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Items: 1 to 50 of 189

1.

Cell Lines as Biological Models: Practical Steps for More Reliable Research.

Capes-Davis A, Bairoch A, Barrett T, Burnett EC, Dirks WG, Hall EM, Healy L, Kniss DA, Korch C, Liu Y, Neve RM, Nims RW, Parodi B, Schweppe RE, Storts DR, Tian F.

Chem Res Toxicol. 2019 Jun 15. doi: 10.1021/acs.chemrestox.9b00215. [Epub ahead of print]

PMID:
31203605
2.

Correction to "Large-Scale Reanalysis of Publicly Available HeLa Cell Proteomics Data in the Context of the Human Proteome Project".

Robin T, Bairoch A, Müller M, Lisacek F, Lane L.

J Proteome Res. 2019 Apr 5;18(4):1926-1927. doi: 10.1021/acs.jproteome.9b00113. Epub 2019 Feb 25. No abstract available.

PMID:
30802063
3.

Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines.

Babic Z, Capes-Davis A, Martone ME, Bairoch A, Ozyurt IB, Gillespie TH, Bandrowski AE.

Elife. 2019 Jan 29;8. pii: e41676. doi: 10.7554/eLife.41676.

4.

Exploring the Uncharacterized Human Proteome Using neXtProt.

Duek P, Gateau A, Bairoch A, Lane L.

J Proteome Res. 2018 Dec 7;17(12):4211-4226. doi: 10.1021/acs.jproteome.8b00537. Epub 2018 Sep 20.

PMID:
30191714
5.

Large-Scale Reanalysis of Publicly Available HeLa Cell Proteomics Data in the Context of the Human Proteome Project.

Robin T, Bairoch A, Müller M, Lisacek F, Lane L.

J Proteome Res. 2018 Dec 7;17(12):4160-4170. doi: 10.1021/acs.jproteome.8b00392. Epub 2018 Sep 17. Erratum in: J Proteome Res. 2019 Apr 5;18(4):1926-1927.

PMID:
30175587
6.

A new bioinformatics tool to help assess the significance of BRCA1 variants.

Cusin I, Teixeira D, Zahn-Zabal M, Rech de Laval V, Gleizes A, Viassolo V, Chappuis PO, Hutter P, Bairoch A, Gaudet P.

Hum Genomics. 2018 Jul 11;12(1):36. doi: 10.1186/s40246-018-0168-0.

7.

The Cellosaurus, a Cell-Line Knowledge Resource.

Bairoch A.

J Biomol Tech. 2018 Jul;29(2):25-38. doi: 10.7171/jbt.18-2902-002. Epub 2018 May 10.

8.

Kinases and Cancer.

Cicenas J, Zalyte E, Bairoch A, Gaudet P.

Cancers (Basel). 2018 Mar 1;10(3). pii: E63. doi: 10.3390/cancers10030063.

9.

A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells.

Kurtz A, Seltmann S, Bairoch A, Bittner MS, Bruce K, Capes-Davis A, Clarke L, Crook JM, Daheron L, Dewender J, Faulconbridge A, Fujibuchi W, Gutteridge A, Hei DJ, Kim YO, Kim JH, Kokocinski AK, Lekschas F, Lomax GP, Loring JF, Ludwig T, Mah N, Matsui T, Müller R, Parkinson H, Sheldon M, Smith K, Stachelscheid H, Stacey G, Streeter I, Veiga A, Xu RH.

Stem Cell Reports. 2018 Jan 9;10(1):1-6. doi: 10.1016/j.stemcr.2017.12.002. Review.

10.

Triage by ranking to support the curation of protein interactions.

Mottin L, Pasche E, Gobeill J, Rech de Laval V, Gleizes A, Michel PA, Bairoch A, Gaudet P, Ruch P.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax040.

11.

Annotation of functional impact of voltage-gated sodium channel mutations.

Hinard V, Britan A, Schaeffer M, Zahn-Zabal M, Thomet U, Rougier JS, Bairoch A, Abriel H, Gaudet P.

Hum Mutat. 2017 May;38(5):485-493. doi: 10.1002/humu.23191. Epub 2017 Feb 28.

12.

The neXtProt knowledgebase on human proteins: 2017 update.

Gaudet P, Michel PA, Zahn-Zabal M, Britan A, Cusin I, Domagalski M, Duek PD, Gateau A, Gleizes A, Hinard V, Rech de Laval V, Lin J, Nikitin F, Schaeffer M, Teixeira D, Lane L, Bairoch A.

