Imperial College London

DrTimothyEbbels

Faculty of MedicineDepartment of Metabolism, Digestion and Reproduction

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

137 results found

Ebbels TMD, Cavill R, 2009, Bioinformatic methods in NMR-based metabolic profiling, PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY, Vol: 55, Pages: 361-374, ISSN: 0079-6565

Journal article

Robinette SL, Veselkov KA, Bohus E, Coen M, Keun HC, Ebbels TMD, Beckonert O, Holmes EC, Lindon JC, Nicholson JKet al., 2009, Cluster Analysis Statistical Spectroscopy Using Nuclear Magnetic Resonance Generated Metabolic Data Sets from Perturbed Biological Systems, ANALYTICAL CHEMISTRY, Vol: 81, Pages: 6581-6589, ISSN: 0003-2700

Journal article

Sands CJ, Coen M, Maher AD, Ebbels TMD, Holmes E, Lindon JC, Nicholson JKet al., 2009, Statistical Total Correlation Spectroscopy Editing of H-1 NMR Spectra of Biofluids: Application to Drug Metabolite Profile Identification and Enhanced Information Recovery, ANALYTICAL CHEMISTRY, Vol: 81, Pages: 6458-6466, ISSN: 0003-2700

Journal article

Loo RL, Coen M, Ebbels T, Cloarec O, Maibaum E, Bictash M, Yap I, Elliott P, Stamler J, Nicholson JK, Holmes Eet al., 2009, Metabolic Profiling and Population Screening of Analgesic Usage in Nuclear Magnetic Resonance Spectroscopy-Based Large-Scale Epidemiologic Studies, ANALYTICAL CHEMISTRY, Vol: 81, Pages: 5119-5129, ISSN: 0003-2700

Journal article

Behrends V, Ebbels TMD, Williams HD, Bundy JGet al., 2009, Time-Resolved Metabolic Footprinting for Nonlinear Modeling of Bacterial Substrate Utilization, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Vol: 75, Pages: 2453-2463, ISSN: 0099-2240

Journal article

Loo R-L, Coen M, Ebbels T, Chan Q, Stamler J, Elliott P, Holmes E, Nicholson Jet al., 2009, Metabonomic Approach to Verify Self-Reported Analgesic Use: INTERMAP Study, Joint Nutrition, Physical Activity and Metabolism Conference/49th Cardiovascular Disease Epidemiology and Prevention of the American-Heart-Association, Publisher: LIPPINCOTT WILLIAMS & WILKINS, Pages: E312-E312, ISSN: 0009-7322

Conference paper

Guo Q, Sidhu JK, Ebbels TMD, Rana F, Spurgeon DJ, Svendsen C, Sturzenbaum SR, Kille P, Morgan AJ, Bundy JGet al., 2009, Validation of metabolomics for toxic mechanism of action screening with the earthworm Lumbricus rubellus, METABOLOMICS, Vol: 5, Pages: 72-83, ISSN: 1573-3882

Journal article

Cavill R, Keun HC, Holmes E, Lindon JC, Nicholson JK, Ebbels TMDet al., 2009, Genetic algorithms for simultaneous variable and sample selection in metabonomics, BIOINFORMATICS, Vol: 25, Pages: 112-118, ISSN: 1367-4803

Journal article

Veselkov KA, Lindon JC, Ebbels TMD, Crockford D, Volynkin VV, Holmes E, Davies DB, Nicholson JKet al., 2009, Recursive Segment-Wise Peak Alignment of Biological H-1 NMR Spectra for Improved Metabolic Biomarker Recovery, ANALYTICAL CHEMISTRY, Vol: 81, Pages: 56-66, ISSN: 0003-2700

Journal article

Garcia-Perez I, Couto Alves A, Angulo S, Li JV, Utzinger J, Ebbels TMD, Legido-Quigley C, Nicholson JK, Holmes E, Barbas Cet al., 2009, Bidirectional correlation of NMR and capillary electrophoresis fingerprints: a new approach to investigating Schistosoma mansoni infection in a mouse model, Analytical chemistry, Vol: 82, Pages: 203-210

Journal article

Couto Alves A, Rantalainen M, Holmes E, Nicholson JK, Ebbels TMDet al., 2009, Analytic properties of statistical total correlation spectroscopy based information recovery in 1H NMR metabolic data sets, Analytical chemistry, Vol: 81, Pages: 2075-2084

