Swiss Institute of Bioinformatics

References to Swiss-Prot/TrEMBL

• Bairoch A., Boeckmann B., Ferro S., Gasteiger E.
  Swiss-Prot: Juggling between evolution and stability
  Brief. Bioinform. 5:39-55(2004).
  PUBMED: 15153305
  Full text (Journal home page: http://www.henrystewart.com/journals/bib/)

• The UniProt Consortium
  The universal protein resource (UniProt).
  Nucleic Acids Res. 36:D190-195(2008).
  PUBMED: 18045787
  Full text - Please read NAR Online's Terms and Conditions for Use.

• Hinz U., Bairoch A.;
  The Impact of 3D Structures on a Protein Knowledgebase: from Proteins to Systems;
  (in) Sussman J.L. and Silman I. (eds): Structural Proteomics and its Impact on the Life Sciences, World Scientific Publishing (2008) pp. 51-77
  Full text - Copyright World Scientific Publishing

• Boeckmann B., Blatter M.-C., Famiglietti L., Hinz U., Lane L., Roechert B., Bairoch A.
  Protein variety and functional diversity: Swiss-Prot annotation in its biological context
  Comptes Rendus Biologies 328:882-99(2005).
  PUBMED: 16286078
  

• Boeckmann B., Bairoch A., Apweiler R., Blatter M.-C., Estreicher A., Gasteiger E., Martin M.J., Michoud K., O'Donovan C., Phan I., Pilbout S., Schneider M.
  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
  Nucleic Acids Res. 31:365-370(2003).
  PUBMED: 12520024
  Full text - Please read NAR Online's Terms and Conditions for Use.

• Apweiler R., Bairoch A., Wu C.H., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., Martin M.J., Natale D.A., O'Donovan C., Redaschi N., Yeh L.S.
  UniProt: the Universal Protein knowledgebase.
  Nucleic Acids Res. 32:D115-119(2004).
  PUBMED: 14681372
  Full text - Please read NAR Online's Terms and Conditions for Use.

• Farriol-Mathis N., Garavelli J.S., Boeckmann B., Duvaud S., Gasteiger E., Gateau A., Veuthey A.-L., Bairoch A.
  Annotation of post-translational modifications in the Swiss-Prot knowledge base
  Proteomics 4:1537-1550(2004).
  PUBMED: 15174124
  Full text

• Yip Y.L., Scheib H., Diemand A.V., Gattiker A., Famiglietti L.M., Gasteiger E., Bairoch A.
  The Swiss-Prot Variant Page and the ModSNP Database: A Resource for Sequence and Structure information on Human Protein Variants
  Hum. Mutat. 23:464-470(2004).
  PUBMED: 15108278
  Full text

• Apweiler R., Bairoch A., Wu C.H.
  Protein sequence databases
  Curr. Opin. Chem. Biol. 8:76-80(2004).
  PUBMED: 15036160

• O'Donovan C., Martin M.J., Gattiker A., Gasteiger E., Bairoch A., Apweiler R.
  High-quality protein knowledge resource: SWISS-PROT and TrEMBL
  Brief. Bioinform. 3:275-284(2002).
  PUBMED: 12230036

• Gasteiger E., Jung E., Bairoch A.
  SWISS-PROT: Connecting biological knowledge via a protein database
  Curr. Issues Mol. Biol. 3:47-55(2001)
  PUBMED: 11488411

• Apweiler R.
  Functional information in SWISS-PROT: the basis for large-scale characterisation of protein sequences
  Brief. Bioinform. 2:9-18(2001)
  PUBMED: 11465066

• Bairoch A., Apweiler R.
  The SWISS-PROT protein sequence database: its relevance to human molecular medical research
  J. Mol. Med. 75:312-316(1997).
  PUBMED: 97325419

• Apweiler R., Gateau A., Contrino S., Martin M.J., Junker V., O'Donovan C., Lang F., Mitaritonna N., Kappus S., Bairoch A.
  Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT + TREMBL
  (In) ISMB-97; Proceedings 5th International Conference on Intelligent Systems for Molecular Biology, pp33-43, AAAI Press, Menlo Park, (1997).
  PUBMED: 97463228

• Bairoch A.
  Proteome databases
  (In) Proteome research: new frontiers in functional genomics, Wilkins M.R., Williams K.L, Appel R.D., Hochstrasser D.H, Eds., pp93-132, Springer Verlag, Heidelberg, (1997).

  ISBN: 3-540-62775-8

• Junker V.L., Apweiler R., Bairoch A.
  Representation of functional information in the SWISS-PROT data bank.
  Bioinformatics 15:1066-1007(1999).
  PUBMED: 20210096

• Kersey P., Hermjakob H., Apweiler R.
  VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL.
  Bioinformatics 16:1048-1049(2000).
  PUBMED: 11159319

• Jung E., Veuthey A.-L., Gasteiger E., Bairoch A.
  Annotation of glycoproteins in the SWISS-PROT database
  Proteomics 1:262-268(2001).
  PUBMED: 11680872

• O'Donovan C., Apweiler R., Bairoch A.
  The human proteomics initiative (HPI).
  Trends Biotechnol. 19:178-81(2001).
  PUBMED:11301130

• Moeller S., Leser U., Fleischmann W., Apweiler R.
  EDITtoTrEMBL: a distributed approach to high-quality automated protein sequence annotation.
  Bioinformatics 15:219-227(1999).
  PUBMED: 99240955

• Fleischmann W., Moeller S., Gateau A., Apweiler R.
  A novel method for automatic functional annotation of proteins.
  Bioinformatics 15:228-233(1999).
  PUBMED: 99240956

• O'Donovan C., Jesus Martin M., Glemet E., Codani J.J., Apweiler R.
  Removing redundancy in SWISS-PROT and TrEMBL.
  Bioinformatics 15:258-259(1999).
  PUBMED: 99240960

• Watanabe K., Harayama S.
  SWISS-PROT: The curated protein sequence database on Internet (in Japanese).
  Protein, Nucleic Acid and Enzyme 46:80-86(2001).

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Last modified 04/Jul/2008 by ELG