AIMC Topic: Biosynthetic Pathways

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Regulation and induction of fungal secondary metabolites: a comprehensive review.

Archives of microbiology Jul 1, 2025
Fungal secondary metabolites (SMs) represent a vast reservoir of bioactive compounds with immense therapeutic, agricultural, and industrial potential. These small molecules, including antibiotics, immunosuppressants, and anticancer agents, are synthe...
Fungi Multigene Family Gene Expression Regulation, Fungal Biosynthetic Pathways Secondary Metabolism Metabolic Engineering
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Toward an integrated omics approach for plant biosynthetic pathway discovery in the age of AI.

Trends in biochemical sciences Feb 24, 2025
Elucidating plant biosynthetic pathways is key to advancing a sustainable bioeconomy by enabling access to complex natural products through synthetic biology. Despite progress from genomic, transcriptomic, and metabolomic approaches, much multiomics ...
Artificial Intelligence Genomics Metabolomics Plants Biosynthetic Pathways
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Artificial Intelligence Methods and Models for Retro-Biosynthesis: A Scoping Review.

ACS synthetic biology Jul 24, 2024
Retrosynthesis aims to efficiently plan the synthesis of desirable chemicals by strategically breaking down molecules into readily available building block compounds. Having a long history in chemistry, retro-biosynthesis has also been used in the fi...
Artificial Intelligence Synthetic Biology Biocatalysis Biosynthetic Pathways
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Unlocking plant bioactive pathways: omics data harnessing and machine learning assisting.

Current opinion in biotechnology May 9, 2024
Plant bioactives hold immense potential in the medicine and food industry. The recent advancements in omics applied in deciphering specialized metabolic pathways underscore the importance of high-quality genome releases and the wealth of data in meta...
Machine Learning Genomics Metabolomics Biological Products Plants Biosynthetic Pathways
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Rational construction of synthetic consortia: Key considerations and model-based methods for guiding the development of a novel biosynthesis platform.

Biotechnology advances Mar 24, 2024
The rapid development of synthetic biology has significantly improved the capabilities of mono-culture systems in converting different substrates into various value-added bio-chemicals through metabolic engineering. However, overexpression of biosynt...
Artificial Intelligence Synthetic Biology Microbial Consortia Biosynthetic Pathways Metabolic Engineering
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Enabling pathway design by multiplex experimentation and machine learning.

Metabolic engineering Nov 30, 2023
The remarkable metabolic diversity observed in nature has provided a foundation for sustainable production of a wide array of valuable molecules. However, transferring the biosynthetic pathway to the desired host often runs into inherent failures tha...
Machine Learning Biosynthetic Pathways Metabolic Engineering
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Design, Evaluation, and Implementation of Synthetic Isopentyldiol Pathways in .

ACS synthetic biology Oct 23, 2023
Isopentyldiol (IPDO) is an important raw material in the cosmetic industry. So far, IPDO is exclusively produced through chemical synthesis. Growing interest in natural personal care products has inspired the quest to develop a biobased process. We p...
Artificial Intelligence Escherichia coli Biosynthetic Pathways Metabolic Engineering
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Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP.

Nature communications Jun 10, 2022
The complete biosynthetic pathways are unknown for most natural products (NPs), it is thus valuable to make computer-aided bio-retrosynthesis predictions. Here, a navigable and user-friendly toolkit, BioNavi-NP, is developed to predict the biosynthet...
Neural Networks, Computer Algorithms Deep Learning Biological Products Biosynthetic Pathways
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Deep Learning to Predict the Biosynthetic Gene Clusters in Bacterial Genomes.

Journal of molecular biology May 6, 2022
Biosynthetic gene clusters (BGCs) in bacterial genomes code for important small molecules and secondary metabolites. Based on the validated BGCs and the corresponding sequences of protein family domains (Pfams), Pfam functions and clan information, w...
Deep Learning Bacteria Multigene Family Biosynthetic Pathways Genome, Bacterial
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NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products.

Journal of natural products Oct 18, 2021
Computational approaches such as genome and metabolome mining are becoming essential to natural products (NPs) research. Consequently, a need exists for an automated structure-type classification system to handle the massive amounts of data appearing...
Neural Networks, Computer Biological Products Biosynthetic Pathways
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