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Results: 1 to 20 of 169

1.

The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience.

Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Perez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaino JA, Hermjakob H.

Mol Cell Proteomics. 2014 Jun 30. pii: mcp.O113.036681. [Epub ahead of print]

PMID:
24980485
[PubMed - as supplied by publisher]
Free Article
2.

qcML: an exchange format for quality control metrics from mass spectrometry experiments.

Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, Vizcaino JA, Hermjakob H, Kohlbacher O, Martens L.

Mol Cell Proteomics. 2014 Apr 23. [Epub ahead of print]

PMID:
24760958
[PubMed - as supplied by publisher]
Free Article
3.

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]
4.

jmzTab: a java interface to the mzTab data standard.

Xu QW, Griss J, Wang R, Jones AR, Hermjakob H, Vizcaíno JA.

Proteomics. 2014 Jun;14(11):1328-32. doi: 10.1002/pmic.201300560. Epub 2014 Apr 29.

PMID:
24659499
[PubMed - in process]
5.

The Reactome pathway knowledgebase.

Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P.

Nucleic Acids Res. 2014 Jan;42(Database issue):D472-7. doi: 10.1093/nar/gkt1102. Epub 2013 Nov 15.

PMID:
24243840
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.

Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H.

Nucleic Acids Res. 2014 Jan;42(Database issue):D358-63. doi: 10.1093/nar/gkt1115. Epub 2013 Nov 13.

PMID:
24234451
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Path2Models: large-scale generation of computational models from biochemical pathway maps.

Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N.

BMC Syst Biol. 2013 Nov 1;7:116. doi: 10.1186/1752-0509-7-116.

PMID:
24180668
[PubMed - in process]
Free Article
8.

Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK.

Orchard S, Binz PA, Jones AR, Vizcaino JA, Deutsch EW, Hermjakob H.

Proteomics. 2013 Oct;13(20):2931-7. doi: 10.1002/pmic.201370166.

PMID:
24108681
[PubMed - indexed for MEDLINE]
9.

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
10.

Capturing cooperative interactions with the PSI-MI format.

Van Roey K, Orchard S, Kerrien S, Dumousseau M, Ricard-Blum S, Hermjakob H, Gibson TJ.

Database (Oxford). 2013 Sep 25;2013:bat066. doi: 10.1093/database/bat066. Print 2013.

PMID:
24067240
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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]
12.

Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML.

Ghali F, Krishna R, Lukasse P, Martínez-Bartolomé S, Reisinger F, Hermjakob H, Vizcaíno JA, Jones AR.

Mol Cell Proteomics. 2013 Nov;12(11):3026-35. doi: 10.1074/mcp.O113.029777. Epub 2013 Jun 28.

PMID:
23813117
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

iAnn: an event sharing platform for the life sciences.

Jimenez RC, Albar JP, Bhak J, Blatter MC, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, van Driel MA, Dunn MJ, Fernandes PL, van Gelder CW, Hermjakob H, Ioannidis V, Judge DP, Kahlem P, Korpelainen E, Kraus HJ, Loveland J, Mayer C, McDowall J, Moran F, Mulder N, Nyronen T, Rother K, Salazar GA, Schneider R, Via A, Villaveces JM, Yu P, Schneider MV, Attwood TK, Corpas M.

Bioinformatics. 2013 Aug 1;29(15):1919-21. doi: 10.1093/bioinformatics/btt306. Epub 2013 Jun 5.

PMID:
23742982
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A new reference implementation of the PSICQUIC web service.

del-Toro N, Dumousseau M, Orchard S, Jimenez RC, Galeota E, Launay G, Goll J, Breuer K, Ono K, Salwinski L, Hermjakob H.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W601-6. doi: 10.1093/nar/gkt392. Epub 2013 May 13.

PMID:
23671334
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
16.

Towards the collaborative curation of the registry underlying Identifiers.org.

Juty N, Le Novère N, Hermjakob H, Laibe C.

Database (Oxford). 2013 Apr 12;2013:bat017. doi: 10.1093/database/bat017. Print 2013.

PMID:
23584831
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

From Peptidome to PRIDE: public proteomics data migration at a large scale.

Csordas A, Wang R, Ríos D, Reisinger F, Foster JM, Slotta DJ, Vizcaíno JA, Hermjakob H.

Proteomics. 2013 May;13(10-11):1692-5. doi: 10.1002/pmic.201200514. Epub 2013 Apr 20.

PMID:
23533138
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.

Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Vizcaíno JA, Hermjakob H, Stephan C, Meyer HE, Eisenacher M; HUPO-PSI Group.

Database (Oxford). 2013 Mar 12;2013:bat009. doi: 10.1093/database/bat009. Print 2013.

PMID:
23482073
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.

Perez-Riverol Y, Wang R, Hermjakob H, Müller M, Vesada V, Vizcaíno JA.

Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):63-76. doi: 10.1016/j.bbapap.2013.02.032. Epub 2013 Mar 1. Review.

PMID:
23467006
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions.

Perez-Riverol Y, Sánchez A, Noda J, Borges D, Carvalho PC, Wang R, Vizcaíno JA, Betancourt L, Ramos Y, Duarte G, Nogueira FC, González LJ, Padrón G, Tabb DL, Hermjakob H, Domont GB, Besada V.

Anal Chem. 2013 Apr 2;85(7):3515-20. doi: 10.1021/ac303239g. Epub 2013 Mar 20.

PMID:
23448308
[PubMed - indexed for MEDLINE]

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