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

117 results found

Castagné R, Boulangé CL, Karaman I, Campanella G, Santos Ferreira DL, 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 (1)H NMR Metabolic Profiling., J Proteome Res, Vol: 16, Pages: 3623-3633

(1)H NMR spectroscopy of biofluids generates reproducible data allowing detection and quantification of small molecules in large population cohorts. Statistical models to analyze such data are now well-established, and the use of univariate metabolome wide association studies (MWAS) investigating the spectral features separately has emerged as a computationally efficient and interpretable alternative to multivariate models. The MWAS rely on the accurate estimation of a metabolome wide significance level (MWSL) to be applied to control the family wise error rate. Subsequent interpretation requires efficient visualization and formal feature annotation, which, in-turn, call for efficient prioritization of spectral variables of interest. Using human serum (1)H NMR spectroscopic profiles from 3948 participants from the Multi-Ethnic Study of Atherosclerosis (MESA), we have performed a series of MWAS for serum levels of glucose. We first propose an extension of the conventional MWSL that yields stable estimates of the MWSL across the different model parameterizations and distributional features of the outcome. We propose both efficient visualization methods and a strategy based on subsampling and internal validation to prioritize the associations. Our work proposes and illustrates practical and scalable solutions to facilitate the implementation of the MWAS approach and improve interpretation in large cohort studies.

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

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

Liebeke M, Hao J, Ebbels TMD, Bundy JGet al., 2013, Combining Spectral Ordering with Peak Fitting for One-Dimensional NMR Quantitative Metabolomics, ANALYTICAL CHEMISTRY, Vol: 85, Pages: 4605-4612, ISSN: 0003-2700

JOURNAL ARTICLE

Stamler J, Brown IJ, Yap IKS, Chan Q, Wijeyesekera A, Garcia-Perez I, Chadeau-Hyam M, Ebbels TMD, De Iorio M, Posma J, Daviglus ML, Carnethon M, Holmes E, Nicholson JK, Elliott Pet al., 2013, Dietary and Urinary Metabonomic Factors Possibly Accounting for Higher Blood Pressure of Black Compared With White Americans Results of International Collaborative Study on Macro-/Micronutrients and Blood Pressure, HYPERTENSION, Vol: 62, Pages: 1074-1080, ISSN: 0194-911X

JOURNAL ARTICLE

Vinken M, Maes M, Cavill R, Valkenborg D, Ellis JK, Decrock E, Leybaert L, Staes A, Gevaert K, Oliveira AG, Menezes GB, Cogliati B, Zaidan Dagli ML, Ebbels TMD, Witters E, Keun HC, Vanhaecke T, Rogiers Vet al., 2013, Proteomic and metabolomic responses to connexin43 silencing in primary hepatocyte cultures, ARCHIVES OF TOXICOLOGY, Vol: 87, Pages: 883-894, ISSN: 0340-5761

JOURNAL ARTICLE

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