BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification

CypReact: A Software Tool for in Silico Reactant Prediction for Human Cytochrome P450 Enzymes

(2018) Siyang Tian et al.   Journal of Chemical Information and Modeling

Demethylation of Polymethoxyflavones by Human Gut Bacterium, Blautia sp. MRG-PMF1

(2017) Supawadee Burapan et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

HMDB 4.0: the human metabolome database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Chemical transformation of xenobiotics by the human gut microbiota

(2017) Nitzan Koppel et al.   SCIENCE

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

(2017) Egon L. Willighagen et al.   Journal of Cheminformatics

Identifying known unknowns using the US EPA’s CompTox Chemistry Dashboard

(2016) Andrew D. McEachran et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Computational Prediction of Electron Ionization Mass Spectra to Assist in GC/MS Compound Identification

(2016) Felicity Allen et al.   ANALYTICAL CHEMISTRY

Computational Metabolomics: A Framework for the Million Metabolome

(2016) Karan Uppal et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Expanding role of gut microbiota in lipid metabolism

(2016) Anatole Ghazalpour et al.   CURRENT OPINION IN LIPIDOLOGY

Antibiotics in Drinking Water in Shanghai and Their Contribution to Antibiotic Exposure of School Children

(2016) Hexing Wang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Emerging applications of metabolomics in drug discovery and precision medicine

(2016) David S. Wishart   NATURE REVIEWS DRUG DISCOVERY

YMDB 2.0: a significantly expanded version of the yeast metabolome database

(2016) Miguel Ramirez-Gaona et al.   NUCLEIC ACIDS RESEARCH

BRENDA in 2017: new perspectives and new tools in BRENDA

(2016) Sandra Placzek et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Xenobiotic Metabolism and Gut Microbiomes

(2016) Anubhav Das et al.   PLoS One

XMetDB: an open access database for xenobiotic metabolism

(2016) Ola Spjuth et al.   Journal of Cheminformatics

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

(2016) Yannick Djoumbou Feunang et al.   Journal of Cheminformatics

MetFrag relaunched: incorporating strategies beyond in silico fragmentation

(2016) Christoph Ruttkies et al.   Journal of Cheminformatics

The Reciprocal Interactions between Polyphenols and Gut Microbiota and Effects on Bioaccessibility

(2016) Tugba Ozdal et al.   Nutrients

Effect of chlorpyrifos on soil microbial diversity and its biotransformation by Streptomyces sp. HP-11

(2016) M. Supreeth et al.   3 Biotech

Effect of chlorpyrifos on soil microbial diversity and its biotransformation by Streptomyces sp. HP-11

(2016) M. Supreeth et al.   3 Biotech

The metabolome of [2-14C](−)-epicatechin in humans: implications for the assessment of efficacy, safety and mechanisms of action of polyphenolic bioactives

(2016) Javier I. Ottaviani et al.   Scientific Reports

Predicting drug metabolism: experiment and/or computation?

(2015) Johannes Kirchmair et al.   NATURE REVIEWS DRUG DISCOVERY

ECMDB 2.0: A richer resource for understanding the biochemistry ofE. coli

(2015) Tanvir Sajed et al.   NUCLEIC ACIDS RESEARCH

enviPath – The environmental contaminant biotransformation pathway resource

(2015) Jörg Wicker et al.   NUCLEIC ACIDS RESEARCH

ChEBI in 2016: Improved services and an expanding collection of metabolites

(2015) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Dereplication strategies in natural product research: How many tools and methodologies behind the same concept?

(2015) Jane Hubert et al.   PHYTOCHEMISTRY REVIEWS

Illuminating the dark matter in metabolomics: Fig. 1.

(2015) Ricardo R. da Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Survey of Modulation of Gut Microbiota by Dietary Polyphenols

(2015) Montserrat Dueñas et al.   Biomed Research International

Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics

(2014) Rachel N. Carmody et al.   JOURNAL OF CLINICAL INVESTIGATION

Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification

(2014) Felicity Allen et al.   Metabolomics

CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra

(2014) Felicity Allen et al.   NUCLEIC ACIDS RESEARCH

T3DB: the toxic exposome database

(2014) David Wishart et al.   NUCLEIC ACIDS RESEARCH

Pharmaceuticals and personal care products found in the Great Lakes above concentrations of environmental concern

(2013) Benjamin D. Blair et al.   CHEMOSPHERE

XenoSite: Accurately Predicting CYP-Mediated Sites of Metabolism with Neural Networks

(2013) Jed Zaretzki et al.   Journal of Chemical Information and Modeling

Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content

(2013) J. A. Rothwell et al.   Database-The Journal of Biological Databases and Curation

Pharmacogenomics Knowledge for Personalized Medicine

(2012) M Whirl-Carrillo et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Reactions and enzymes in the metabolism of drugs and other xenobiotics

(2012) Bernard Testa et al.   DRUG DISCOVERY TODAY

Impact of chronic exposure to low doses of chlorpyrifos on the intestinal microbiota in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) and in the rat

(2012) Claire Joly et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

2D SMARTCyp Reactivity-Based Site of Metabolism Prediction for Major Drug-Metabolizing Cytochrome P450 Enzymes

(2012) Ruifeng Liu et al.   Journal of Chemical Information and Modeling

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Biological Denitrification of High Nitrate Processing Wastewaters from Explosives Production Plant

(2011) Paweł Cyplik et al.   WATER AIR AND SOIL POLLUTION

Predicting biodegradation products and pathways: a hybrid knowledge- and machine learning-based approach

(2010) J. Wicker et al.   BIOINFORMATICS

The SMARTCyp cytochrome P450 metabolism prediction server

(2010) Patrik Rydberg et al.   BIOINFORMATICS

Drug Metabolism for the Perplexed Medicinal Chemist

(2009) Bernard Testa   CHEMISTRY & BIODIVERSITY

PHARMACEUTICAL METABOLITES IN THE ENVIRONMENT: ANALYTICAL CHALLENGES AND ECOLOGICAL RISKS

(2009) Mary D. Celiz et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Interaction between Phenolics and Gut Microbiota: Role in Human Health

(2009) María V. Selma et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Computational strategies for metabolite identification in metabolomics

(2009) David S Wishart   Bioanalysis

Data-driven extraction of relative reasoning rules to limit combinatorial explosion in biodegradation pathway prediction

(2008) Kathrin Fenner et al.   BIOINFORMATICS

SyGMa: Combining Expert Knowledge and Empirical Scoring in the Prediction of Metabolites

(2008) Lars Ridder et al.   ChemMedChem

The University of Minnesota pathway prediction system: predicting metabolic logic

(2008) Lynda B.M. Ellis et al.   NUCLEIC ACIDS RESEARCH

In Silico Tools for Sharing Data and Knowledge on Toxicity and Metabolism: Derek for Windows, Meteor, and Vitic

(2008) Carol A. Marchant et al.   TOXICOLOGY MECHANISMS AND METHODS