A5061514282- Metabolomics and Mass Spectrometry Studies
- Advanced Chemical Sensor Technologies
- Computational Drug Discovery Methods
- Microbial Metabolic Engineering and Bioproduction
- Advanced Proteomics Techniques and Applications
- Analytical Chemistry and Chromatography
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Berberine and alkaloids research
- Biomedical Text Mining and Ontologies
- Alkaloids: synthesis and pharmacology
- Health disparities and outcomes
- Chronic Disease Management Strategies
- Mass Spectrometry Techniques and Applications
- Plant-based Medicinal Research
- Gut microbiota and health
University of Alberta
2018-2024
Jena University Hospital
2022
Uppsala University
2022
Latvijas Organiskās Sintēzes Institūts
2022
Abstract The Human Metabolome Database or HMDB (https://hmdb.ca) has been providing comprehensive reference information about human metabolites and their associated biological, physiological chemical properties since 2007. Over the past 15 years, grown evolved significantly to meet needs of metabolomics community respond continuing changes in internet computing technology. This year's update, 5.0, brings a number important improvements upgrades database. These should make more useful...
First released in 2006, DrugBank (https://go.drugbank.com) has grown to become the 'gold standard' knowledge resource for drug, drug-target and related pharmaceutical information. is widely used across many diverse biomedical research clinical applications, averages more than 30 million views/year. Since its last update 2018, we have been actively enhancing quantity quality of drug data this knowledgebase. In latest release (DrugBank 6.0), number FDA approved drugs from 2646 4563 (a 72%...
In the field of metabolomics, mass spectrometry (MS) is method most commonly used for identifying and annotating metabolites. As this typically involves matching a given MS spectrum against an experimentally acquired reference spectral library, approach limited by coverage size such libraries (which number in thousands). These experimental can be greatly extended predicting spectra known chemical structures millions) to create computational libraries. To facilitate generation predicted...
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 CFM-ID 4.0 web server (https://cfmid.wishartlab.com) is an online tool for predicting, annotating and interpreting tandem mass (MS/MS) spectra of small molecules. It specifically designed to assist researchers pursuing studies in metabolomics, exposomics analytical chemistry. More specifically, supports the: 1) prediction electrospray ionization quadrupole time-of-flight (ESI-QTOF-MS/MS) molecules over multiple collision energies (10 eV, 20 40 eV); 2) annotation ESI-QTOF-MS/MS given the...
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,...
In silico metabolism prediction is a cheminformatic task of autonomously predicting the set metabolic byproducts produced from specified molecule and enzymes or reactions. Here, we describe novel machine learned in cytochrome P450 (CYP450) suite, called CyProduct, that accurately predicts for human CYP450 isoform. It includes three modules: (1) CypReact, tool if query compound reacts with given enzyme, (2) CypBoM, "bond site" reaction (i.e., which specific bonds within react CYP isoform),...
Despite decades of study, large parts the mammalian metabolome remain unexplored. Mass spectrometry-based metabolomics routinely detects thousands small molecule-associated peaks within human tissues and biofluids, but typically only a fraction these can be identified, structure elucidation novel metabolites remains low-throughput endeavor. Biochemical language models have transformed interpretation DNA, RNA, protein sequences, not yet had comparable impact on understanding molecule...
Methods for assessing compound identification confidence in metabolomics and related studies have been debated actively researched the past two decades. The earliest effort 2007 focused primarily on mass spectrometry nuclear magnetic resonance spectroscopy resulted four recommended levels of metabolite - Metabolite Standards Initiative (MSI) Levels. In 2014, original MSI Levels were expanded to five (including sublevels) facilitate communication high resolution studies. Further refinement...
One year after identifying the first case of 2019 coronavirus disease (COVID-19) in Canada, federal and provincial governments are still struggling to manage pandemic. Provincial across Canada have experimented with widely varying policies order limit burden COVID-19. However, date, effectiveness these has been difficult ascertain. This is partly due lack a publicly available, high-quality dataset on COVID-19 interventions outcomes for Canada. The present paper provides containing important,...