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Items: 1 to 50 of 103

1.

Interoperable and scalable data analysis with microservices: Applications in Metabolomics.

Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M, Carone M, Cascante M, de Atauri P, Foguet C, Gonzalez-Beltran A, Hankemeier T, Haug K, He S, Herman S, Johnson D, Kale N, Larsson A, Neumann S, Peters K, Pireddu L, Rocca-Serra P, Roger P, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Schober D, Selivanov V, Thévenot EA, van Vliet M, Zanetti G, Steinbeck C, Kultima K, Spjuth O.

Bioinformatics. 2019 Mar 9. pii: btz160. doi: 10.1093/bioinformatics/btz160. [Epub ahead of print]

PMID:
30851093
2.

PhenoMeNal: processing and analysis of metabolomics data in the cloud.

Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M, de Atauri P, Ebbels TMD, Foguet C, Glen R, Gonzalez-Beltran A, Günther UL, Handakas E, Hankemeier T, Haug K, Herman S, Holub P, Izzo M, Jacob D, Johnson D, Jourdan F, Kale N, Karaman I, Khalili B, Emami Khonsari P, Kultima K, Lampa S, Larsson A, Ludwig C, Moreno P, Neumann S, Novella JA, O'Donovan C, Pearce JTM, Peluso A, Piras ME, Pireddu L, Reed MAC, Rocca-Serra P, Roger P, Rosato A, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Selivanov V, Spjuth O, Schober D, Thévenot EA, Tomasoni M, van Rijswijk M, van Vliet M, Viant MR, Weber RJM, Zanetti G, Steinbeck C.

Gigascience. 2019 Feb 1;8(2). pii: giy149. doi: 10.1093/gigascience/giy149.

3.

Correction: The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.

McAlpine JB, Chen SN, Kutateladze A, MacMillan JB, Appendino G, Barison A, Beniddir MA, Biavatti MW, Bluml S, Boufridi A, Butler MS, Capon RJ, Choi YH, Coppage D, Crews P, Crimmins MT, Csete M, Dewapriya P, Egan JM, Garson MJ, Genta-Jouve G, Gerwick WH, Gross H, Harper MK, Hermanto P, Hook JM, Hunter L, Jeannerat D, Ji NY, Johnson TA, Kingston DGI, Koshino H, Lee HW, Lewin G, Li J, Linington RG, Liu M, McPhail KL, Molinski TF, Moore BS, Nam JW, Neupane RP, Niemitz M, Nuzillard JM, Oberlies NH, Ocampos FMM, Pan G, Quinn RJ, Reddy DS, Renault JH, Rivera-Chávez J, Robien W, Saunders CM, Schmidt TJ, Seger C, Shen B, Steinbeck C, Stuppner H, Sturm S, Taglialatela-Scafati O, Tantillo DJ, Verpoorte R, Wang BG, Williams CM, Williams PG, Wist J, Yue JM, Zhang C, Xu Z, Simmler C, Lankin DC, Bisson J, Pauli GF.

Nat Prod Rep. 2019 Jan 1;36(1):248-249. doi: 10.1039/c8np90041h. Epub 2018 Nov 23.

PMID:
30468235
4.

The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.

McAlpine JB, Chen SN, Kutateladze A, MacMillan JB, Appendino G, Barison A, Beniddir MA, Biavatti MW, Bluml S, Boufridi A, Butler MS, Capon RJ, Choi YH, Coppage D, Crews P, Crimmins MT, Csete M, Dewapriya P, Egan JM, Garson MJ, Genta-Jouve G, Gerwick WH, Gross H, Harper MK, Hermanto P, Hook JM, Hunter L, Jeannerat D, Ji NY, Johnson TA, Kingston DGI, Koshino H, Lee HW, Lewin G, Li J, Linington RG, Liu M, McPhail KL, Molinski TF, Moore BS, Nam JW, Neupane RP, Niemitz M, Nuzillard JM, Oberlies NH, Ocampos FMM, Pan G, Quinn RJ, Reddy DS, Renault JH, Rivera-Chávez J, Robien W, Saunders CM, Schmidt TJ, Seger C, Shen B, Steinbeck C, Stuppner H, Sturm S, Taglialatela-Scafati O, Tantillo DJ, Verpoorte R, Wang BG, Williams CM, Williams PG, Wist J, Yue JM, Zhang C, Xu Z, Simmler C, Lankin DC, Bisson J, Pauli GF.

