scale biological data for function inference . Briefings in Bioinformatics , 2 ( 4 ) : 363 – 374 .
  • Masys , D. R. 2001 . Linking microarray data to the literature . Nature Genetics , 28 ( 1 ) : 9 – 10 .
  • 2003 . National Center for Biotechnology Information , http://www.ncbi.nlm.nih.gov/entrez/query/static/overview.htmlPubMed Overview
  • NCBI . 2003a . Microarrays: Chipping away at the mysteries of science and medicine , http://www.ncbi.nlm.nih.gov/About/primer/microarrays.html
  • NCBI . 2003b . Molecular modeling: A method for unraveling protein structure and function , www.ncbi.nlm.nih.gov/About/primer/molecularmod.html
  • NCBI . 2003c . What is a genome? , http://www.ncbi.nlm.nih.gov/About/primer/genetics_genome.html
  • Office of Management and Budget. 2002 . Guidelines for ensuring and maximizing the quality, objectivity, utility, and integrity of information disseminated by Federal Agencies; Notice; Republication . Federal Register , 67 ( 36 ) : 8451 – 8460 .
  • Park , J. H. 2002 . Network biology: Data mining biological networks . IEEE Intelligent Systems , 17 ( 3 ) : 68 – 70 .
  • Pennisi , E. 1999 . Keeping genome database clean and up to date . Science , 268 ( 5439 ) : 447 – 450 .
  • Plant Ontology Consortium. 2002 . Plant Ontology Consortium and plant ontology . Comparative and Functional Genomics , 3 ( 2 ) : 137 – 142 .
  • Random House. 1998 . Random House Webster's Unabridged Dictionary , New York : Random House .
  • Raychaudhuri , S. and Altman , R. B. 2003 . A literature-based method for assessing the functional coherence of a gene group . Bioinformatics , 19 ( 3 ) : 1 – 6 .
  • Raychaudhuri , S. , Sutphin , P. D. , Stuart , J. M. and Altman , R. B. 2000 . CLEAVER: Analyzing microarray data using known biological categories http://www-smi.stanford.edu/pubs/SMI_Reports/SMI-2000–0839.pdf
  • 2002 . Research Collaboratory for Structural Bioinformatics , http://www.rcsb.org/pdb/annual_report02.pdfPDB Protein Data Bank Annual Report
  • Schonbach , C. 2000 . Data warehousing in molecular biology . Briefings in Bioinformatics , 1 ( 2 ) : 190 – 198 .
  • Shatkay , H. , Edwards , S. and Boguski , M. 2002 . Information retrieval meets gene analysis . IEEE Intelligent Systems , 17 ( 2 ) : 45 – 53 .
  • Sherlock , G. 2001 . Analysis of large-scale gene expression data . Briefings in Bioinformatics , 2 ( 4 ) : 350 – 362 .
  • Slonim , D. K. 2002 . From patterns to pathways: Gene expression data analysis comes of age . Nature Genetics , 32 : 502 – 508 . Supplement
  • Stevens , R. , Goble , C. A. and Bechhofer , S. 2000 . Ontology-based knowledge representation for bioinformatics . Briefings in Bioinformatics , 1 ( 4 ) : 398 – 414 .
  • Tamames , J. , Clark , D. , Herrero , J. , Dopazo , J. , Blaschke , C. , Fernandez , J. M. , Oliveros , J. C. and Valencia , A. 2002 . Bioinformatics methods for the analysis of expression arrays: Data clustering and information extraction . Journal of Biotechnology , 98 ( 2–3 ) : 269 – 283 .
  • Tsoka , S. , Promponas , V. and Ouzounis , C. A. 1999 . Reproducibility in genome sequence annotation: The Plasmodium falciparum chromosome 2 case . FEBS Letters , 451 ( 3 ) : 354 – 355 .
  • Uehling , M. D. 2003a . Digging into digital quarries . Bio-IT World , : 38 – 42 . (October 2003)
  • Uehling , M. D. 2003b . Is data quality really job 1? . Bio-IT World , : 11 (February 2003)
  • University of Chicago Press. 2003 . The Chicago Manual of Style, , 15th ed. , Chicago : University of Chicago Press .
  • Winker , K. 1999 . How to bring collections data into the net . Nature , 401 October 7 : 524
  • Wittig , U. and Beuckelar , A. 2001 . Analysis and comparison of metabolic pathway databases . Briefings in Bioinformatics , 2 ( 2 ) : 126 – 142 .
  • Wojcik , J. and Schachter , V. 2000 . Proteomic databases and software on the Web . Briefings in Bioinformatics , 1 ( 3 ) : 250 – 59 .
  • Wu , L. F. , Hughes , T. R. , Davierwala , A. P. , Robinson , M. D. , Stoughton , R. and Altschuler , S. J. 2002 . Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters . Nature Genetics , 31 ( 3 ) : 255 – 265 .
  • Xie , H. , Wasserman , A. , Levine , Z. , Novik , A. , Grebinskiy , V. , Shoshan , A. and Mintz , L. 2002 . Large-scale protein annotation through Gene Ontology . Genome Research , 12 ( 5 ) : 785 – 794 .
  • Yandell , M. D. and Majoros , W. H. 2002 . Genomics and natural language processing . Nature Reviews Genetics , 3 ( 8 ) : 601 – 610 .

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