OBJECTIVE: Familial adenomatous polyposis (FAP) is one major type of inherited duodenal cancer. The estimate of duodenal cancer risk in patients with FAP is critical for selecting the optimal treatment strategy.
Mechanistic models explicitly represent hypothesized biological knowledge. As such, they offer more generalizability than data-driven models. However, identifying model curation efforts that improve performance for mechanistic models is nontrivial. H...
Journal of chemical information and modeling
32040319
Metabolism of drugs affects their absorption, distribution, efficacy, excretion, and toxicity profiles. Metabolism is routinely assessed experimentally using recombinant enzymes, human liver microsome, and animal models. Unfortunately, these experime...
Metabolomics : Official journal of the Metabolomic Society
32215752
INTRODUCTION: To interpret metabolomic and lipidomic profiles, it is necessary to identify the metabolic reactions that connect the measured molecules. This can be achieved by putting them in the context of genome-scale metabolic network reconstructi...
Welding generates and releases fumes that are hazardous to human health. Welding fumes (WFs) are a complex mix of metallic oxides, fluorides and silicates that can cause or exacerbate health problems in exposed individuals. In particular, WF inhalati...
MOTIVATION: Understanding the mechanisms and structural mappings between molecules and pathway classes are critical for design of reaction predictors for synthesizing new molecules. This article studies the problem of prediction of classes of metabol...
Plant science : an international journal of experimental plant biology
32563466
Gene or pathway functional similarities are important information for researchers. However, these similarities are often described sparsely and qualitatively. The latent semantic analysis of Arabidopsis thaliana (Arabidopsis) Gene Ontology (GO) data ...
The numerous interconnected biochemical pathways that make up the metabolism of a living cell comprise a fuzzy logic system because of its high level of complexity and our inability to fully understand, predict, and model the many activities, how the...
Through advanced mechanistic modeling and the generation of large high-quality datasets, machine learning is becoming an integral part of understanding and engineering living systems. Here we show that mechanistic and machine learning models can be c...
Metabolic inference from genomic sequence information is a necessary step in determining the capacity of cells to make a living in the world at different levels of biological organization. A common method for determining the metabolic potential encod...