Nucleic Acids Res. 2017 Jan 4;45(D1):D177-D182. doi: 10.1093/nar/gkw1062. Epub 2016 Nov 29.

13.

Missing Protein Landscape of Human Chromosomes 2 and 14: Progress and Current Status.

Duek P, Bairoch A, Gateau A, Vandenbrouck Y, Lane L.

J Proteome Res. 2016 Nov 4;15(11):3971-3978. Epub 2016 Aug 17.

PMID:
27487287
14.

ICEPO: the ion channel electrophysiology ontology.

Hinard V, Britan A, Rougier JS, Bairoch A, Abriel H, Gaudet P.

Database (Oxford). 2016 Apr 7;2016. pii: baw017. doi: 10.1093/database/baw017. Print 2016.

15.

Deep Question Answering for protein annotation.

Gobeill J, Gaudinat A, Pasche E, Vishnyakova D, Gaudet P, Bairoch A, Ruch P.

Database (Oxford). 2015 Sep 16;2015. pii: bav081. doi: 10.1093/database/bav081. Print 2015. Review.

16.

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.

Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Finn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Kaas Q, Landsman D, Lenfant N, Manning G, Nagano N, Srinivasan N, O'Donovan C, Pruitt KD, Sowdhamini R, Rawlings ND, Saier MH Jr, Sharman JL, Spedding M, Tsirigos KD, Vastermark A, Vriend G.

Database (Oxford). 2015 Jul 11;2015:bav063. doi: 10.1093/database/bav063. eCollection 2015.

17.

N-terminome analysis of the human mitochondrial proteome.

Vaca Jacome AS, Rabilloud T, Schaeffer-Reiss C, Rompais M, Ayoub D, Lane L, Bairoch A, Van Dorsselaer A, Carapito C.

Proteomics. 2015 Jul;15(14):2519-24. doi: 10.1002/pmic.201400617. Epub 2015 Jun 8.

PMID:
25944712
18.

Key challenges for the creation and maintenance of specialist protein resources.

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.

Proteins. 2015 Jun;83(6):1005-13. doi: 10.1002/prot.24803. Epub 2015 Apr 22.

19.

C11orf83, a mitochondrial cardiolipin-binding protein involved in bc1 complex assembly and supercomplex stabilization.

Desmurs M, Foti M, Raemy E, Vaz FM, Martinou JC, Bairoch A, Lane L.

Mol Cell Biol. 2015 Apr;35(7):1139-56. doi: 10.1128/MCB.01047-14. Epub 2015 Jan 20.

20.

The neXtProt knowledgebase on human proteins: current status.

Gaudet P, Michel PA, Zahn-Zabal M, Cusin I, Duek PD, Evalet O, Gateau A, Gleizes A, Pereira M, Teixeira D, Zhang Y, Lane L, Bairoch A.

Nucleic Acids Res. 2015 Jan;43(Database issue):D764-70. doi: 10.1093/nar/gku1178.

21.

DERA is the human deoxyribose phosphate aldolase and is involved in stress response.

Salleron L, Magistrelli G, Mary C, Fischer N, Bairoch A, Lane L.

Biochim Biophys Acta. 2014 Dec;1843(12):2913-25. doi: 10.1016/j.bbamcr.2014.09.007. Epub 2014 Sep 16.

22.

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.

Stockinger H, Altenhoff AM, Arnold K, Bairoch A, Bastian F, Bergmann S, Bougueleret L, Bucher P, Delorenzi M, Lane L, Le Mercier P, Lisacek F, Michielin O, Palagi PM, Rougemont J, Schwede T, von Mering C, van Nimwegen E, Walther D, Xenarios I, Zavolan M, Zdobnov EM, Zoete V, Appel RD.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W436-41. doi: 10.1093/nar/gku380. Epub 2014 May 3.

23.

C2orf62 and TTC17 are involved in actin organization and ciliogenesis in zebrafish and human.

Bontems F, Fish RJ, Borlat I, Lembo F, Chocu S, Chalmel F, Borg JP, Pineau C, Neerman-Arbez M, Bairoch A, Lane L.

PLoS One. 2014 Jan 27;9(1):e86476. doi: 10.1371/journal.pone.0086476. eCollection 2014.

24.

Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins.

Lane L, Bairoch A, Beavis RC, Deutsch EW, Gaudet P, Lundberg E, Omenn GS.

J Proteome Res. 2014 Jan 3;13(1):15-20. doi: 10.1021/pr401144x. Epub 2013 Dec 23.

25.