Nat Prod Rep. 2019 Jan 1;36(1):35-107. doi: 10.1039/c7np00064b. Epub 2018 Jul 13. Erratum in: Nat Prod Rep. 2018 Nov 23;:.

5.

A decade after the metabolomics standards initiative it's time for a revision.

Spicer RA, Salek R, Steinbeck C.

Sci Data. 2017 Sep 26;4:170138. doi: 10.1038/sdata.2017.138. No abstract available.

6.

Expanding the Rubterolone Family: Intrinsic Reactivity and Directed Diversification of PKS-derived Pyrans.

Guo H, Benndorf R, König S, Leichnitz D, Weigel C, Peschel G, Berthel P, Kaiser M, Steinbeck C, Werz O, Poulsen M, Beemelmanns C.

Chemistry. 2018 Aug 6;24(44):11319-11324. doi: 10.1002/chem.201802066. Epub 2018 Jul 16.

PMID:
29846024
7.

Current Challenges in Plant Eco-Metabolomics.

Peters K, Worrich A, Weinhold A, Alka O, Balcke G, Birkemeyer C, Bruelheide H, Calf OW, Dietz S, Dührkop K, Gaquerel E, Heinig U, Kücklich M, Macel M, Müller C, Poeschl Y, Pohnert G, Ristok C, Rodríguez VM, Ruttkies C, Schuman M, Schweiger R, Shahaf N, Steinbeck C, Tortosa M, Treutler H, Ueberschaar N, Velasco P, Weiß BM, Widdig A, Neumann S, Dam NMV.

Int J Mol Sci. 2018 May 6;19(5). pii: E1385. doi: 10.3390/ijms19051385. Review.

8.

NMReDATA, a standard to report the NMR assignment and parameters of organic compounds.

Pupier M, Nuzillard JM, Wist J, Schlörer NE, Kuhn S, Erdelyi M, Steinbeck C, Williams AJ, Butts C, Claridge TDW, Mikhova B, Robien W, Dashti H, Eghbalnia HR, Farès C, Adam C, Kessler P, Moriaud F, Elyashberg M, Argyropoulos D, Pérez M, Giraudeau P, Gil RR, Trevorrow P, Jeannerat D.

Magn Reson Chem. 2018 Aug;56(8):703-715. doi: 10.1002/mrc.4737. Epub 2018 May 16.

9.

In vivo and in vitro identification of Z-BOX C - a new bilirubin oxidation end product.

Ritter M, Neupane S, Seidel RA, Steinbeck C, Pohnert G.

Org Biomol Chem. 2018 May 15;16(19):3553-3555. doi: 10.1039/c8ob00164b.

PMID:
29532847
10.

A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it.

Spicer RA, Steinbeck C.

Metabolomics. 2018;14(1):16. doi: 10.1007/s11306-017-1309-5. Epub 2017 Dec 26.

11.

The future of metabolomics in ELIXIR.

van Rijswijk M, Beirnaert C, Caron C, Cascante M, Dominguez V, Dunn WB, Ebbels TMD, Giacomoni F, Gonzalez-Beltran A, Hankemeier T, Haug K, Izquierdo-Garcia JL, Jimenez RC, Jourdan F, Kale N, Klapa MI, Kohlbacher O, Koort K, Kultima K, Le Corguillé G, Moreno P, Moschonas NK, Neumann S, O'Donovan C, Reczko M, Rocca-Serra P, Rosato A, Salek RM, Sansone SA, Satagopam V, Schober D, Shimmo R, Spicer RA, Spjuth O, Thévenot EA, Viant MR, Weber RJM, Willighagen EL, Zanetti G, Steinbeck C.

Version 2. F1000Res. 2017 Sep 6 [revised 2017 Jan 1];6. pii: ELIXIR-1649. doi: 10.12688/f1000research.12342.2. eCollection 2017.

12.

Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.

Willighagen EL, Mayfield JW, Alvarsson J, Berg A, Carlsson L, Jeliazkova N, Kuhn S, Pluskal T, Rojas-Chertó M, Spjuth O, Torrance G, Evelo CT, Guha R, Steinbeck C.

J Cheminform. 2017 Sep 20;9(1):53. doi: 10.1186/s13321-017-0231-1. No abstract available.

13.

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.

