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Results: 1 to 20 of 203

1.

Representing kidney development using the gene ontology.

Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall CJ, O'Donovan C, Apweiler R, Huntley RP.

PLoS One. 2014 Jun 18;9(6):e99864. doi: 10.1371/journal.pone.0099864. eCollection 2014.

PMID:
24941002
[PubMed - in process]
Free PMC Article
2.

ProteomeXchange provides globally coordinated proteomics data submission and dissemination.

Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H.

Nat Biotechnol. 2014 Mar;32(3):223-6. doi: 10.1038/nbt.2839. No abstract available.

PMID:
24727771
[PubMed - in process]
3.

The European Bioinformatics Institute's data resources 2014.

Brooksbank C, Bergman MT, Apweiler R, Birney E, Thornton J.

Nucleic Acids Res. 2014 Jan;42(Database issue):D18-25. doi: 10.1093/nar/gkt1206. Epub 2013 Nov 23.

PMID:
24271396
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Characterization, design, and function of the mitochondrial proteome: from organs to organisms.

Lotz C, Lin AJ, Black CM, Zhang J, Lau E, Deng N, Wang Y, Zong NC, Choi JH, Xu T, Liem DA, Korge P, Weiss JN, Hermjakob H, Yates JR 3rd, Apweiler R, Ping P.

J Proteome Res. 2014 Feb 7;13(2):433-46. doi: 10.1021/pr400539j. Epub 2013 Dec 12.

PMID:
24070373
[PubMed - in process]
Free PMC Article
5.

Integration of cardiac proteome biology and medicine by a specialized knowledgebase.

Zong NC, Li H, Li H, Lam MP, Jimenez RC, Kim CS, Deng N, Kim AK, Choi JH, Zelaya I, Liem D, Meyer D, Odeberg J, Fang C, Lu HJ, Xu T, Weiss J, Duan H, Uhlen M, Yates JR 3rd, Apweiler R, Ge J, Hermjakob H, Ping P.

Circ Res. 2013 Oct 12;113(9):1043-53. doi: 10.1161/CIRCRESAHA.113.301151. Epub 2013 Aug 21.

PMID:
23965338
[PubMed - indexed for MEDLINE]
6.

Cellular resolution models for even skipped regulation in the entire Drosophila embryo.

Ilsley GR, Fisher J, Apweiler R, Depace AH, Luscombe NM.

Elife (Cambridge). 2013 Aug 6;2:e00522. doi: 10.7554/eLife.00522.

PMID:
23930223
[PubMed]
Free PMC Article
7.

LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.

Foster JM, Moreno P, Fabregat A, Hermjakob H, Steinbeck C, Apweiler R, Wakelam MJ, Vizcaíno JA.

PLoS One. 2013 May 7;8(5):e61951. doi: 10.1371/journal.pone.0061951. Print 2013.

PMID:
23667450
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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

Mutowo-Meullenet P, Huntley RP, Dimmer EC, Alam-Faruque Y, Sawford T, Jesus Martin M, O'Donovan C, Apweiler R.

Database (Oxford). 2013 Jan 17;2013:bas062. doi: 10.1093/database/bas062. Print 2013.

PMID:
23327938
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Gene Ontology annotations and resources.

Gene Ontology Consortium, Blake JA, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L, Carbon S, Dietze H, Ireland A, Lewis SE, Mungall CJ, Gaudet P, Chrisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Bely B, Blatter M-, Bonilla C, Bouguerleret L, Boutet E, Breuza L, Bridge A, Chan WM, Chavali G, Coudert E, Dimmer E, Estreicher A, Famiglietti L, Feuermann M, Gos A, Gruaz-Gumowski N, Hieta R, Hinz C, Hulo C, Huntley R, James J, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P, Mutowo-Muellenet P, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Porras Millán P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulgar R, Lomax J, Roncaglia P, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Giglio MG, Chang H-, Hunter S, McAnulla C, Mitchell A, Sangrador A, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall DM, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-, Petri V, Lowry T, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hitz BC, Hong EL, Karra K, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Huala E, Mi H, Thomas PD, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M.

Nucleic Acids Res. 2013 Jan;41(Database issue):D530-5. doi: 10.1093/nar/gks1050. Epub 2012 Nov 17.

PMID:
23161678
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

The HUPO initiative on Model Organism Proteomes, iMOP.

Jones AM, Aebersold R, Ahrens CH, Apweiler R, Baerenfaller K, Baker M, Bendixen E, Briggs S, Brownridge P, Brunner E, Daube M, Deutsch EW, Grossniklaus U, Heazlewood J, Hengartner MO, Hermjakob H, Jovanovic M, Lawless C, Lochnit G, Martens L, Ravnsborg C, Schrimpf SP, Shim YH, Subasic D, Tholey A, Wijk Kv, Mering Cv, Weiss M, Zheng X.