A large-scale evaluation of computational protein function prediction.

Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I.

Nat Methods. 2013 Mar;10(3):221-7. doi: 10.1038/nmeth.2340. Epub 2013 Jan 27.

26.

Functional identification of APIP as human mtnB, a key enzyme in the methionine salvage pathway.

Mary C, Duek P, Salleron L, Tienz P, Bumann D, Bairoch A, Lane L.

PLoS One. 2012;7(12):e52877. doi: 10.1371/journal.pone.0052877. Epub 2012 Dec 28.

27.

A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17.

Liu S, Im H, Bairoch A, Cristofanilli M, Chen R, Deutsch EW, Dalton S, Fenyo D, Fanayan S, Gates C, Gaudet P, Hincapie M, Hanash S, Kim H, Jeong SK, Lundberg E, Mias G, Menon R, Mu Z, Nice E, Paik YK, Uhlen M, Wells L, Wu SL, Yan F, Zhang F, Zhang Y, Snyder M, Omenn GS, Beavis RC, Hancock WS.

J Proteome Res. 2013 Jan 4;12(1):45-57. doi: 10.1021/pr300985j. Epub 2012 Dec 21.

28.

neXtProt: organizing protein knowledge in the context of human proteome projects.

Gaudet P, Argoud-Puy G, Cusin I, Duek P, Evalet O, Gateau A, Gleizes A, Pereira M, Zahn-Zabal M, Zwahlen C, Bairoch A, Lane L.

J Proteome Res. 2013 Jan 4;12(1):293-8. doi: 10.1021/pr300830v. Epub 2012 Dec 3.

PMID:
23205526
29.

Standard guidelines for the chromosome-centric human proteome project.

Paik YK, Omenn GS, Uhlen M, Hanash S, Marko-Varga G, Aebersold R, Bairoch A, Yamamoto T, Legrain P, Lee HJ, Na K, Jeong SK, He F, Binz PA, Nishimura T, Keown P, Baker MS, Yoo JS, Garin J, Archakov A, Bergeron J, Salekdeh GH, Hancock WS.

J Proteome Res. 2012 Apr 6;11(4):2005-13. doi: 10.1021/pr200824a. Epub 2012 Mar 26.

PMID:
22443261
30.

The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome.

Paik YK, Jeong SK, Omenn GS, Uhlen M, Hanash S, Cho SY, Lee HJ, Na K, Choi EY, Yan F, Zhang F, Zhang Y, Snyder M, Cheng Y, Chen R, Marko-Varga G, Deutsch EW, Kim H, Kwon JY, Aebersold R, Bairoch A, Taylor AD, Kim KY, Lee EY, Hochstrasser D, Legrain P, Hancock WS.

Nat Biotechnol. 2012 Mar 7;30(3):221-3. doi: 10.1038/nbt.2152. No abstract available.

PMID:
22398612
31.

neXtProt: a knowledge platform for human proteins.

Lane L, Argoud-Puy G, Britan A, Cusin I, Duek PD, Evalet O, Gateau A, Gaudet P, Gleizes A, Masselot A, Zwahlen C, Bairoch A.

Nucleic Acids Res. 2012 Jan;40(Database issue):D76-83. doi: 10.1093/nar/gkr1179. Epub 2011 Dec 1.

32.

UniPathway: a resource for the exploration and annotation of metabolic pathways.

Morgat A, Coissac E, Coudert E, Axelsen KB, Keller G, Bairoch A, Bridge A, Bougueleret L, Xenarios I, Viari A.

Nucleic Acids Res. 2012 Jan;40(Database issue):D761-9. doi: 10.1093/nar/gkr1023. Epub 2011 Nov 18.

33.

The human proteome project: current state and future direction.

Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L, Bergeron J, Borchers CH, Corthals GL, Costello CE, Deutsch EW, Domon B, Hancock W, He F, Hochstrasser D, Marko-Varga G, Salekdeh GH, Sechi S, Snyder M, Srivastava S, Uhlén M, Wu CH, Yamamoto T, Paik YK, Omenn GS.

Mol Cell Proteomics. 2011 Jul;10(7):M111.009993. doi: 10.1074/mcp.M111.009993.

34.

The human proteome project: Current state and future direction.

Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L, Bergeron J, Borchers C, Corthals GL, Costello CE, Deutsch EW, Domon B, Hancock W, He F, Hochstrasser D, Marko-Varga G, Salekdeh GH, Sechi S, Snyder M, Srivastava S, Uhlen M, Hu CH, Yamamoto T, Paik YK, Omenn GS.

