Journal of bioinformatics and computational biology
Jul 20, 2024
Drugs often target specific metabolic pathways to produce a therapeutic effect. However, these pathways are complex and interconnected, making it challenging to predict a drug's potential effects on an organism's overall metabolism. The mapping of dr...
BACKGROUND: Genome-scale metabolic models (GEMs) serve as effective tools for understanding cellular phenotypes and predicting engineering targets in the development of industrial strain. Enzyme-constrained genome-scale metabolic models (ecGEMs) have...
The genome-scale metabolic model (GEM) has emerged as one of the leading modeling approaches for systems-level metabolic studies and has been widely explored for a broad range of organisms and applications. Owing to the development of genome sequenci...
The mapping of metabolite-specific data to pathways within cellular metabolism is a major data analysis step needed for biochemical interpretation. A variety of machine learning approaches, particularly deep learning approaches, have been used to pre...
Proceedings of the National Academy of Sciences of the United States of America
Apr 26, 2024
How genomic differences contribute to phenotypic differences is a major question in biology. The recently characterized genomes, isolation environments, and qualitative patterns of growth on 122 sources and conditions of 1,154 strains from 1,049 fung...
Ferroptosis is a unique form of cell death reliant on iron and lipid peroxidation. It disrupts redox balance, causing cell death by damaging the plasma membrane, with inducers acting through enzymatic pathways or transport systems. In cancer treatmen...
Understanding the interactions between microorganisms and their impact on bacterial behavior at the community level is a key research topic in microbiology. Different methods, relying on experimental or mathematical approaches based on the diverse pr...
Immune thrombocytopenia (ITP) is an autoimmune disease characterized by antibody-mediated platelet destruction and impaired platelet production. The mechanisms underlying ITP and biomarkers predicting the response of drug treatments are elusive. We p...
BACKGROUND: Metabolic pathway prediction is one possible approach to address the problem in system biology of reconstructing an organism's metabolic network from its genome sequence. Recently there have been developments in machine learning-based pat...
Critical reviews in food science and nutrition
Dec 21, 2023
Preservatives are added as antimicrobial agents to extend the shelf life of meat. Adding preservatives to meat products can affect their flavor and nutrition. This review clarifies the effects of preservatives on metabolic pathways and network molecu...
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