Carin Li
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View article: PathBank 2.0—the pathway database for model organism metabolomics
PathBank 2.0—the pathway database for model organism metabolomics Open
PathBank (https://pathbank.org) and its predecessor database, the Small Molecule Pathway Database (SMPDB), have been providing comprehensive metabolite pathway information for the metabolomics community since 2010. Over the past 14 years, …
View article: CyProduct: A Software Tool for Accurately Predicting the Byproducts of Human Cytochrome P450 Metabolism
CyProduct: A Software Tool for Accurately Predicting the Byproducts of Human Cytochrome P450 Metabolism Open
In silico metabolism prediction is a cheminformatic task of autonomously predicting the set of metabolic byproducts produced from a specified molecule and a set of enzymes or reactions. Here, we describe a novel machine learned i…
View article: The Bovine Metabolome
The Bovine Metabolome Open
From an animal health perspective, relatively little is known about the typical or healthy ranges of concentrations for many metabolites in bovine biofluids and tissues. Here, we describe the results of a comprehensive, quantitative metabo…
View article: Assessing the performance of genome-wide association studies for predicting disease risk
Assessing the performance of genome-wide association studies for predicting disease risk Open
To date more than 3700 genome-wide association studies (GWAS) have been published that look at the genetic contributions of single nucleotide polymorphisms (SNPs) to human conditions or human phenotypes. Through these studies many highly s…
View article: PathBank: a comprehensive pathway database for model organisms
PathBank: a comprehensive pathway database for model organisms Open
PathBank (www.pathbank.org) is a new, comprehensive, visually rich pathway database containing more than 110 000 machine-readable pathways found in 10 model organisms (Homo sapiens, Bos taurus, Rattus norvegicus, Mus musculus, Drosophila m…
View article: Assessing the performance of genome-wide association studies for predicting disease risk
Assessing the performance of genome-wide association studies for predicting disease risk Open
To date more than 3700 genome-wide association studies (GWAS) have been published that look at the genetic contributions of single nucleotide polymorphisms (SNPs) to human conditions or human phenotypes. Through these studies many highly s…
View article: CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification
CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification Open
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…
View article: MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis Open
We present a new update to MetaboAnalyst (version 4.0) for comprehensive metabolomic data analysis, interpretation, and integration with other omics data. Since the last major update in 2015, MetaboAnalyst has continued to evolve based on …
View article: DrugBank 5.0: a major update to the DrugBank database for 2018
DrugBank 5.0: a major update to the DrugBank database for 2018 Open
DrugBank (www.drugbank.ca) is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets. First described in 2006, DrugBank has continued to evolve over the pas…
View article: HMDB 4.0: the human metabolome database for 2018
HMDB 4.0: the human metabolome database for 2018 Open
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, c…