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Items: 1 to 20 of 82


ClassyFire: automated chemical classification with a comprehensive, computable taxonomy.

Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, Wishart DS.

J Cheminform. 2016 Nov 4;8:61.


SPLASH, a hashed identifier for mass spectra.

Wohlgemuth G, Mehta SS, Mejia RF, Neumann S, Pedrosa D, Pluskal T, Schymanski EL, Willighagen EL, Wilson M, Wishart DS, Arita M, Dorrestein PC, Bandeira N, Wang M, Schulze T, Salek RM, Steinbeck C, Nainala VC, Mistrik R, Nishioka T, Fiehn O.

Nat Biotechnol. 2016 Nov 8;34(11):1099-1101. doi: 10.1038/nbt.3689. No abstract available.


Reaction Decoder Tool (RDT): extracting features from chemical reactions.

Rahman SA, Torrance G, Baldacci L, Martínez Cuesta S, Fenninger F, Gopal N, Choudhary S, May JW, Holliday GL, Steinbeck C, Thornton JM.

Bioinformatics. 2016 Jul 1;32(13):2065-6. doi: 10.1093/bioinformatics/btw096.


MetaboLights: An Open-Access Database Repository for Metabolomics Data.

Kale NS, Haug K, Conesa P, Jayseelan K, Moreno P, Rocca-Serra P, Nainala VC, Spicer RA, Williams M, Li X, Salek RM, Griffin JL, Steinbeck C.

Curr Protoc Bioinformatics. 2016 Mar 24;53:14.13.1-18. doi: 10.1002/0471250953.bi1413s53.


libChEBI: an API for accessing the ChEBI database.

Swainston N, Hastings J, Dekker A, Muthukrishnan V, May J, Steinbeck C, Mendes P.

J Cheminform. 2016 Mar 1;8:11. doi: 10.1186/s13321-016-0123-9.


The Time Is Right to Focus on Model Organism Metabolomes.

Edison AS, Hall RD, Junot C, Karp PD, Kurland IJ, Mistrik R, Reed LK, Saito K, Salek RM, Steinbeck C, Sumner LW, Viant MR.

Metabolites. 2016 Feb 15;6(1). pii: E8. doi: 10.3390/metabo6010008.


Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis.

Emwas AH, Roy R, McKay RT, Ryan D, Brennan L, Tenori L, Luchinat C, Gao X, Zeri AC, Gowda GA, Raftery D, Steinbeck C, Salek RM, Wishart DS.

J Proteome Res. 2016 Feb 5;15(2):360-73. doi: 10.1021/acs.jproteome.5b00885. Review.


Data standards can boost metabolomics research, and if there is a will, there is a way.

Rocca-Serra P, Salek RM, Arita M, Correa E, Dayalan S, Gonzalez-Beltran A, Ebbels T, Goodacre R, Hastings J, Haug K, Koulman A, Nikolski M, Oresic M, Sansone SA, Schober D, Smith J, Steinbeck C, Viant MR, Neumann S.

Metabolomics. 2016;12(1):14. Review.


COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.

Salek RM, Neumann S, Schober D, Hummel J, Billiau K, Kopka J, Correa E, Reijmers T, Rosato A, Tenori L, Turano P, Marin S, Deborde C, Jacob D, Rolin D, Dartigues B, Conesa P, Haug K, Rocca-Serra P, O'Hagan S, Hao J, van Vliet M, Sysi-Aho M, Ludwig C, Bouwman J, Cascante M, Ebbels T, Griffin JL, Moing A, Nikolski M, Oresic M, Sansone SA, Viant MR, Goodacre R, Günther UL, Hankemeier T, Luchinat C, Walther D, Steinbeck C.

Metabolomics. 2015;11(6):1587-1597.


ChEBI in 2016: Improved services and an expanding collection of metabolites.

Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1214-9. doi: 10.1093/nar/gkv1031.


SpeckTackle: JavaScript charts for spectroscopy.

Beisken S, Conesa P, Haug K, Salek RM, Steinbeck C.

J Cheminform. 2015 May 9;7:17. doi: 10.1186/s13321-015-0065-7.


BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.

Moreno P, Beisken S, Harsha B, Muthukrishnan V, Tudose I, Dekker A, Dornfeldt S, Taruttis F, Grosse I, Hastings J, Neumann S, Steinbeck C.

BMC Bioinformatics. 2015 Feb 21;16:56. doi: 10.1186/s12859-015-0486-3.


eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment.

Hastings J, Jeliazkova N, Owen G, Tsiliki G, Munteanu CR, Steinbeck C, Willighagen E.

J Biomed Semantics. 2015 Mar 21;6:10. doi: 10.1186/s13326-015-0005-5.


Ten recommendations for software engineering in research.

Hastings J, Haug K, Steinbeck C.

Gigascience. 2014 Dec 4;3(1):31. doi: 10.1186/2047-217X-3-31.


A molecular fragment cheminformatics roadmap for mesoscopic simulation.

Truszkowski A, Daniel M, Kuhn H, Neumann S, Steinbeck C, Zielesny A, Epple M.

J Cheminform. 2014 Oct 4;6(1):45.


The potential utility of predicted one bond carbon-proton coupling constants in the structure elucidation of small organic molecules by NMR spectroscopy.

Venkata C, Forster MJ, Howe PW, Steinbeck C.

PLoS One. 2014 Nov 3;9(11):e111576. doi: 10.1371/journal.pone.0111576.


Updates in Rhea--a manually curated resource of biochemical reactions.

Morgat A, Axelsen KB, Lombardot T, Alcántara R, Aimo L, Zerara M, Niknejad A, Belda E, Hyka-Nouspikel N, Coudert E, Redaschi N, Bougueleret L, Steinbeck C, Xenarios I, Bridge A.

Nucleic Acids Res. 2015 Jan;43(Database issue):D459-64. doi: 10.1093/nar/gku961.


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

Jayaseelan KV, Steinbeck C.

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


The mzTab data exchange format: communicating mass-spectrometry-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, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H.

Mol Cell Proteomics. 2014 Oct;13(10):2765-75. doi: 10.1074/mcp.O113.036681.


MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics.

Beisken S, Earll M, Portwood D, Seymour M, Steinbeck C.

Mol Inform. 2014 Apr;33(4):307-310.

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