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Items: 1 to 50 of 54

1.

The metaRbolomics Toolbox in Bioconductor and beyond.

Stanstrup J, Broeckling CD, Helmus R, Hoffmann N, Mathé E, Naake T, Nicolotti L, Peters K, Rainer J, Salek RM, Schulze T, Schymanski EL, Stravs MA, Thévenot EA, Treutler H, Weber RJM, Willighagen E, Witting M, Neumann S.

Metabolites. 2019 Sep 23;9(10). pii: E200. doi: 10.3390/metabo9100200. Review.

2.

Use cases, best practice and reporting standards for metabolomics in regulatory toxicology.

Viant MR, Ebbels TMD, Beger RD, Ekman DR, Epps DJT, Kamp H, Leonards PEG, Loizou GD, MacRae JI, van Ravenzwaay B, Rocca-Serra P, Salek RM, Walk T, Weber RJM.

Nat Commun. 2019 Jul 10;10(1):3041. doi: 10.1038/s41467-019-10900-y. Review.

3.

The Metabolomics Society-Current State of the Membership and Future Directions.

Zanetti KA, Hall RD, Griffin JL, Putri S, Salek RM, Styczynski MP, Tugizimana F, van der Hooft JJJ.

Metabolites. 2019 May 3;9(5). pii: E89. doi: 10.3390/metabo9050089.

4.

Metabolomics in early detection and prognosis of acute coronary syndrome.

Pouralijan Amiri M, Khoshkam M, Salek RM, Madadi R, Faghanzadeh Ganji G, Ramazani A.

Clin Chim Acta. 2019 Aug;495:43-53. doi: 10.1016/j.cca.2019.03.1632. Epub 2019 Mar 27. Review.

PMID:
30928571
5.

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 AN, 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 Oct 1;35(19):3752-3760. doi: 10.1093/bioinformatics/btz160.

6.

A Tool to Encourage Minimum Reporting Guideline Uptake for Data Analysis in Metabolomics.

Considine EC, Salek RM.

Metabolites. 2019 Mar 5;9(3). pii: E43. doi: 10.3390/metabo9030043.

7.

mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics.

Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O, Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y, Vizcaíno JA, Salek RM, Neumann S, Jones AR.

Anal Chem. 2019 Mar 5;91(5):3302-3310. doi: 10.1021/acs.analchem.8b04310. Epub 2019 Feb 13.

8.

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.

9.

Expanding the Use of Spectral Libraries in Proteomics.

Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, Jehmlich N, Vissers JPC, Wolan DW, Wang AY, Mendoza L, Shofstahl J, Dowsey AW, Griss J, Salek RM, Neumann S, Binz PA, Lam H, Vizcaíno JA, Bandeira N, Röst H.

J Proteome Res. 2018 Dec 7;17(12):4051-4060. doi: 10.1021/acs.jproteome.8b00485. Epub 2018 Oct 11. Review.

10.

Mind the Gap: Mapping Mass Spectral Databases in Genome-Scale Metabolic Networks Reveals Poorly Covered Areas.

Frainay C, Schymanski EL, Neumann S, Merlet B, Salek RM, Jourdan F, Yanes O.

Metabolites. 2018 Sep 15;8(3). pii: E51. doi: 10.3390/metabo8030051.

11.

Improving sample classification by harnessing the potential of 1H-NMR signal chemical shifts.

Cañueto D, Salek RM, Correig X, Cañellas N.

Sci Rep. 2018 Aug 8;8(1):11886. doi: 10.1038/s41598-018-30351-7.

12.

rDolphin: a GUI R package for proficient automatic profiling of 1D 1H-NMR spectra of study datasets.

Cañueto D, Gómez J, Salek RM, Correig X, Cañellas N.

Metabolomics. 2018 Jan 31;14(3):24. doi: 10.1007/s11306-018-1319-y.

PMID:
30830320
13.

Assessing Public Metabolomics Metadata, Towards Improving Quality.

Ferreira JD, Inácio B, Salek RM, Couto FM.

J Integr Bioinform. 2017 Dec 13;14(4). pii: /j/jib.2017.14.issue-4/jib-2017-0054/jib-2017-0054.xml. doi: 10.1515/jib-2017-0054.

14.

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.

15.

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.

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.

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, Walzer M, Jones AR.

J Proteome Res. 2017 Dec 1;16(12):4288-4298. doi: 10.1021/acs.jproteome.7b00370. Epub 2017 Sep 15.

18.

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.

19.

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.

20.

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.

21.

The Human Proteome Organization-Proteomics Standards Initiative Quality Control Working Group: Making Quality Control More Accessible for Biological Mass Spectrometry.

Bittremieux W, Walzer M, Tenzer S, Zhu W, Salek RM, Eisenacher M, Tabb DL.