Willighagen EL, Mayfield JW, Alvarsson J, Berg A, Carlsson L, Jeliazkova N, Kuhn S, Pluskal T, Rojas-Chertó M, Spjuth O, Torrance G, Evelo CT, Guha R, Steinbeck C.

J Cheminform. 2017 Jun 6;9(1):33. doi: 10.1186/s13321-017-0220-4. Erratum in: J Cheminform. 2017 Sep 20;9(1):53.

14.

nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.

Schober D, Jacob D, Wilson M, Cruz JA, Marcu A, Grant JR, Moing A, Deborde C, de Figueiredo LF, Haug K, Rocca-Serra P, Easton J, Ebbels TMD, Hao J, Ludwig C, Günther UL, Rosato A, Klein MS, Lewis IA, Luchinat C, Jones AR, Grauslys A, Larralde M, Yokochi M, Kobayashi N, Porzel A, Griffin JL, Viant MR, Wishart DS, Steinbeck C, Salek RM, Neumann S.

Anal Chem. 2018 Jan 2;90(1):649-656. doi: 10.1021/acs.analchem.7b02795. Epub 2017 Dec 14.

15.

Compliance with minimum information guidelines in public metabolomics repositories.

Spicer RA, Salek R, Steinbeck C.

Sci Data. 2017 Sep 26;4:170137. doi: 10.1038/sdata.2017.137.

16.

Navigating freely-available software tools for metabolomics analysis.

Spicer R, Salek RM, Moreno P, Cañueto D, Steinbeck C.

Metabolomics. 2017;13(9):106. doi: 10.1007/s11306-017-1242-7. Epub 2017 Aug 9. Review.

17.

Automated assembly of species metabolomes through data submission into a public repository.

Salek RM, Conesa P, Cochrane K, Haug K, Williams M, Kale N, Moreno P, Jayaseelan KV, Macias JR, Nainala VC, Hall RD, Reed LK, Viant MR, O'Donovan C, Steinbeck C.

Gigascience. 2017 Aug 1;6(8):1-4. doi: 10.1093/gigascience/gix062.

18.

Discovering and linking public omics data sets using the Omics Discovery Index.

Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H.

Nat Biotechnol. 2017 May 9;35(5):406-409. doi: 10.1038/nbt.3790. No abstract available.

19.

mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.

Larralde M, Lawson TN, Weber RJM, Moreno P, Haug K, Rocca-Serra P, Viant MR, Steinbeck C, Salek RM.

Bioinformatics. 2017 Aug 15;33(16):2598-2600. doi: 10.1093/bioinformatics/btx169.

20.

Global open data management in metabolomics.

Haug K, Salek RM, Steinbeck C.

Curr Opin Chem Biol. 2017 Feb;36:58-63. doi: 10.1016/j.cbpa.2016.12.024. Epub 2017 Jan 13. Review.

21.

Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy.

Weber RJM, Lawson TN, Salek RM, Ebbels TMD, Glen RC, Goodacre R, Griffin JL, Haug K, Koulman A, Moreno P, Ralser M, Steinbeck C, Dunn WB, Viant MR.

Metabolomics. 2017;13(2):12. doi: 10.1007/s11306-016-1147-x. Epub 2016 Dec 27. No abstract available.

22.

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. eCollection 2016.

23.

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.

24.

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. Epub 2016 Feb 22.

25.

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.

PMID:
27010336
26.

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. eCollection 2016.

27.

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.

28.

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. Epub 2016 Jan 20. Review.

29.

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;12:14. doi: 10.1007/s11306-015-0879-3. Epub 2015 Nov 17. Review.

30.

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. Epub 2015 May 26.

31.

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. Epub 2015 Oct 13.

32.

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. eCollection 2015.

33.

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.

34.

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. eCollection 2015.

35.

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. eCollection 2014.

36.

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. eCollection 2014 Dec.

37.

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. eCollection 2014.

38.

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. Epub 2014 Oct 20.

39.

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.

40.

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. Epub 2014 Jun 30.

41.

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. Epub 2014 Apr 22.

42.

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.

43.

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.

44.

Metabolic differences in ripening of Solanum lycopersicum 'Ailsa Craig' and three monogenic mutants.

Beisken S, Earll M, Baxter C, Portwood D, Ament Z, Kende A, Hodgman C, Seymour G, Smith R, Fraser P, Seymour M, Salek RM, Steinbeck C.

Sci Data. 2014 Sep 16;1:140029. doi: 10.1038/sdata.2014.29. eCollection 2014.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

50.

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.

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