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Results: 16

References for PMC Articles for PubMed (Select 22544604)

1.

The IntAct molecular interaction database in 2012.

Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, Pedruzzi I, Pfeiffenberger E, Porras P, Raghunath A, Roechert B, Orchard S, Hermjakob H.

Nucleic Acids Res. 2012 Jan;40(Database issue):D841-6. doi: 10.1093/nar/gkr1088. Epub 2011 Nov 24.

2.

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy.

Pruitt KD, Tatusova T, Brown GR, Maglott DR.

Nucleic Acids Res. 2012 Jan;40(Database issue):D130-5. doi: 10.1093/nar/gkr1079. Epub 2011 Nov 24.

3.

Ensembl 2012.

Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri AK, Keefe D, Keenan S, Kinsella R, Komorowska M, Koscielny G, Kulesha E, Larsson P, Longden I, McLaren W, Muffato M, Overduin B, Pignatelli M, Pritchard B, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sobral D, Tang YA, Taylor K, Trevanion S, Vandrovcova J, White S, Wilson M, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Harrow J, Herrero J, Hubbard TJ, Parker A, Proctor G, Spudich G, Vogel J, Yates A, Zadissa A, Searle SM.

Nucleic Acids Res. 2012 Jan;40(Database issue):D84-90. doi: 10.1093/nar/gkr991. Epub 2011 Nov 15.

4.

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.

Kersey PJ, Staines DM, Lawson D, Kulesha E, Derwent P, Humphrey JC, Hughes DS, Keenan S, Kerhornou A, Koscielny G, Langridge N, McDowall MD, Megy K, Maheswari U, Nuhn M, Paulini M, Pedro H, Toneva I, Wilson D, Yates A, Birney E.

Nucleic Acids Res. 2012 Jan;40(Database issue):D91-7. doi: 10.1093/nar/gkr895. Epub 2011 Nov 8.

5.

Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets.

Griss J, Martín M, O'Donovan C, Apweiler R, Hermjakob H, Vizcaíno JA.

Proteomics. 2011 Nov;11(22):4434-8. doi: 10.1002/pmic.201100363. Epub 2011 Oct 17.

6.

Published and perished? The influence of the searched protein database on the long-term storage of proteomics data.

Griss J, Côté RG, Gerner C, Hermjakob H, Vizcaíno JA.

Mol Cell Proteomics. 2011 Sep;10(9):M111.008490. doi: 10.1074/mcp.M111.008490. Epub 2011 Jun 23.

7.

Ongoing and future developments at the Universal Protein Resource.

UniProt Consortium.

Nucleic Acids Res. 2011 Jan;39(Database issue):D214-9. doi: 10.1093/nar/gkq1020. Epub 2010 Nov 4.

8.

A new bioinformatics analysis tools framework at EMBL-EBI.

Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W695-9. doi: 10.1093/nar/gkq313. Epub 2010 May 3.

9.

The Proteomics Identifications database: 2010 update.

Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L.

Nucleic Acids Res. 2010 Jan;38(Database issue):D736-42. doi: 10.1093/nar/gkp964. Epub 2009 Nov 11.

10.

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.

Huang da W, Sherman BT, Lempicki RA.

Nat Protoc. 2009;4(1):44-57. doi: 10.1038/nprot.2008.211.

PMID:
19131956
11.

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.

Côté RG, Jones P, Martens L, Kerrien S, Reisinger F, Lin Q, Leinonen R, Apweiler R, Hermjakob H.

BMC Bioinformatics. 2007 Oct 18;8:401.

12.

IDconverter and IDClight: conversion and annotation of gene and protein IDs.

Alibés A, Yankilevich P, Cañada A, Díaz-Uriarte R.

BMC Bioinformatics. 2007 Jan 10;8:9.

13.

A database of unique protein sequence identifiers for proteome studies.

Babnigg G, Giometti CS.

Proteomics. 2006 Aug;6(16):4514-22.

PMID:
16858731
14.

Globally distributed object identification for biological knowledgebases.

Clark T, Martin S, Liefeld T.

Brief Bioinform. 2004 Mar;5(1):59-70.

15.

UniProt archive.

Leinonen R, Diez FG, Binns D, Fleischmann W, Lopez R, Apweiler R.

Bioinformatics. 2004 Nov 22;20(17):3236-7. Epub 2004 Mar 25.

16.

MatchMiner: a tool for batch navigation among gene and gene product identifiers.

Bussey KJ, Kane D, Sunshine M, Narasimhan S, Nishizuka S, Reinhold WC, Zeeberg B, Ajay W, Weinstein JN.

Genome Biol. 2003;4(4):R27. Epub 2003 Mar 25.

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