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David Wishart   Dr.  Senior Scientist or Principal Investigator 
Timeline See timeline
David Wishart published an article in February 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
Fergus Shanahan

722 shared publications

APC Microbiome Ireland, University College Cork, National University of Ireland; Cork Ireland

Claudio Luchinat

632 shared publications

Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy

Reynolds Ross

524 shared publications

APC Microbiome Ireland, University College Cork, Cork, Ireland

Edith J. M. Feskens

438 shared publications

Division of Human Nutrition, Wageningen University & Research, Wageningen, The Netherlands

Catherine Stanton

318 shared publications

Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland

371
Publications
41
Reads
5
Downloads
3797
Citations
Publication Record
Distribution of Articles published per year 
(1994 - 2018)
Total number of journals
published in
 
27
 
Publications See all
Article 0 Reads 0 Citations Solvent Composition Effects on the Structural Properties of the Aβ42 Monomer from the 3D-RISM-KH Molecular Theory of Sol... Nikolay Blinov, David S. Wishart, Andriy Kovalenko Published: 27 February 2019
The Journal of Physical Chemistry B, doi: 10.1021/acs.jpcb.9b00480
DOI See at publisher website
Article 1 Read 0 Citations Edible nuts deliver polyphenols and their transformation products to the large intestine: An in vitro fermentation model... Gabriele Rocchetti, Sudarshana Reddy Bhumireddy, Gianluca Gi... Published: 01 February 2019
Food Research International, doi: 10.1016/j.foodres.2018.09.012
DOI See at publisher website
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 https://bitbucket.org/djoumbou/biotransformerjar/ . Moreover, it is also freely available as an open access RESTful application at www.biotransformer.ca , which allows users to manually or programmatically submit queries, and retrieve metabolism predictions or compound identification data.
Article 1 Read 0 Citations CEU Mass Mediator 3.0: A Metabolite Annotation Tool Alberto Gil-De-La Fuente, Joanna Godzien, Sergio Saugar, Rod... Published: 21 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 1 Citation 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
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