AIMC Topic: Metabolic Networks and Pathways
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Neural Metabolic Networks: Key Elements of Healthy Brain Function.
Journal of neurochemistry
Jun 1, 2025
Neural networks are responsible for processing sensory stimuli and driving the synaptic activity required for brain function and behavior. This computational capacity is expensive and requires a steady supply of energy and building blocks to operate....
Decoding the role of the arginine dihydrolase pathway in shaping human gut community assembly and health-relevant metabolites.
Cell systems
May 21, 2025
The arginine dihydrolase pathway (arc operon) provides a metabolic niche by transforming arginine into metabolic byproducts. We investigate the role of the arc operon in probiotic Escherichia coli Nissle 1917 on human gut community assembly and healt...
A machine-learning approach for predicting butyrate production by microbial consortia using metabolic network information.
PeerJ
Jan 1, 2025
Understanding the behavior of microbial consortia is crucial for predicting metabolite production by microorganisms. Genome-scale network reconstructions enable the computation of metabolic interactions and specific associations within microbial cons...
BPP: a platform for automatic biochemical pathway prediction.
Briefings in bioinformatics
Jul 25, 2024
A biochemical pathway consists of a series of interconnected biochemical reactions to accomplish specific life activities. The participating reactants and resultant products of a pathway, including gene fragments, proteins, and small molecules, coale...
Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis.
Nucleic acids research
Jan 5, 2024
Plant Reactome (https://plantreactome.gramene.org) is a freely accessible, comprehensive plant pathway knowledgebase. It provides curated reference pathways from rice (Oryza sativa) and gene-orthology-based pathway projections to 129 additional speci...
The Reactome Pathway Knowledgebase 2024.
Nucleic acids research
Jan 5, 2024
The Reactome Knowledgebase (https://reactome.org), an Elixir and GCBR core biological data resource, provides manually curated molecular details of a broad range of normal and disease-related biological processes. Processes are annotated as an ordere...
A Machine Learning Approach for Predicting Essentiality of Metabolic Genes.
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2024
The identification of essential genes is a key challenge in systems and synthetic biology, particularly for engineering metabolic pathways that convert feedstocks into valuable products. Assessment of gene essentiality at a genome scale requires larg...
PiDeeL: metabolic pathway-informed deep learning model for survival analysis and pathological classification of gliomas.
Bioinformatics (Oxford, England)
Nov 1, 2023
MOTIVATION: Online assessment of tumor characteristics during surgery is important and has the potential to establish an intra-operative surgeon feedback mechanism. With the availability of such feedback, surgeons could decide to be more liberal or c...
MVML-MPI: Multi-View Multi-Label Learning for Metabolic Pathway Inference.
Briefings in bioinformatics
Sep 22, 2023
Development of robust and effective strategies for synthesizing new compounds, drug targeting and constructing GEnome-scale Metabolic models (GEMs) requires a deep understanding of the underlying biological processes. A critical step in achieving thi...
An integrated deep learning framework for the interpretation of untargeted metabolomics data.
Briefings in bioinformatics
Jul 20, 2023
Untargeted metabolomics is gaining widespread applications. The key aspects of the data analysis include modeling complex activities of the metabolic network, selecting metabolites associated with clinical outcome and finding critical metabolic pathw...
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