120 results found
Buesen R, Chorley BN, da Silva Lima B, et 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.
Castagne R, Boulange CL, Karaman I, et 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
Chan Q, Loo RL, Ebbels TMD, et 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
Kauffmann HM, Kamp H, Fuchs R, et 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.
© 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.
Weber RJM, Lawson TN, Salek RM, et al., 2017, Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy, METABOLOMICS, Vol: 13, ISSN: 1573-3882
Blaise BJ, Correia G, Tin A, et al., 2016, Power Analysis and Sample Size Determination in Metabolic Phenotyping, ANALYTICAL CHEMISTRY, Vol: 88, Pages: 5179-5188, ISSN: 0003-2700
David R, Ebbels T, Gooderham N, 2016, Synergistic and Antagonistic Mutation Responses of Human MCL-5 Cells to Mixtures of Benzo[a]pyrene and 2-Amino-1-Methyl-6-Phenylimidazo[4,5-b]pyridine: Dose-Related Variation in the Joint Effects of Common Dietary Carcinogens, ENVIRONMENTAL HEALTH PERSPECTIVES, Vol: 124, Pages: 88-96, ISSN: 0091-6765
Griep LMO, Chekmeneva E, Stamler J, et 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
Karaman I, Ferreira DLS, Boulange CL, et 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
Rocca-Serra P, Salek RM, Arita M, et al., 2016, Data standards can boost metabolomics research, and if there is a will, there is a way, METABOLOMICS, Vol: 12, ISSN: 1573-3882
Tredwell GD, Bundy JG, De Iorio M, et al., 2016, Modelling the acid/base H-1 NMR chemical shift limits of metabolites in human urine, METABOLOMICS, Vol: 12, ISSN: 1573-3882
Hendrickx DM, Aerts HJWL, Caiment F, et al., 2015, diXa: a data infrastructure for chemical safety assessment, BIOINFORMATICS, Vol: 31, Pages: 1505-1507, ISSN: 1367-4803
Pomyen Y, Segura M, Ebbels TMD, et 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
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
Roessner U, Ebbels T, 2015, One minute with the Metabolomics Society's Honorary Fellows 2015, METABOLOMICS, Vol: 11, Pages: 779-781, ISSN: 1573-3882
Salek RM, Arita M, Dayalan S, et al., 2015, Embedding standards in metabolomics: the Metabolomics Society data standards task group, METABOLOMICS, Vol: 11, Pages: 782-783, ISSN: 1573-3882
Salek RM, Neumann S, Schober D, et al., 2015, COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access, METABOLOMICS, Vol: 11, Pages: 1587-1597, ISSN: 1573-3882
Salek RM, Neumann S, Schober D, et 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
Hao J, Liebeke M, Astle W, et 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
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
Liebeke M, Bruford MW, Donnelly RK, et al., 2014, Identifying biochemical phenotypic differences between cryptic species, BIOLOGY LETTERS, Vol: 10, ISSN: 1744-9561
Milner JJ, Wang J, Sheridan PA, et 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
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
Tzoulaki I, Ebbels TMD, Valdes A, et 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
Valcarcel B, Ebbels TMD, Kangas AJ, et 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
Blazquez M, Carretero A, Ellis JK, et 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
Cantor GH, Beckonert O, Bollard ME, et 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
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
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