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Publications on UniProt

Last modified September 23, 2016

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If you find UniProt useful, please consider citing our latest publication:

The UniProt Consortium

UniProt: a hub for protein information

Nucleic Acids Res. 43: D204-D212 (2015)

...or choose the publication that best covers the UniProt aspects or components you used in your work:

Publications on UniProt databases

Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, Lewis SE, Niknejad A, Orchard S, Poux S, Skunca N, Robinson-Rechavi M.

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations

Database (Oxford) bav043 (2016)

Boutet E, Lieberherr D, Tognolli M, Schneider M, Bansal P, Bridge AJ, Poux S, Bougueleret L, Xenarios I.

UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View

Methods Mol. Biol. 1374:23-54 (2016)

Alpi E, Griss J, da Silva AW, Bely B, Antunes R, Zellner H, Rios D, O’Donovan C, Vizcaino JA, Martin MJ.

Analysis of the tryptic search space in UniProt databases

Proteomics 15:48-57 (2015)

Foulger RE, Osumi-Sutherland D, McIntosh BK, Hulo C, Masson P, Poux S, Le Mercier P, Lomax J.

Representing virus-host interactions and other multi-organism processes in the Gene Ontology

BMC Microbiol. 15:146 (2015)

Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Manning G, Nagano N, O’Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, Spedding M, Srinivasan N, Vriend G, Babbitt PC, Bateman A.

Key challenges for the creation and maintenance of specialist protein resources

Proteins 83:1005-1013 (2015)

Huntley RP, Sawford T, Mutowo-Meullenet P, Shypitsyna A, Bonilla C, Martin MJ, O’Donovan C.

The GOA database: gene Ontology annotation updates for 2015

Nucleic Acids Res. 43:d1057-1063 (2015)

Pundir S, Magrane M, Martin MJ, O’Donovan C, UniProt Consortium.

Searching and Navigating UniProt Databases

Curr. Protoc. Bioinformatics 50:1.27.1-1.27.10 (2015)

Suzek BE, Wang Y, Huang H, McGarvey PB, Wu CH, UniProt Consortium.

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

Bioinformatics 31:926-32 (2015)

Famiglietti ML, Estreicher A, Gos A, Bolleman J, Gehant S, Breuza L, Bridge A, Poux S, Redaschi N, Bougueleret L, Xenarios I.

Genetic Variations and Diseases in UniProtKB/Swiss-Prot: The Ins and Outs of Expert Manual Curation.

Hum. Mutat. 35:927-935 (2014)

Huntley RP, Sawford T, Martin MJ, O?Donovan C.

Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt

Gigascience 3:4 (2014)

Masson P, Hulo C, de Castro E, Foulger R, Poux S, Bridge A, Lomax J, Bougueleret L, Xenarios I, Le Mercier P.

An Integrated Ontology Resource to Explore and Study Host-Virus Relationships

PLoS One 9(9):e108075 (2014)

Poux S, Magrane M, Arighi CN, Bridge A, O?Donovan C, Laiho K, The UniProt Consortium.

Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data

Database (Oxford) bau016 (2014)

Chen C, Li Z, Huang H, Suzek BE, Wu CH; UniProt Consortium.

A fast Peptide Match service for UniProt Knowledgebase

Bioinformatics 29:2808-2809 (2013)

Mutowo-Meullenet P, Huntley RP, Dimmer EC, Alam-Faruque Y, Sawford T, Martin MJ, O?Donovan C, Apweiler R.

Use of Gene Ontology Annotation to understand the peroxisome proteome in humans

Database (Oxford) bas062 (2013)

Magrane M. and the UniProt consortium

UniProt Knowledgebase: a hub of integrated protein data

Database, 2011: bar009 (2011).

Jain E., Bairoch A., Duvaud S., Phan I., Redaschi N., Suzek B.E., Martin M.J., McGarvey P., Gasteiger E.

Infrastructure for the life sciences: design and implementation of the UniProt website

BMC Bioinformatics 10:136 (2009)

Suzek B.E., Huang H., McGarvey P., Mazumder R., Wu C.H.

UniRef: Comprehensive and Non-Redundant UniProt Reference Clusters

Bioinformatics 23:1282-1288 (2007)

Leinonen R., Nardone F., Zhu W., Apweiler R.

UniSave: the UniProtKB Sequence/Annotation Version database

Bioinformatics 22:1284-1285 (2006)

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

C. R. Biol. 328:882-899 (2005)

Apweiler R., Bairoch A., Wu C.H.

Protein sequence databases

Curr. Opin. Chem. Biol. 8:76-80 (2004)

Bairoch A., Boeckmann B., Ferro S., Gasteiger E.

Swiss-Prot: juggling between evolution and stability

Brief. Bioinform. 5:39-55 (2004)

Leinonen R., Diez F.G., Binns D., Fleischmann W., Lopez R., Apweiler R.

UniProt Archive

Bioinformatics 20:3236-3237 (2004)

Publications on annotation projects

Breuza L, Poux S, Estreicher A, Famiglietti ML, Magrane M, Tognolli M, Bridge A, Baratin D, Redaschi N, The UniProt Consortium

The UniProtKB guide to the human proteome

Database (Oxford) bav120

Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, Baratin D, Cuche BA, Bougueleret L, Poux S, Redaschi N, Xenarios I, Bridge A.

HAMAP in 2015: updates to the protein family classification and annotation system

Nucleic Acids Res. 43:D1064-1070 (2015)

Schneider M., Poux S., UniProt Consortium.

UniProtKB amid the turmoil of plant proteomics research front

Front. Plant Sci. 3:270-270 (2012)

Jungo F., Bougueleret L., Xenarios I., Poux S.

The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data

Toxicon 60:551-557 (2012)

Hinz U., UniProt Consortium.

From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase

Cell. Mol. Life Sci. 67:1049-1064 (2010)

Braconi Quintaje S., Orchard S.

The annotation of both human and mouse kinomes in UniProtKB/Swiss-Prot: one small step in manual annotation, one giant leap for full comprehension of genomes

Mol. Cell. Proteomics 7:1409-1419 (2008)

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 knowledgebase

Proteomics 4:1537-1550 (2004)

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)

Gattiker A., Michoud K., Rivoire C., Auchincloss A.H., Coudert E., Lima T., Kersey P., Pagni M., Sigrist C.J., Lachaize C., Veuthey A.-L., Gasteiger E., Bairoch A.

Automated annotation of microbial proteomes in Swiss-Prot

Comput. Biol. Chem. 27:49-58 (2003)

See also: Past publications