Imperial College London

DrTimothyEbbels

Faculty of MedicineDepartment of Surgery & Cancer

Reader in Computational Bioinformatics
 
 
 
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Contact

 

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

 
 
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Location

 

131Sir Alexander Fleming BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

120 results found

Buesen R, Chorley BN, da Silva Lima B, Daston G, Deferme L, Ebbels T, Gant TW, Goetz A, Greally J, Gribaldo L, Hackermüller J, Hubesch B, Jennen D, Johnson K, Kanno J, Kauffmann HM, 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, ISSN: 0273-2300

© 2017. Prevailing knowledge gaps in linking specific molecular changes to apical outcomes and methodological uncertainties in the generation, storage, processing, and interpretation of 'omics data limit the application of 'omics technologies in regulatory toxicology. Against this background, the European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC) convened a workshop Applying 'omics technologies in chemicals risk assessment that is reported herein. Ahead of the workshop, multi-expert teams drafted frameworks on best practices for (i) a Good-Laboratory Practice-like context for collecting, storing and curating 'omics data; (ii) the processing of 'omics data; and (iii) weight-of-evidence approaches for integrating 'omics data. The workshop participants confirmed the relevance of these Frameworks to facilitate the regulatory applicability and use of 'omics data, and the workshop discussions provided input for their further elaboration. Additionally, the key objective (iv) to establish approaches to connect 'omics perturbations to phenotypic alterations was addressed. Generally, it was considered promising to strive to link gene expression changes and pathway perturbations to the phenotype by mapping them to specific adverse outcome pathways. While further work is necessary before gene expression changes can be used to establish safe levels of substance exposure, the ECETOC workshop provided important incentives towards achieving this goal.

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 HM, Kamp H, Fuchs R, Chorley BN, Deferme L, Ebbels T, Hackermüller 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, ISSN: 0273-2300

© 2017 Elsevier Inc. 'Omics technologies are gaining importance to support regulatory toxicity studies. Prerequisites for performing 'omics studies considering GLP principles were discussed at the European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC) Workshop Applying 'omics technologies in Chemical Risk Assessment. A GLP environment comprises a standard operating procedure system, proper pre-planning and documentation, and inspections of independent quality assurance staff. To prevent uncontrolled data changes, the raw data obtained in the respective 'omics data recording systems have to be specifically defined. Further requirements include transparent and reproducible data processing steps, and safe data storage and archiving procedures. The software for data recording and processing should be validated, and data changes should be traceable or disabled. GLP-compliant quality assurance of 'omics technologies appears feasible for many GLP requirements. However, challenges include (i) defining, storing, and archiving the raw data; (ii) transparent descriptions of data processing steps; (iii) software validation; and (iv) ensuring complete reproducibility of final results with respect to raw data. Nevertheless, 'omics studies can be supported by quality measures (e.g., GLP principles) to ensure quality control, reproducibility and traceability of experiments. This enables regulators to use 'omics data in a fit-for-purpose context, which enhances their applicability for risk assessment.

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

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

Milner JJ, Wang J, Sheridan PA, Ebbels T, Beck MA, Saric Jet al., 2014, H-1 NMR-Based Profiling Reveals Differential Immune-Metabolic Networks during Influenza Virus Infection in Obese Mice, PLOS ONE, Vol: 9, ISSN: 1932-6203

JOURNAL ARTICLE

Salamanca BV, Ebbels TMD, De Iorio M, 2014, Variance and covariance heterogeneity analysis for detection of metabolites associated with cadmium exposure, STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY, Vol: 13, Pages: 191-201, ISSN: 2194-6302

JOURNAL ARTICLE

Tzoulaki I, Ebbels TMD, Valdes A, Elliott P, Ioannidis JPAet al., 2014, Design and Analysis of Metabolomics Studies in Epidemiologic Research: A Primer on -Omic Technologies, AMERICAN JOURNAL OF EPIDEMIOLOGY, Vol: 180, Pages: 129-139, ISSN: 0002-9262

JOURNAL ARTICLE

Valcarcel B, Ebbels TMD, Kangas AJ, Soininen P, Elliot P, Ala-Korpela M, Jarvelin M-R, de Iorio Met al., 2014, Genome metabolome integrated network analysis to uncover connections between genetic variants and complex traits: an application to obesity, JOURNAL OF THE ROYAL SOCIETY INTERFACE, Vol: 11, ISSN: 1742-5689

JOURNAL ARTICLE

Blazquez M, Carretero A, Ellis JK, Athersuch TJ, Cavill R, Ebbels TMD, Keun HC, Castell JV, Lahoz A, Bort Ret al., 2013, A Combination of Transcriptomics and Metabolomics Uncovers Enhanced Bile Acid Biosynthesis in HepG2 Cells Expressing CCAAT/Enhancer-Binding Protein beta (C/EBP beta), Hepatocyte Nuclear Factor 4 alpha (HNF4 alpha), and Constitutive Androstane Receptor (CAR), JOURNAL OF PROTEOME RESEARCH, Vol: 12, Pages: 2732-2741, ISSN: 1535-3893

JOURNAL ARTICLE

Cantor GH, Beckonert O, Bollard ME, Keun HC, Ebbels TMD, Antti H, Wijsman JA, Bible RH, Breau AP, Cockerell GL, Holmes E, Lindon JC, Nicholson JKet al., 2013, Integrated Histopathological and Urinary Metabonomic Investigation of the Pathogenesis of Microcystin-LR Toxicosis, VETERINARY PATHOLOGY, Vol: 50, Pages: 159-171, ISSN: 0300-9858

JOURNAL ARTICLE

Ebbels T, Dunn W, 2013, Report on the 9th Annual International Conference of the Metabolomics Society, METABOLOMICS, Vol: 9, Pages: 935-937, ISSN: 1573-3882

JOURNAL ARTICLE

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