Proteomics. 2012 Feb;12(3):340-5. doi: 10.1002/pmic.201290014.

PMID:
22290800
[PubMed - indexed for MEDLINE]
11.

The impact of focused Gene Ontology curation of specific mammalian systems.

Alam-Faruque Y, Huntley RP, Khodiyar VK, Camon EB, Dimmer EC, Sawford T, Martin MJ, O'Donovan C, Talmud PJ, Scambler P, Apweiler R, Lovering RC.

PLoS One. 2011;6(12):e27541. doi: 10.1371/journal.pone.0027541. Epub 2011 Dec 9.

PMID:
22174742
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

The UniProt-GO Annotation database in 2011.

Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane M, Pichler K, Poggioli D, Sehra H, Auchincloss A, Axelsen K, Blatter MC, Boutet E, Braconi-Quintaje S, Breuza L, Bridge A, Coudert E, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, James J, Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Masson P, Moinat M, Pedruzzi I, Poux S, Rivoire C, Roechert B, Schneider M, Stutz A, Sundaram S, Tognolli M, Bougueleret L, Argoud-Puy G, Cusin I, Duek-Roggli P, Xenarios I, Apweiler R.

Nucleic Acids Res. 2012 Jan;40(Database issue):D565-70. doi: 10.1093/nar/gkr1048. Epub 2011 Nov 28.

PMID:
22123736
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

InterPro in 2011: new developments in the family and domain prediction database.

Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY.

Nucleic Acids Res. 2012 Jan;40(Database issue):D306-12. doi: 10.1093/nar/gkr948. Epub 2011 Nov 16.

PMID:
22096229
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
21932440
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

A posteriori quality control for the curation and reuse of public proteomics data.

Foster JM, Degroeve S, Gatto L, Visser M, Wang R, Griss J, Apweiler R, Martens L.

Proteomics. 2011 Jun;11(11):2182-94. doi: 10.1002/pmic.201000602. Epub 2011 May 2.

PMID:
21538885
[PubMed - indexed for MEDLINE]
16.

A guide to UniProt for protein scientists.

O'Donovan C, Apweiler R.

Methods Mol Biol. 2011;694:25-35. doi: 10.1007/978-1-60761-977-2_2.

PMID:
21082425
[PubMed - indexed for MEDLINE]
17.

A large-scale protein-function database.

Apweiler R, Armstrong R, Bairoch A, Cornish-Bowden A, Halling PJ, Hofmeyr JH, Kettner C, Leyh TS, Rohwer J, Schomburg D, Steinbeck C, Tipton K.

Nat Chem Biol. 2010 Nov;6(11):785. doi: 10.1038/nchembio.460. No abstract available.

PMID:
20956966
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

"4D Biology for health and disease" workshop report.

Abrahams JP, Apweiler R, Balling R, Bertero MG, Bujnicki JM, Chayen NE, Chène P, Corthals GL, Dyląg T, Förster F, Heck AJ, Henderson PJ, Herwig R, Jehenson P, Kokalj SJ, Laue E, Legrain P, Martens L, Migliorini C, Musacchio A, Podobnik M, Schertler GF, Schreiber G, Sixma TK, Smit AB, Stuart D, Svergun DI, Taussig MJ.

N Biotechnol. 2011 Jul;28(4):291-3. doi: 10.1016/j.nbt.2010.10.003. Epub 2010 Oct 15.

PMID:
20951846
[PubMed - indexed for MEDLINE]
19.

The Renal Gene Ontology Annotation Initiative.

Alam-Faruque Y, Dimmer EC, Huntley RP, O'Donovan C, Scambler P, Apweiler R.

Organogenesis. 2010 Apr-Jun;6(2):71-5. Review.

PMID:
20885853
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Recommendations for biomarker identification and qualification in clinical proteomics.

Mischak H, Allmaier G, Apweiler R, Attwood T, Baumann M, Benigni A, Bennett SE, Bischoff R, Bongcam-Rudloff E, Capasso G, Coon JJ, D'Haese P, Dominiczak AF, Dakna M, Dihazi H, Ehrich JH, Fernandez-Llama P, Fliser D, Frokiaer J, Garin J, Girolami M, Hancock WS, Haubitz M, Hochstrasser D, Holman RR, Ioannidis JP, Jankowski J, Julian BA, Klein JB, Kolch W, Luider T, Massy Z, Mattes WB, Molina F, Monsarrat B, Novak J, Peter K, Rossing P, Sánchez-Carbayo M, Schanstra JP, Semmes OJ, Spasovski G, Theodorescu D, Thongboonkerd V, Vanholder R, Veenstra TD, Weissinger E, Yamamoto T, Vlahou A.

Sci Transl Med. 2010 Aug 25;2(46):46ps42. doi: 10.1126/scitranslmed.3001249.

PMID:
20739680
[PubMed - indexed for MEDLINE]

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