A5065759390- Metabolomics and Mass Spectrometry Studies
- Microbial Metabolic Engineering and Bioproduction
- Computational Drug Discovery Methods
- Analytical Chemistry and Chromatography
- Bioinformatics and Genomic Networks
- Mass Spectrometry Techniques and Applications
- Forensic and Genetic Research
- Isotope Analysis in Ecology
- Gut microbiota and health
- Biomedical Text Mining and Ontologies
- Pharmacogenetics and Drug Metabolism
- Fermentation and Sensory Analysis
- Health, Environment, Cognitive Aging
- Nutrition, Genetics, and Disease
- Nutritional Studies and Diet
- Analytical chemistry methods development
- Plant biochemistry and biosynthesis
- Pharmacological Effects and Assays
- Insect Resistance and Genetics
- Catalysis and Oxidation Reactions
- Diet and metabolism studies
- Pharmaceutical and Antibiotic Environmental Impacts
- Insect and Pesticide Research
- Advanced Chemical Sensor Technologies
- Genetics, Bioinformatics, and Biomedical Research
Corteva (United States)
2020-2023
University of Alberta
2009-2019
Unité de Nutrition Humaine
2017
National Institute for Nanotechnology
2009-2013
Centre International de Recherche sur le Cancer
2012
DrugBank (www.drugbank.ca) is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, interactions and targets. First described in 2006, has continued to evolve over the past 12 years response marked improvements web standards changing needs for drug research development. This year's update, 5.0, represents most significant upgrade more than 10 years. In many cases, existing data content grown by 100% or last update. For instance, total number of...
The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the now considered standard resource for studies. Over past decade has continued to grow evolve response emerging needs metabolomics researchers continuing changes web...
The Human Metabolome Database (HMDB) (www.hmdb.ca) is a resource dedicated to providing scientists with the most current and comprehensive coverage of human metabolome. Since its first release in 2007, HMDB has been used facilitate research for nearly 1000 published studies metabolomics, clinical biochemistry systems biology. recent (version 3.0) significantly expanded enhanced over 2009 2.0). In particular, number annotated metabolite entries grown from 6500 more than 40 000 (a 600%...
DrugBank (http://www.drugbank.ca) is a comprehensive online database containing extensive biochemical and pharmacological information about drugs, their mechanisms targets. Since it was first described in 2006, has rapidly evolved, both response to user requests changing trends drug research development. Previous versions of have been widely used facilitate silico target discovery. The latest update, 4.0, further expanded contain data on metabolism, absorption, distribution, excretion...
DrugBank ( http://www.drugbank.ca ) is a richly annotated database of drug and target information. It contains extensive data on the nomenclature, ontology, chemistry, structure, function, action, pharmacology, pharmacokinetics, metabolism pharmaceutical properties both small molecule large (biotech) drugs. also comprehensive information diseases, proteins, genes organisms which these drugs act. First released in 2006, has become widely used by pharmacists, medicinal chemists, researchers,...
Scientists have long been driven by the desire to describe, organize, classify, and compare objects using taxonomies and/or ontologies. In contrast biology, geology, many other scientific disciplines, world of chemistry still lacks a standardized chemical ontology or taxonomy. Several attempts at classification made; but they mostly limited either manual, semi-automated proof-of-principle applications. This is regrettable as comprehensive description tools could not only improve our...
The Small Molecule Pathway Database (SMPDB, http://www.smpdb.ca) is a comprehensive, colorful, fully searchable and highly interactive database for visualizing human metabolic, drug action, metabolism, physiological activity metabolic disease pathways. SMPDB contains >600 pathways with nearly 75% of its not found in any other database. All pathway diagrams are extensively hyperlinked include detailed information on the relevant tissues, organs, organelles, subcellular compartments, protein...
A number of computational tools for metabolism prediction have been developed over the last 20 years to predict structures small molecules undergoing biological transformation or environmental degradation. These were largely facilitate absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies, although there is now a growing interest in using such metabolomics exposomics studies. However, their use widespread adoption still hampered by several factors, including limited...
The exposome is defined as the totality of all human environmental exposures from conception to death. It often regarded complement genome, with interaction between and genome ultimately determining one's phenotype. 'toxic exposome' complete collection chronically or acutely toxic compounds which humans can be exposed. Considerable interest in defining has been spurred on by realization that most injuries, deaths diseases are directly indirectly caused substances found air, water, food, home...