Mol Cell Proteomics. 2011 Apr 29. [Epub ahead of print]

35.

Towards BioDBcore: a community-defined information specification for biological databases.

Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C; BioDBCore Working Group.

Database (Oxford). 2011 Jan 4;2011:baq027. doi: 10.1093/database/baq027. Print 2011.

36.

Towards BioDBcore: a community-defined information specification for biological databases.

Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C; BioDBCore Working Group.

Nucleic Acids Res. 2011 Jan;39(Database issue):D7-10. doi: 10.1093/nar/gkq1173. Epub 2010 Nov 18.

37.

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.

38.

ViralZone: a knowledge resource to understand virus diversity.

Hulo C, de Castro E, Masson P, Bougueleret L, Bairoch A, Xenarios I, Le Mercier P.

Nucleic Acids Res. 2011 Jan;39(Database issue):D576-82. doi: 10.1093/nar/gkq901. Epub 2010 Oct 14.

39.

Mass spectrometry in high-throughput proteomics: ready for the big time.

Nilsson T, Mann M, Aebersold R, Yates JR 3rd, Bairoch A, Bergeron JJ.

Nat Methods. 2010 Sep;7(9):681-5. doi: 10.1038/nmeth0910-681.

PMID:
20805795
40.

OpenFluDB, a database for human and animal influenza virus.

Liechti R, Gleizes A, Kuznetsov D, Bougueleret L, Le Mercier P, Bairoch A, Xenarios I.

Database (Oxford). 2010 Jul 6;2010:baq004. doi: 10.1093/database/baq004.

41.

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.

42.

Animal Toxins: How is Complexity Represented in Databases?

Jungo F, Estreicher A, Bairoch A, Bougueleret L, Xenarios I.

Toxins (Basel). 2010 Feb;2(2):262-82. doi: 10.3390/toxins2020262. Epub 2010 Feb 21.

43.

PROSITE, a protein domain database for functional characterization and annotation.

Sigrist CJ, Cerutti L, de Castro E, Langendijk-Genevaux PS, Bulliard V, Bairoch A, Hulo N.

Nucleic Acids Res. 2010 Jan;38(Database issue):D161-6. doi: 10.1093/nar/gkp885. Epub 2009 Oct 25.

44.

Human aldehyde dehydrogenase genes: alternatively spliced transcriptional variants and their suggested nomenclature.

Black WJ, Stagos D, Marchitti SA, Nebert DW, Tipton KF, Bairoch A, Vasiliou V.

Pharmacogenet Genomics. 2009 Nov;19(11):893-902. doi: 10.1097/FPC.0b013e3283329023.

45.

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

Jain E, Bairoch A, Duvaud S, Phan I, Redaschi N, Suzek BE, Martin MJ, McGarvey P, Gasteiger E.

BMC Bioinformatics. 2009 May 8;10:136. doi: 10.1186/1471-2105-10-136.

46.

Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands.

Orchard S, Hoogland C, Bairoch A, Eisenacher M, Kraus HJ, Binz PA.

Proteomics. 2009 Feb;9(3):499-501. doi: 10.1002/pmic.200800838.

PMID:
19132688
47.

The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program.

Schneider M, Lane L, Boutet E, Lieberherr D, Tognolli M, Bougueleret L, Bairoch A.

J Proteomics. 2009 Apr 13;72(3):567-73. doi: 10.1016/j.jprot.2008.11.010. Epub 2008 Nov 24.

48.

InterPro: the integrative protein signature database.

Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.

Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5. doi: 10.1093/nar/gkn785. Epub 2008 Oct 21.

49.

HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot.

Lima T, Auchincloss AH, Coudert E, Keller G, Michoud K, Rivoire C, Bulliard V, de Castro E, Lachaize C, Baratin D, Phan I, Bougueleret L, Bairoch A.

Nucleic Acids Res. 2009 Jan;37(Database issue):D471-8. doi: 10.1093/nar/gkn661. Epub 2008 Oct 11.

50.

CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens.

Almeida LG, Sakabe NJ, deOliveira AR, Silva MC, Mundstein AS, Cohen T, Chen YT, Chua R, Gurung S, Gnjatic S, Jungbluth AA, Caballero OL, Bairoch A, Kiesler E, White SL, Simpson AJ, Old LJ, Camargo AA, Vasconcelos AT.

Nucleic Acids Res. 2009 Jan;37(Database issue):D816-9. doi: 10.1093/nar/gkn673. Epub 2008 Oct 5.

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