Anal Chem. 2017 Apr 18;89(8):4474-4479. doi: 10.1021/acs.analchem.6b04310. Epub 2017 Mar 30.

PMID:
28318237
22.

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.

23.

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.

24.

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.

25.

Editorial: Metabolome Informatics and Statistics: Current State and Emerging Trends.

Carroll AJ, Salek RM, Arita M, Kopka J, Walther D.

Front Bioeng Biotechnol. 2016 Jul 19;4:63. doi: 10.3389/fbioe.2016.00063. eCollection 2016. No abstract available.

26.

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
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.

Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review.

Emwas AH, Luchinat C, Turano P, Tenori L, Roy R, Salek RM, Ryan D, Merzaban JS, Kaddurah-Daouk R, Zeri AC, Nagana Gowda GA, Raftery D, Wang Y, Brennan L, Wishart DS.

Metabolomics. 2015;11(4):872-894. Epub 2014 Nov 21. Review.

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.

Behavioural and molecular endophenotypes in psychotic disorders reveal heritable abnormalities in glutamatergic neurotransmission.

Scoriels L, Salek RM, Goodby E, Grainger D, Dean AM, West JA, Griffin JL, Suckling J, Nathan PJ, Lennox BR, Murray GK, Bullmore ET, Jones PB.

Transl Psychiatry. 2015 Mar 31;5:e540. doi: 10.1038/tp.2015.26.

34.

Dolphin: a tool for automatic targeted metabolite profiling using 1D and 2D (1)H-NMR data.

Gómez J, Brezmes J, Mallol R, Rodríguez MA, Vinaixa M, Salek RM, Correig X, Cañellas N.

Anal Bioanal Chem. 2014 Dec;406(30):7967-76. doi: 10.1007/s00216-014-8225-6. Epub 2014 Nov 5.

PMID:
25370160
35.

Getting the right answers: understanding metabolomics challenges.

Beisken S, Eiden M, Salek RM.

Expert Rev Mol Diagn. 2015 Jan;15(1):97-109. doi: 10.1586/14737159.2015.974562. Epub 2014 Oct 30. Review.

PMID:
25354566
36.

Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany.

Orchard S, Albar JP, Binz PA, Kettner C, Jones AR, Salek RM, Vizcaino JA, Deutsch EW, Hermjakob H.

Proteomics. 2014 Nov;14(21-22):2363-8. doi: 10.1002/pmic.201470164. Epub 2014 Oct 9.

PMID:
25297050
37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

45.

Remodeling of central metabolism in invasive breast cancer compared to normal breast tissue - a GC-TOFMS based metabolomics study.

Budczies J, Denkert C, Müller BM, Brockmöller SF, Klauschen F, Györffy B, Dietel M, Richter-Ehrenstein C, Marten U, Salek RM, Griffin JL, Hilvo M, Orešič M, Wohlgemuth G, Fiehn O.

BMC Genomics. 2012 Jul 23;13:334. doi: 10.1186/1471-2164-13-334.

46.

A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human.".

Griffin JL, Atherton HJ, Steinbeck C, Salek RM.

BMC Res Notes. 2011 Jul 29;4:272. doi: 10.1186/1756-0500-4-272.

47.

A metabolomic comparison of mouse models of the Neuronal Ceroid Lipofuscinoses.

Salek RM, Pears MR, Cooper JD, Mitchison HM, Pearce DA, Mortishire-Smith RJ, Griffin JL.

J Biomol NMR. 2011 Apr;49(3-4):175-84. doi: 10.1007/s10858-011-9491-7. Epub 2011 Apr 3.

48.

¹H nuclear magnetic resonance spectroscopy characterisation of metabolic phenotypes in the medulloblastoma of the SMO transgenic mice.

Hekmatyar SK, Wilson M, Jerome N, Salek RM, Griffin JL, Peet A, Kauppinen RA.

Br J Cancer. 2010 Oct 12;103(8):1297-304. doi: 10.1038/sj.bjc.6605890. Epub 2010 Sep 14.

49.

A metabolomic study of the CRND8 transgenic mouse model of Alzheimer's disease.

Salek RM, Xia J, Innes A, Sweatman BC, Adalbert R, Randle S, McGowan E, Emson PC, Griffin JL.

Neurochem Int. 2010 Jul;56(8):937-47. doi: 10.1016/j.neuint.2010.04.001. Epub 2010 Apr 14.

PMID:
20398713
50.

A metabolomic study of brain tissues from aged mice with low expression of the vesicular monoamine transporter 2 (VMAT2) gene.

Salek RM, Colebrooke RE, Macintosh R, Lynch PJ, Sweatman BC, Emson PC, Griffin JL.

Neurochem Res. 2008 Feb;33(2):292-300. Epub 2007 Nov 29.

PMID:
18041582

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