Imperial College London

DrTimothyEbbels

Faculty of MedicineDepartment of Surgery & Cancer

Reader in Computational Bioinformatics
 
 
 
//

Contact

 

+44 (0)20 7594 3160t.ebbels Website

 
 
//

Location

 

131Sir Alexander Fleming BuildingSouth Kensington Campus

//

Summary

 

Publications

Publication Type
Year
to

127 results found

Ebbels TMD, Rodriguez-Martinez A, Dumas ME, Keun HCet al., 2018, CHAPTER 12: Advances in Computational Analysis of Metabolomic NMR Data, New Developments in NMR, Pages: 310-323

© The Royal Society of Chemistry 2018. In this chapter we discuss some of the more recent developments in preprocessing and statistical analysis of NMR spectra in metabolomics. Bayesian methods for analyzing NMR spectra are summarized and we describe one particular approach, BATMAN, in more detail. We consider techniques based on statistical associations, such as correlation spectroscopy (e.g. STOCSY and recent variants), as well as approaches that model the associations as a network and how these change under different biological conditions. The link between metabolism and genotype is explored by looking at metabolic GWAS and related techniques. Finally, we describe the relevance and current status of data standards for NMR metabolomics.

BOOK CHAPTER

Harada S, Hirayama A, Chan Q, Kurihara A, Fukai K, Iida M, Kato S, Sugiyama D, Kuwabara K, Takeuchi A, Akiyama M, Okamura T, Ebbels TMD, Elliott P, Tomita M, Sato A, Suzuki C, Sugimoto M, Soga T, Takebayashi Tet al., 2018, Reliability of plasma polar metabolite concentrations in a large-scale cohort study using capillary electrophoresis-mass spectrometry, PLOS ONE, Vol: 13, ISSN: 1932-6203

JOURNAL ARTICLE

Kaluarachchi M, Boulange CL, Karaman I, Lindon JC, Ebbels TMD, Elliott P, Tracy RP, Olson NCet al., 2018, A comparison of human serum and plasma metabolites using untargeted H-1 NMR spectroscopy and UPLC-MS, METABOLOMICS, Vol: 14, ISSN: 1573-3882

JOURNAL ARTICLE

Posma JM, Garcia-Perez I, Ebbels TMD, Lindon JC, Stamler J, Elliott P, Holmes E, Nicholson JKet al., 2018, Optimized Phenotypic Biomarker Discovery and Confounder Elimination via Covariate-Adjusted Projection to Latent Structures from Metabolic Spectroscopy Data, JOURNAL OF PROTEOME RESEARCH, Vol: 17, Pages: 1586-1595, ISSN: 1535-3893

JOURNAL ARTICLE

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, Guenther 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 Set al., 2018, nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data, ANALYTICAL CHEMISTRY, Vol: 90, Pages: 649-656, ISSN: 0003-2700

JOURNAL ARTICLE

Ye L, De Iorio M, Ebbels TMD, 2018, Bayesian estimation of the number of protonation sites for urinary metabolites from NMR spectroscopic data, METABOLOMICS, Vol: 14, ISSN: 1573-3882

JOURNAL ARTICLE

Buesen R, Chorley BN, Lima BDS, Daston G, Deferme L, Ebbels T, Gant TW, Goetz A, Greally J, Gribaldo L, Hackermueller J, Hubesch B, Jennen D, Johnson K, Kanno J, Kauffmann H-M, Laffont M, McMullen P, Meehan R, Pemberton M, Perdichizzi S, Piersma AH, Sauer UG, Schmidt K, Seitz H, Sumida K, Tollefsen KE, Tong W, Tralau T, van Ravenzwaay B, Weber RJM, Worth A, Yauk C, Poole Aet al., 2017, Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop, REGULATORY TOXICOLOGY AND PHARMACOLOGY, Vol: 91, Pages: S3-S13, ISSN: 0273-2300

JOURNAL ARTICLE

Castagne R, Boulange CL, Karaman I, Campanella G, Ferreira DLS, Kaluarachchi MR, Lehne B, Moayyeri A, Lewis MR, Spagou K, Dona AC, Evangelos V, Tracy R, Greenland P, Lindon JC, Herrington D, Ebbels TMD, Elliott P, Tzoulaki I, Chadeau-Hyam Met al., 2017, Improving Visualization and Interpretation of Metabolome-Wide Association Studies: An Application in a Population-Based Cohort Using Untargeted H-1 NMR Metabolic Profiling, JOURNAL OF PROTEOME RESEARCH, Vol: 16, Pages: 3623-3633, ISSN: 1535-3893