Metabolite identification for untargeted metabolomics is often hampered by the lack of experimentally collected reference spectra from tandem mass spectrometry (MS/MS). To circumvent this problem, Competitive Fragmentation Modeling-ID (CFM-ID) was developed to accurately predict electrospray ionization-MS/MS (ESI-MS/MS) chemical structures and aid in compound via MS/MS spectral matching. While earlier versions CFM-ID performed very well, CFM-ID’s performance predicting certain classes...
Abstract Background The NORMAN Association ( https://www.norman-network.com/ ) initiated the Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/ in 2015, following collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange information chemicals that are expected to occur environment, along with accompanying expert knowledge and references, has become a valuable base for “suspect screening” lists....
BioTransformer 3.0 (https://biotransformer.ca) is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. It combines machine learning approaches with rule-based system to predict small-molecule human tissues, the gut as well external environment (soil water microbiota). Simply stated, takes molecular structure input (SMILES or SDF) outputs an interactively sortable table of predicted metabolites transformation products (SMILES, PNG...
The Yeast Metabolome Database (YMDB, http://www.ymdb.ca) is a richly annotated 'metabolomic' database containing detailed information about the metabolome of Saccharomyces cerevisiae. Modeled closely after Human Database, YMDB contains >2000 metabolites with links to 995 different genes/proteins, including enzymes and transporters. in has been gathered from hundreds books, journal articles electronic databases. In addition its comprehensive literature-derived data, also an extensive...
YMDB or the Yeast Metabolome Database (http://www.ymdb.ca/) is a comprehensive database containing extensive information on genome and metabolome of Saccharomyces cerevisiae Initially released in 2012, has gone through significant expansion number improvements over past 4 years. This manuscript describes most recent version (YMDB 2.0). More specifically, it provides an updated description that was previously described 2012 NAR Issue details many additions made to time. Some important changes...
The Escherichia coli Metabolome Database (ECMDB, http://www.ecmdb.ca) is a comprehensively annotated metabolomic database containing detailed information about the metabolome of E. (K-12). Modelled closely on Human and Yeast Databases, ECMDB contains >2600 metabolites with links to ∼1500 different genes proteins, including enzymes transporters. in has been collected from dozens textbooks, journal articles electronic databases. Each metabolite entry an average 75 separate data fields,...
In an effort to capture meaningful biological, chemical and mechanistic information about clinically relevant, commonly encountered or important toxins, we have developed the Toxin Toxin-Target Database (T3DB). The T3DB is a unique bioinformatics resource that compiles comprehensive common ubiquitous toxins their toxin-targets into single electronic repository. database currently contains over 2900 small molecule peptide 1300 more than 33 000 toxin-target associations. Each record (ToxCard)...
ECMDB or the Escherichia coli Metabolome Database (http://www.ecmdb.ca) is a comprehensive database containing detailed information about genome and metabolome of E. (K-12). First released in 2012, has undergone substantial expansion many modifications over past 4 years. This manuscript describes most recent version (ECMDB 2.0). In particular, it provides update that was previously described 2013 NAR Issue details additions improvements made to time. Some important significant enhancements...
In silico metabolism prediction requires first predicting whether a specific molecule will interact with one or more metabolizing enzymes, then the result of each enzymatic reaction. Here, we provide computational tool, CypReact, for performing this task reactant prediction. Specifically, CypReact takes as input an arbitrary (specified SMILES string standard SDF file) and any nine most important human cytochrome P450 (CYP450) enzymes—CYP1A2, CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6,...
Abstract The Chemical Functional Ontology (ChemFOnt), located at https://www.chemfont.ca, is a hierarchical, OWL-compatible ontology describing the functions and actions of >341 000 biologically important chemicals. These include primary metabolites, secondary natural products, food chemicals, synthetic additives, drugs, herbicides, pesticides environmental ChemFOnt FAIR-compliant resource intended to bring same rigor, standardization formal structure terms terminology used in...
Abstract Background: The NORMAN Association (https://www.norman-network.com/) initiated the Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange information chemicals that are expected to occur environment, along with accompanying expert knowledge and references, has become a valuable base for “suspect screening” lists....
Abstract We report the major conclusions of online open-access workshop “Computational Applications in Secondary Metabolite Discovery (CAiSMD)” that took place from 08 to 10 March 2021. Invited speakers academia and industry about 200 registered participants five continents (Africa, Asia, Europe, South America, North America) part workshop. The highlighted potential applications computational methodologies search for secondary metabolites (SMs) or natural products (NPs) as drugs drug leads....