ArticleNature communications2025
Designing pathways for bioproducing complex chemicals by combining tools for pathway extraction and ranking.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
4 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Microbial bioleaching of rare earth elements from phosphate minerals: a biotechnology-driven systematic review of mechanisms, bioprocess determinants, and opportunities for sustainable recovery.BMC biotechnology · 2026Pooled it
- Nature-Inspired Enzymatic Cascades: Emerging Strategies for Sustainable Chemistry.Molecules (Basel, Switzerland) · 2026Review
- Computational tools for nonnatural pathway design: Algorithms, applications, and challenges.Biodesign research · 2025Review
- Designing pathways for bioproducing complex chemicals by combining tools for pathway extraction and ranking.Nature communications · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The synthesis of many important biochemicals involves complex molecules and numerous reactions. The design and optimization of whole-cell biocatalysts for the production of these molecules requires metabolic modeling to extract production pathways from biochemical databases and integrate them into genome-scale models of the host. However, the synthesis of such complex molecules often requires reactions from multiple pathways operating in balanced subnetworks that are not assembled in existing databases. Here, we present SubNetX, a computational algorithm that extracts reactions from a database and assembles balanced subnetworks to produce a target biochemical from selected precursor metabolites, energy currencies, and cofactors. These subnetworks can be integrated into whole-cell models, allowing the reconstruction and ranking of alternative biosynthetic pathways based on yield, length, and other design goals. We apply SubNetX to 70 industrially relevant natural and synthetic chemicals to demonstrate the application of this pipeline.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.