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Items: 28

1.

An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar.

Famiglietti ML, Estreicher A, Breuza L, Poux S, Redaschi N, Xenarios I, Bridge A; UniProt Consortium.

Database (Oxford). 2019 Jan 1;2019. pii: baz040. doi: 10.1093/database/baz040.

2.

Annotation of gene product function from high-throughput studies using the Gene Ontology.

Attrill H, Gaudet P, Huntley RP, Lovering RC, Engel SR, Poux S, Van Auken KM, Georghiou G, Chibucos MC, Berardini TZ, Wood V, Drabkin H, Fey P, Garmiri P, Harris MA, Sawford T, Reiser L, Tauber R, Toro S; Gene Ontology Consortium.

Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/baz007.

3.

Scaling up data curation using deep learning: An application to literature triage in genomic variation resources.

Lee K, Famiglietti ML, McMahon A, Wei CH, MacArthur JAL, Poux S, Breuza L, Bridge A, Cunningham F, Xenarios I, Lu Z.

PLoS Comput Biol. 2018 Aug 13;14(8):e1006390. doi: 10.1371/journal.pcbi.1006390. eCollection 2018 Aug.

4.

On expert curation and scalability: UniProtKB/Swiss-Prot as a case study.

Poux S, Arighi CN, Magrane M, Bateman A, Wei CH, Lu Z, Boutet E, Bye-A-Jee H, Famiglietti ML, Roechert B, UniProt Consortium T.

Bioinformatics. 2017 Nov 1;33(21):3454-3460. doi: 10.1093/bioinformatics/btx439.

5.

Bacterial Virus Ontology; Coordinating across Databases.

Hulo C, Masson P, Toussaint A, Osumi-Sutherland D, de Castro E, Auchincloss AH, Poux S, Bougueleret L, Xenarios I, Le Mercier P.

Viruses. 2017 May 23;9(6). pii: E126. doi: 10.3390/v9060126.

6.

The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection.

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

PLoS One. 2017 Feb 16;12(2):e0171746. doi: 10.1371/journal.pone.0171746. eCollection 2017.

7.

Best Practices in Manual Annotation with the Gene Ontology.

Poux S, Gaudet P.

Methods Mol Biol. 2017;1446:41-54.

PMID:
27812934
8.

The UniProtKB guide to the human proteome.

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

Database (Oxford). 2016 Feb 20;2016. pii: bav120. doi: 10.1093/database/bav120. Print 2016.

9.

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

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

Methods Mol Biol. 2016;1374:23-54. doi: 10.1007/978-1-4939-3167-5_2.

PMID:
26519399
10.

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

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

BMC Microbiol. 2015 Jul 28;15:146. doi: 10.1186/s12866-015-0481-x.

11.

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

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.

Database (Oxford). 2015 May 9;2015:bav043. doi: 10.1093/database/bav043. Print 2015.

12.

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

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.

Nucleic Acids Res. 2015 Jan;43(Database issue):D1064-70. doi: 10.1093/nar/gku1002. Epub 2014 Oct 27.

13.

An integrated ontology resource to explore and study host-virus relationships.

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

PLoS One. 2014 Sep 18;9(9):e108075. doi: 10.1371/journal.pone.0108075. eCollection 2014.

14.

Genetic variations and diseases in UniProtKB/Swiss-Prot: the ins and outs of expert manual curation.

Famiglietti ML, Estreicher A, Gos A, Bolleman J, Géhant S, Breuza L, Bridge A, Poux S, Redaschi N, Bougueleret L, Xenarios I; UniProt Consortium.

Hum Mutat. 2014 Aug;35(8):927-35. doi: 10.1002/humu.22594. Epub 2014 Jun 24. Review.

15.

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

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

Database (Oxford). 2014 Mar 12;2014:bau016. doi: 10.1093/database/bau016. Print 2014.

16.

UniProtKB amid the turmoil of plant proteomics research.

Schneider M; UniProt Consortium, Poux S.

Front Plant Sci. 2012 Dec 6;3:270. doi: 10.3389/fpls.2012.00270. eCollection 2012.

17.

HAMAP in 2013, new developments in the protein family classification and annotation system.

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; UniProt Consortium.

Nucleic Acids Res. 2013 Jan;41(Database issue):D584-9. doi: 10.1093/nar/gks1157. Epub 2012 Nov 27.

18.

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.

19.

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

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

Toxicon. 2012 Sep 15;60(4):551-7. doi: 10.1016/j.toxicon.2012.03.010. Epub 2012 Mar 23.

20.

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.

21.

Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase.

Gaudet P, Lane L, Fey P, Bridge A, Poux S, Auchincloss A, Axelsen K, Braconi Quintaje S, Boutet E, Brown P, Coudert E, Datta RS, de Lima WC, de Oliveira Lima T, Duvaud S, Farriol-Mathis N, Ferro Rojas S, Feuermann M, Gateau A, Hinz U, Hulo C, James J, Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Moinat M, Nikolskaya A, Pedruzzi I, Rivoire C, Roechert B, Schneider M, Stanley E, Tognolli M, Sjölander K, Bougueleret L, Chisholm RL, Bairoch A.

Database (Oxford). 2009;2009:bap016. Epub 2009 Oct 15.

22.

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.

Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R.

Nat Biotechnol. 2004 Feb;22(2):177-83.

PMID:
14755292
23.

Assembly of Polycomb complexes and silencing mechanisms.

Pirrotta V, Poux S, Melfi R, Pilyugin M.

Genetica. 2003 Mar;117(2-3):191-7. Review.

PMID:
12723698
24.

The Drosophila trithorax protein is a coactivator required to prevent re-establishment of polycomb silencing.

Poux S, Horard B, Sigrist CJ, Pirrotta V.

Development. 2002 May;129(10):2483-93.

25.

Establishment of Polycomb silencing requires a transient interaction between PC and ESC.

Poux S, Melfi R, Pirrotta V.

Genes Dev. 2001 Oct 1;15(19):2509-14.

26.

Recruitment of components of Polycomb Group chromatin complexes in Drosophila.

Poux S, McCabe D, Pirrotta V.

Development. 2001 Jan;128(1):75-85.

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