AIMC Topic: Metabolic Networks and Pathways

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MPI-VGAE: protein-metabolite enzymatic reaction link learning by variational graph autoencoders.

Briefings in bioinformatics Jul 20, 2023
Enzymatic reactions are crucial to explore the mechanistic function of metabolites and proteins in cellular processes and to understand the etiology of diseases. The increasing number of interconnected metabolic reactions allows the development of in...
Machine Learning Molecular Docking Simulation Metabolic Networks and Pathways Cell Physiological Phenomena
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A Machine Learning-Based Approach Using Multi-omics Data to Predict Metabolic Pathways.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2023
The integrative method approaches are continuously evolving to provide accurate insights from the data that is received through experimentation on various biological systems. Multi-omics data can be integrated with predictive machine learning algorit...
Machine Learning Algorithms Metabolic Networks and Pathways
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Synthetic Biology Meets Machine Learning.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2023
This chapter outlines the myriad applications of machine learning (ML) in synthetic biology, specifically in engineering cell and protein activity, and metabolic pathways. Though by no means comprehensive, the chapter highlights several prominent com...
Machine Learning Algorithms Metabolic Networks and Pathways Synthetic Biology
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Multi-omic integration by machine learning (MIMaL).

Bioinformatics (Oxford, England) Oct 31, 2022
MOTIVATION: Cells respond to environments by regulating gene expression to exploit resources optimally. Recent advances in technologies allow for measuring the abundances of RNA, proteins, lipids and metabolites. These highly complex datasets reflect...
Machine Learning Proteome Cluster Analysis Metabolic Networks and Pathways
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MLGL-MP: a Multi-Label Graph Learning framework enhanced by pathway interdependence for Metabolic Pathway prediction.

Bioinformatics (Oxford, England) Jun 24, 2022
MOTIVATION: During lead compound optimization, it is crucial to identify pathways where a drug-like compound is metabolized. Recently, machine learning-based methods have achieved inspiring progress to predict potential metabolic pathways for drug-li...
Neural Networks, Computer Machine Learning Software Drug Discovery Metabolic Networks and Pathways
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Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2022
Plant Reactome (https://plantreactome.gramene.org) and PubChem ( https://pubchem.ncbi.nlm.nih.gov ) are two reference data portals and resources for curated plant pathways, small molecules, metabolites, gene products, and macromolecular interactions....
Databases, Factual Proteins Metabolic Networks and Pathways Plants Knowledge Bases
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[Construction of Escherichia coli cell factories].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology May 25, 2021
As an important model industrial microorganism, Escherichia coli has been widely used in pharmaceutical, chemical industry and agriculture. In the past 30 years, a variety of new strategies and techniques, including artificial intelligence, gene edit...
Artificial Intelligence Escherichia coli Metabolic Networks and Pathways Gene Editing Metabolic Engineering
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Hybrid modelling of biological systems using fuzzy continuous Petri nets.

Briefings in bioinformatics Jan 18, 2021
Integrated modelling of biological systems is challenged by composing components with sufficient kinetic data and components with insufficient kinetic data or components built only using experts' experience and knowledge. Fuzzy continuous Petri nets ...
Humans Computational Biology Fuzzy Logic Metabolic Networks and Pathways Mercaptopurine
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A deep learning architecture for metabolic pathway prediction.

Bioinformatics (Oxford, England) Apr 15, 2020
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...
Neural Networks, Computer Machine Learning Software Deep Learning Metabolic Networks and Pathways
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The reactome pathway knowledgebase.

Nucleic acids research Jan 8, 2020
The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations in a single consistent data mo...
Humans Software Protein Interaction Maps Signal Transduction Metabolic Networks and Pathways Knowledge Bases Databases, Chemical Genome, Human Databases, Pharmaceutical
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