JOURNAL ARTICLE

Chan Q, Loo RL, Ebbels TMD, Van Horn L, Daviglus ML, Stamler J, Nicholson JK, Holmes E, Elliott Pet al., 2017, Metabolic phenotyping for discovery of urinary biomarkers of diet, xenobiotics and blood pressure in the INTERMAP Study: an overview, HYPERTENSION RESEARCH, Vol: 40, Pages: 336-345, ISSN: 0916-9636

JOURNAL ARTICLE

Kauffmann H-M, Kamp H, Fuchs R, Chorley BN, Deferme L, Ebbels T, Hackermueller J, Perdichizzi S, Poole A, Sauer UG, Tollefsen KE, Tralau T, Yauk C, van Ravenzwaay Bet al., 2017, Framework for the quality assurance of 'omics technologies considering GLP requirements, REGULATORY TOXICOLOGY AND PHARMACOLOGY, Vol: 91, Pages: S27-S35, ISSN: 0273-2300

JOURNAL ARTICLE

Steinbeck C, 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, 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 Get al., 2017, The future of metabolomics in ELIXIR, F1000Research, Vol: 6, ISSN: 2046-1402

© 2017 van Rijswijk M et al. Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the "Future of metabolomics in ELIXIR" was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases.

JOURNAL ARTICLE

Tan LSL, Jasra A, De Iorio M, Ebbels TMDet al., 2017, BAYESIAN INFERENCE FOR MULTIPLE GAUSSIAN GRAPHICAL MODELS WITH APPLICATION TO METABOLIC ASSOCIATION NETWORKS, ANNALS OF APPLIED STATISTICS, Vol: 11, Pages: 2222-2251, ISSN: 1932-6157

JOURNAL ARTICLE

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 MRet al., 2017, Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy, METABOLOMICS, Vol: 13, ISSN: 1573-3882

JOURNAL ARTICLE

Blaise BJ, Correia G, Tin A, Young JH, Vergnaud A-C, Lewis M, Pearce JTM, Elliott P, Nicholson JK, Holmes E, Ebbels TMDet al., 2016, Power Analysis and Sample Size Determination in Metabolic Phenotyping, ANALYTICAL CHEMISTRY, Vol: 88, Pages: 5179-5188, ISSN: 0003-2700

JOURNAL ARTICLE

Griep LMO, Chekmeneva E, Stamler J, Van Horn L, Chan Q, Ebbels TMD, Holmes E, Frost GS, Elliott Pet al., 2016, Urinary hippurate and proline betaine relative to fruit intake, blood pressure, and body mass index, Publisher: CAMBRIDGE UNIV PRESS, Pages: E178-E178, ISSN: 0029-6651

CONFERENCE PAPER

Karaman I, Ferreira DLS, Boulange CL, Kaluarachchi MR, Herrington D, Dona AC, Castagne R, Moayyeri A, Lehne B, Loh M, de Vries PS, Dehghan A, Franco OH, Hofman A, Evangelou E, Tzoulaki I, Elliott P, Lindon JC, Ebbels TMDet al., 2016, Workflow for Integrated Processing of Multicohort Untargeted H-1 NMR Metabolomics Data in Large-Scale Metabolic Epidemiology, JOURNAL OF PROTEOME RESEARCH, Vol: 15, Pages: 4188-4194, ISSN: 1535-3893

JOURNAL ARTICLE

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 S-A, Schober D, Smith J, Steinbeck C, Viant MR, Neumann Set al., 2016, Data standards can boost metabolomics research, and if there is a will, there is a way, METABOLOMICS, Vol: 12, ISSN: 1573-3882

JOURNAL ARTICLE

Tredwell GD, Bundy JG, De Iorio M, Ebbels TMDet al., 2016, Modelling the acid/base H-1 NMR chemical shift limits of metabolites in human urine, METABOLOMICS, Vol: 12, ISSN: 1573-3882

JOURNAL ARTICLE

Elliott P, Posma JM, Chan Q, Garcia-Perez I, Wijeyesekera A, Bictash M, Ebbels TMD, Ueshima H, Zhao L, van Horn L, Daviglus M, Stamler J, Holmes E, Nicholson JKet al., 2015, Urinary metabolic signatures of human adiposity, SCIENCE TRANSLATIONAL MEDICINE, Vol: 7, ISSN: 1946-6234