Journal article

Bohus E, Coen M, Keun HC, Ebbels TMD, Beckonert O, Lindon JC, Holmes E, Noszal B, Nicholson JKet al., 2008, Temporal metabonomic modeling of L-arginine-induced exocrine pancreatitis, JOURNAL OF PROTEOME RESEARCH, Vol: 7, Pages: 4435-4445, ISSN: 1535-3893

Journal article

Pearce JTM, Athersuch TJ, Ebbels TMD, Lindon JC, Nicholson JK, Keun HCet al., 2008, Robust algorithms for automated chemical shift calibration of 1D H-1 NMR spectra of blood serum, ANALYTICAL CHEMISTRY, Vol: 80, Pages: 7158-7162, ISSN: 0003-2700

Journal article

Vinken M, Doktorova T, Ellinger-Ziegelbauer H, Ahr H-J, Lock E, Carmichael P, Roggen E, van Delft J, Kleinjans J, Castell J, Bort R, Donato T, Ryan M, Corvi R, Keun H, Ebbels T, Athersuch T, Sansone S-A, Rocca-Serra P, Stierum R, Jennings P, Pfaller W, Gmuender H, Vanhaecke T, Rogiers Vet al., 2008, The carcinoGENOMICS project: Critical selection of model compounds for the development of omics-based in vitro carcinogenicity screening assays, MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH, Vol: 659, Pages: 202-210, ISSN: 1383-5742

Journal article

Holmes E, Loo RL, Stamler J, Bictash M, Yap IKS, Chan Q, Ebbels T, De Iorio M, Brown IJ, Veselkov KA, Daviglus ML, Kesteloot H, Ueshima H, Zhao L, Nicholson JK, Elliott Pet al., 2008, Human metabolic phenotype diversity and its association with diet and blood pressure, NATURE, Vol: 453, Pages: 396-U50, ISSN: 0028-0836

Journal article

De Iorio M, Ebbels TMD, Stephens DA, 2008, Statistical Techniques in Metabolic Profiling, Vol: 1, Pages: 347-373

Journal article

Rantalainen M, Cloarec O, Ebbels TMD, Lundstedt T, Nicholson JK, Holmes E, Trygg Jet al., 2008, Piecewise multivariate modelling of sequential metabolic profiling data, BMC BIOINFORMATICS, Vol: 9, ISSN: 1471-2105

Journal article

Nicholson J, Keun H, Ebbels T, 2007, COMET and the challenge of drug safety screening, JOURNAL OF PROTEOME RESEARCH, Vol: 6, Pages: 4098-4099, ISSN: 1535-3893

Journal article

Ebbels TMD, Keun HC, Beckonert OP, Bollard ME, Lindon JC, Holmes E, Nicholson JKet al., 2007, Prediction and Classification of Drug Toxicity Using Probabilistic Modeling of Temporal Metabolic Data: The Consortium on Metabonomic Toxicology Screening Approach, Journal of Proteome Research, Vol: 6, Pages: 3944-3951

Journal article

Goodacre R, Broadhurst D, Smilde AK, Kristal BS, Baker JD, Beger R, Bessant C, Connor S, Calmani G, Craig A, Ebbels T, Kell DB, Manetti C, Newton J, Paternostro G, Somorjai R, Sjostrom M, Trygg J, Wulfert Fet al., 2007, Proposed minimum reporting standards for data analysis in metabolomics, METABOLOMICS, Vol: 3, Pages: 231-241, ISSN: 1573-3882

Journal article

De Iorio M, Ebbels, T M D, Stephens D Aet al., 2007, Statistical Techniques in Metabolic Profiling, Handbook of Statistical Genetics, Editors: Balding, Cannings, Bishop M, Publisher: Wiley, Pages: 1-1616, ISBN: 978-0-470-05830-5

Book chapter

Allen E, Hooks M, Moing A, Marcourt M, Tomos D, Rolin D, Ebbels Tet al., 2007, Metabolite regulation of gene expression during the heterotrophic to autotrophic transition in developing seedling of Arabidopsis, COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY, Vol: 146, Pages: S252-S252, ISSN: 1095-6433

Journal article

Beckonert O, Keun HC, Ebbels TMD, Bundy JG, Holmes E, Lindon JC, Nicholson JKet al., 2007, Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts, NATURE PROTOCOLS, Vol: 2, Pages: 2692-2703, ISSN: 1754-2189

