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David Wishart   Dr.  Senior Scientist or Principal Investigator 
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David Wishart published an article in January 2019.
Research Keywords & Expertise See all
0 A
0 Biomarkers
0 Mass Spectrometry
0 Metabolomics
0 Serum
0 high performance liquid chromatography
Top co-authors See all
Claudio Luchinat

382 shared publications

Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, Italy

E.J.M. Feskens

282 shared publications

Division of Human Nutrition and Health, Wageningen University, 6700 AA Wageningen, The Netherlands

Christoph Borchers

236 shared publications

University of Victoria - Genome British Columbia Proteomics Centre, Victoria, BC, Canada

Jean-Luc Wolfender

225 shared publications

School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, CMU, 1, Rue Michel Servet, 1211 Geneva, Switzerland

Catherine Stanton

189 shared publications

APC Microbiome Ireland, Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Cork, Ireland

Publication Record
Distribution of Articles published per year 
(1994 - 2018)
Total number of journals
published in
Publications See all
Article 0 Reads 0 Citations BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identificatio... Yannick Djoumbou-Feunang, Jarlei Fiamoncini, Alberto Gil-De-... Published: 05 January 2019
Journal of Cheminformatics, doi: 10.1186/s13321-018-0324-5
DOI See at publisher website PubMed View at PubMed ABS Show/hide abstract
A number of computational tools for metabolism prediction have been developed over the last 20 years to predict the structures of small molecules undergoing biological transformation or environmental degradation. These tools were largely developed to facilitate absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies, although there is now a growing interest in using such tools to facilitate metabolomics and exposomics studies. However, their use and widespread adoption is still hampered by several factors, including their limited scope, breath of coverage, availability, and performance. To address these limitations, we have developed BioTransformer, a freely available software package for accurate, rapid, and comprehensive in silico metabolism prediction and compound identification. BioTransformer combines a machine learning approach with a knowledge-based approach to predict small molecule metabolism in human tissues (e.g. liver tissue), the human gut as well as the environment (soil and water microbiota), via its metabolism prediction tool. A comprehensive evaluation of BioTransformer showed that it was able to outperform two state-of-the-art commercially available tools (Meteor Nexus and ADMET Predictor), with precision and recall values up to 7 times better than those obtained for Meteor Nexus or ADMET Predictor on the same sets of pharmaceuticals, pesticides, phytochemicals or endobiotics under similar or identical constraints. Furthermore BioTransformer was able to reproduce 100% of the transformations and metabolites predicted by the EAWAG pathway prediction system. Using mass spectrometry data obtained from a rat experimental study with epicatechin supplementation, BioTransformer was also able to correctly identify 39 previously reported epicatechin metabolites via its metabolism identification tool, and suggest 28 potential metabolites, 17 of which matched nine monoisotopic masses for which no evidence of a previous report could be found. BioTransformer can be used as an open access command-line tool, or a software library. It is freely available at . Moreover, it is also freely available as an open access RESTful application at , which allows users to manually or programmatically submit queries, and retrieve metabolism predictions or compound identification data.
Article 0 Reads 0 Citations CEU Mass Mediator 3.0: A Metabolite Annotation Tool Alberto Gil-De-La Fuente, Joanna Godzien, Sergio Saugar, Rod... Published: 31 December 2018
Journal of Proteome Research, doi: 10.1021/acs.jproteome.8b00720
DOI See at publisher website
Article 0 Reads 0 Citations Preface David Wishart, Guowang Xu Published: 01 December 2018
Analytica Chimica Acta, doi: 10.1016/j.aca.2018.09.046
DOI See at publisher website
Article 0 Reads 0 Citations A sensitive, high-throughput LC-MS/MS method for measuring catecholamines in low volume serum Jiamin Zheng, Rupasri Mandal, David S. Wishart Published: 01 December 2018
Analytica Chimica Acta, doi: 10.1016/j.aca.2018.01.021
DOI See at publisher website
Article 0 Reads 0 Citations A Simple and Convenient Synthesis of Unlabeled and 13C-Labeled 3-(3-Hydroxyphenyl)-3-Hydroxypropionic Acid and Its Quant... Yeganeh Khaniani, Matthias Lipfert, Dipanjan Bhattacharyya, ... Published: 21 November 2018
Metabolites, doi: 10.3390/metabo8040080
DOI See at publisher website ABS Show/hide abstract
An improved method to synthesize the highly abundant and biomedically important urinary metabolite 3-(3-hydroxyphenyl)-3-hydroxypropionic acid (HPHPA) is reported. The modified protocol is based on an indium-mediated sonochemical Reformatsky reaction. The synthesis is a simple two-step route as opposed to a complex four-step route previously reported in the literature that requires specialized equipment, flammable materials, and high-pressure reaction vessels. The described procedure also provides an expedient route to prepare a 13C isotopically labeled HPHPA that can be used as a standard for quantitative LC-MS analysis. This report also illustrates how the synthesized metabolite standard was used to detect and accurately quantify its presence in human urine samples using both NMR and LC-MS techniques.
Article 1 Read 0 Citations Erratum to Residue-specific mobility changes in soluble oligomers of the prion protein define regions involved in aggreg... John Paul Glaves, Carol L. Ladner-Keay, Trent C. Bjorndahl, ... Published: 01 November 2018
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, doi: 10.1016/j.bbapap.2018.07.008
DOI See at publisher website