JOURNAL ARTICLE

Hendrickx DM, Aerts HJWL, Caiment F, Clark D, Ebbels TMD, Evelo CT, Gmuender H, Hebels DGAJ, Herwig R, Hescheler J, Jennen DGJ, Jetten MJA, Kanterakis S, Keun HC, Matser V, Overington JP, Pilicheva E, Sarkans U, Segura-Lepe MP, Sotiriadou I, Wittenberger T, Wittwehr C, Zanzi A, Kleinjans JCSet al., 2015, diXa: a data infrastructure for chemical safety assessment, BIOINFORMATICS, Vol: 31, Pages: 1505-1507, ISSN: 1367-4803

JOURNAL ARTICLE

Pomyen Y, Segura M, Ebbels TMD, Keun HCet al., 2015, Over-representation of correlation analysis (ORCA): a method for identifying associations between variable sets, BIOINFORMATICS, Vol: 31, Pages: 102-108, ISSN: 1367-4803

JOURNAL ARTICLE

Roessner U, Bearden DW, Ebbels T, 2015, The international Metabolomics Society in 2015: the path forward to success, METABOLOMICS, Vol: 11, Pages: 1-2, ISSN: 1573-3882

JOURNAL ARTICLE

Roessner U, Ebbels T, 2015, One minute with the Metabolomics Society's Honorary Fellows 2015, METABOLOMICS, Vol: 11, Pages: 779-781, ISSN: 1573-3882

JOURNAL ARTICLE

Salek RM, Arita M, Dayalan S, Ebbels T, Jones AR, Neumann S, Rocca-Serra P, Viant MR, Vizcaino J-Aet al., 2015, Embedding standards in metabolomics: the Metabolomics Society data standards task group, METABOLOMICS, Vol: 11, Pages: 782-783, ISSN: 1573-3882

JOURNAL ARTICLE

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, Vliet MV, Sysi-Aho M, Ludwig C, Bouwman J, Cascante M, Ebbels T, Griffin JL, Moing A, Nikolski M, Oresic M, Sansone S-A, Viant MR, Goodacre R, Guenther UL, Hankemeier T, Luchinat C, Walther D, Steinbeck Cet al., 2015, COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access, METABOLOMICS, Vol: 11, Pages: 1587-1597, ISSN: 1573-3882

JOURNAL ARTICLE

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 S-A, Viant MR, Goodacre R, Guenther UL, Hankemeier T, Luchinat C, Walther D, Steinbeck Cet al., 2015, Coordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access (vol 11, pg 1587, 2015), METABOLOMICS, Vol: 11, Pages: 1598-1599, ISSN: 1573-3882

JOURNAL ARTICLE

Hao J, Liebeke M, Astle W, De Iorio M, Bundy JG, Ebbels TMDet al., 2014, Bayesian deconvolution and quantification of metabolites in complex 1D NMR spectra using BATMAN, NATURE PROTOCOLS, Vol: 9, Pages: 1416-1427, ISSN: 1754-2189

JOURNAL ARTICLE

Ipsen A, Ebbels TMD, 2014, Orders of Magnitude Extension of the Effective Dynamic Range of TDC-Based TOFMS Data Through Maximum Likelihood Estimation, JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, Vol: 25, Pages: 1824-1827, ISSN: 1044-0305

JOURNAL ARTICLE

Liebeke M, Bruford MW, Donnelly RK, Ebbels TMD, Hao J, Kille P, Lahive E, Madison RM, Morgan AJ, Pinto-Juma GA, Spurgeon DJ, Svendsen C, Bundy JGet al., 2014, Identifying biochemical phenotypic differences between cryptic species, BIOLOGY LETTERS, Vol: 10, ISSN: 1744-9561

JOURNAL ARTICLE

This data is extracted from the Web of Science and reproduced under a licence from Thomson Reuters. You may not copy or re-distribute this data in whole or in part without the written consent of the Science business of Thomson Reuters.

Request URL: http://wlsprd.imperial.ac.uk:80/respub/WEB-INF/jsp/search-html.jsp Request URI: /respub/WEB-INF/jsp/search-html.jsp Query String: respub-action=search.html&id=00170564&limit=30&person=true