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Results: 1 to 20 of 63

1.

Building blocks for automated elucidation of metabolites: natural product-likeness for candidate ranking.

Jayaseelan KV, Steinbeck C.

BMC Bioinformatics. 2014 Jul 5;15(1):234. doi: 10.1186/1471-2105-15-234.

PMID:
24996690
[PubMed - in process]
Free Article
2.

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
3.

Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links.

Rueedi R, Ledda M, Nicholls AW, Salek RM, Marques-Vidal P, Morya E, Sameshima K, Montoliu I, Da Silva L, Collino S, Martin FP, Rezzi S, Steinbeck C, Waterworth DM, Waeber G, Vollenweider P, Beckmann JS, Le Coutre J, Mooser V, Bergmann S, Genick UK, Kutalik Z.

PLoS Genet. 2014 Feb 20;10(2):e1004132. doi: 10.1371/journal.pgen.1004132. eCollection 2014 Feb.

PMID:
24586186
[PubMed - in process]
Free PMC Article
4.

Efficient ring perception for the Chemistry Development Kit.

May JW, Steinbeck C.

J Cheminform. 2014 Jan 30;6(1):3. doi: 10.1186/1758-2946-6-3.

PMID:
24479757
[PubMed]
Free PMC Article
5.

The role of reporting standards for metabolite annotation and identification in metabolomic studies.

Salek RM, Steinbeck C, Viant MR, Goodacre R, Dunn WB.

Gigascience. 2013 Oct 16;2(1):13. doi: 10.1186/2047-217X-2-13.

PMID:
24131531
[PubMed]
Free PMC Article
6.

KNIME-CDK: Workflow-driven cheminformatics.

Beisken S, Meinl T, Wiswedel B, de Figueiredo LF, Berthold M, Steinbeck C.

BMC Bioinformatics. 2013 Aug 22;14:257. doi: 10.1186/1471-2105-14-257.

PMID:
24103053
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

OntoQuery: easy-to-use web-based OWL querying.

Tudose I, Hastings J, Muthukrishnan V, Owen G, Turner S, Dekker A, Kale N, Ennis M, Steinbeck C.

Bioinformatics. 2013 Nov 15;29(22):2955-7. doi: 10.1093/bioinformatics/btt514. Epub 2013 Sep 5.

PMID:
24008420
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.

Hill DP, Adams N, Bada M, Batchelor C, Berardini TZ, Dietze H, Drabkin HJ, Ennis M, Foulger RE, Harris MA, Hastings J, Kale NS, de Matos P, Mungall CJ, Owen G, Roncaglia P, Steinbeck C, Turner S, Lomax J.

BMC Genomics. 2013 Jul 29;14:513. doi: 10.1186/1471-2164-14-513.

PMID:
23895341
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Metingear: a development environment for annotating genome-scale metabolic models.

May JW, James AG, Steinbeck C.

Bioinformatics. 2013 Sep 1;29(17):2213-5. doi: 10.1093/bioinformatics/btt342. Epub 2013 Jun 13.

PMID:
23766418
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Dissemination of metabolomics results: role of MetaboLights and COSMOS.

Salek RM, Haug K, Steinbeck C.

Gigascience. 2013 May 17;2(1):8. doi: 10.1186/2047-217X-2-8.

PMID:
23683662
[PubMed]
Free PMC Article
11.

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
12.

The MetaboLights repository: curation challenges in metabolomics.

Salek RM, Haug K, Conesa P, Hastings J, Williams M, Mahendraker T, Maguire E, González-Beltrán AN, Rocca-Serra P, Sansone SA, Steinbeck C.

Database (Oxford). 2013 Apr 29;2013:bat029. doi: 10.1093/database/bat029. Print 2013.

PMID:
23630246
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics.

de Matos P, Cham JA, Cao H, Alcántara R, Rowland F, Lopez R, Steinbeck C.

BMC Bioinformatics. 2013 Mar 20;14:103. doi: 10.1186/1471-2105-14-103.