Journal article

Ebbels TMD, 2007, Nonlinear Methods for the Analysis of Metabolic Profiles, The Handbook of Metabonomics and Metabolomics, Editors: Lindon, Holmes, Nicholson K, Publisher: Elsevier

Book chapter

Ebbels TMD, Buxton BF, Jones DT, 2006, springScape: visualisation of microarray and contextual bioinformatic data using spring embedding and an 'information landscape'., Bioinformatics, Vol: 22, Pages: e99-107

The interpretation of microarray and other high-throughput data is highly dependent on the biological context of experiments. However, standard analysis packages are poor at simultaneously presenting both the array and related bioinformatic data. We have addressed this challenge by developing a system springScape based on 'spring embedding' and an 'information landscape' allowing several related data sources to be dynamically combined while highlighting one particular feature. Each data source is represented as a network of nodes connected by weighted edges. The networks are combined and embedded in the 2-D plane by spring embedding such that nodes with a high similarity are drawn close together. Complex relationships can be discovered by varying the weight of each data source and observing the dynamic response of the spring network. By modifying Procrustes analysis, we find that the visualizations have an acceptable degree of reproducibility. The 'information landscape' highlights one particular data source, displaying it as a smooth surface whose height is proportional to both the information being viewed and the density of nodes. The algorithm is demonstrated using several microarray data sets in combination with protein-protein interaction data and GO annotations. Among the features revealed are the spatio-temporal profile of gene expression and the identification of GO terms correlated with gene expression and protein interactions. The power of this combined display lies in its interactive feedback and exploitation of human visual pattern recognition. Overall, springScape shows promise as a tool for the interpretation of microarray data in the context of relevant bioinformatic information.

Journal article

Loo RL, Holmes E, Maibaum E, Coen M, Ebbels T, Chan Q, Elliott P, Ueshima H, Zhou B, Stamler Jet al., 2006, Metabonomics to assess self-reported data: The international study on macronutrients and blood pressure (INTERMAP), 14th Meeting of the International-Society-of-Atherosclerosis, Publisher: ELSEVIER IRELAND LTD, Pages: 430-431, ISSN: 1567-5688

Conference paper

Loo R, Ebbels T, Coen M, Holmes E, Maibaum E, Chan Q, Elliott P, Ueshima H, Zhou B, Stamler Jet al., 2006, Metabonomic applications to self-reported data in epidemiology studies, EUROPEAN JOURNAL OF EPIDEMIOLOGY, Vol: 21, Pages: 110-110, ISSN: 0393-2990

Journal article

Bollard ME, Keun HC, Beckonert O, Ebbels TMD, Antti H, Nicholls AW, Shockcor JP, Cantor GH, Stevens G, Lindon JC, Holmes E, Nicholson JKet al., 2005, Comparative metabonomics of differential hydrazine toxicity in the rat and mouse, TOXICOLOGY AND APPLIED PHARMACOLOGY, Vol: 204, Pages: 135-151, ISSN: 0041-008X

Journal article

Lindon JC, Keun HC, Ebbels TMD, Pearce JTM, Holmes EC, Nicholson JKet al., 2005, The Consortium for Metabonomic Toxicology (comet): aims, activities and achievements., Pharmacogenomics, Vol: 6, Pages: 691-9

The utility of metabonomics in the evaluation of xenobiotic toxicity has been comprehensively assessed by the Consortium for Metabonomic Toxicology (COMET), formed between five major pharmaceutical companies and Imperial College London, UK. The main objectives were to assess methodologies, to generate a metabonomic database using (1)H nuclear magnetic resonance (NMR) spectroscopy of rodent urine and blood serum and to build a predictive expert system for target organ toxicity. The analytic and biologic variation that might arise through the use of metabonomics was evaluated and a high degree of robustness demonstrated. With the completion of 147 studies, the chief deliverables of a curated database of rodent biofluid NMR spectra and computer-based expert systems for the prediction of kidney or liver toxicity in rat and mouse based on the spectral data have been generated, and delivered to the sponsoring companies. The project, with its relatively modest resources, has met and exceeded all of its targets and was judged a resounding success by the sponsoring companies who are, in many cases, already enhancing and making use of the data in their in-house studies.

Journal article

Ebbels TMD, Holmes E, Lindon JC, Nicholson JKet al., 2004, Evaluation of metabolic variation in normal rat strains from a statistical analysis of (1)H NMR spectra of urine, JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS, Vol: 36, Pages: 823-833, ISSN: 0731-7085

Journal article

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