PMID:
23514033
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.

Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, Muthukrishnan V, Owen G, Turner S, Williams M, Steinbeck C.

Nucleic Acids Res. 2013 Jan;41(Database issue):D456-63. doi: 10.1093/nar/gks1146. Epub 2012 Nov 24.

PMID:
23180789
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

The EBI enzyme portal.

Alcántara R, Onwubiko J, Cao H, Matos Pd, Cham JA, Jacobsen J, Holliday GL, Fischer JD, Rahman SA, Jassal B, Goujon M, Rowland F, Velankar S, López R, Overington JP, Kleywegt GJ, Hermjakob H, O'Donovan C, Martín MJ, Thornton JM, Steinbeck C.

Nucleic Acids Res. 2013 Jan;41(Database issue):D773-80. doi: 10.1093/nar/gks1112. Epub 2012 Nov 21.

PMID:
23175605
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data.

Haug K, Salek RM, Conesa P, Hastings J, de Matos P, Rijnbeek M, Mahendraker T, Williams M, Neumann S, Rocca-Serra P, Maguire E, González-Beltrán A, Sansone SA, Griffin JL, Steinbeck C.

Nucleic Acids Res. 2013 Jan;41(Database issue):D781-6. doi: 10.1093/nar/gks1004. Epub 2012 Oct 29.

PMID:
23109552
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

MetaboLights: towards a new COSMOS of metabolomics data management.

Steinbeck C, Conesa P, Haug K, Mahendraker T, Williams M, Maguire E, Rocca-Serra P, Sansone SA, Salek RM, Griffin JL.

Metabolomics. 2012 Oct;8(5):757-760. Epub 2012 Sep 25.

PMID:
23060735
[PubMed]
Free PMC Article
18.

Accessing and using chemical property databases.

Hastings J, Josephs Z, Steinbeck C.

Methods Mol Biol. 2012;929:193-219.

PMID:
23007431
[PubMed - indexed for MEDLINE]
19.

In support of the BMRB.

Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski MW, Case D, Chazin WJ, Cross TA, Dames S, Kessler H, Lange O, Madl T, Reif B, Sattler M, Eliezer D, Fersht A, Forman-Kay J, Kay LE, Fraser J, Gross J, Kortemme T, Sali A, Fujiwara T, Gardner K, Luo X, Rizo-Rey J, Rosen M, Gil RR, Ho C, Rule G, Gronenborn AM, Ishima R, Klein-Seetharaman J, Tang P, van der Wel P, Xu Y, Grzesiek S, Hiller S, Seelig J, Laue ED, Mott H, Nietlispach D, Barsukov I, Lian LY, Middleton D, Blumenschein T, Moore G, Campbell I, Schnell J, Vakonakis IJ, Watts A, Conte MR, Mason J, Pfuhl M, Sanderson MR, Craven J, Williamson M, Dominguez C, Roberts G, Günther U, Overduin M, Werner J, Williamson P, Blindauer C, Crump M, Driscoll P, Frenkiel T, Golovanov A, Matthews S, Parkinson J, Uhrin D, Williams M, Neuhaus D, Oschkinat H, Ramos A, Shaw DE, Steinbeck C, Vendruscolo M, Vuister GW, Walters KJ, Weinstein H, Wüthrich K, Yokoyama S.

Nat Struct Mol Biol. 2012 Sep;19(9):854-60. doi: 10.1038/nsmb.2371. No abstract available.

PMID:
22955930
[PubMed - indexed for MEDLINE]
20.

Bioinformatics meets user-centred design: a perspective.

Pavelin K, Cham JA, de Matos P, Brooksbank C, Cameron G, Steinbeck C.

PLoS Comput Biol. 2012;8(7):e1002554. doi: 10.1371/journal.pcbi.1002554. Epub 2012 Jul 12.

PMID:
22807660
[PubMed - indexed for MEDLINE]
Free PMC Article

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