ReviewSynthetic and systems biotechnology2017
A review of computational tools for design and reconstruction of metabolic pathways.
Review in Synthetic and systems biotechnology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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The trial behind it
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Who cites it
43 citing papers in PubMed.
- Predicting the pathway involvement of metabolites annotated in the MetaCyc knowledgebase.BMC bioinformatics · 2026Article
- Productive chaos and precision engineering: decoupling discovery from manufacturing to revolutionize plant-inspired therapeutics.Frontiers in plant science · 2026Article
- NOCTIS: open-source toolkit that turns reaction data into actionable graph networks.Journal of cheminformatics · 2025Article
- novoStoic2.0: An integrated framework for pathway synthesis, thermodynamic evaluation, and enzyme selection.PLoS computational biology · 2025Article
- Designing pathways for bioproducing complex chemicals by combining tools for pathway extraction and ranking.Nature communications · 2025Article
- Review
- Quantification of total uncertainty in the physics-informed reconstruction of CVSim-6 physiology.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2025Article
- Recent advances in genetic engineering and chemical production in yeast species.FEMS yeast research · 2025Review
- Evolutionary engineering ofScience advances · 2024Article
- BayesianSSA: a Bayesian statistical model based on structural sensitivity analysis for predicting responses to enzyme perturbations in metabolic networks.BMC bioinformatics · 2024Article
- Quantification of total uncertainty in the physics-informed reconstruction of CVSim-6 physiology.ArXiv · 2024Article
- A deep learning architecture for metabolic pathway prediction.Bioinformatics (Oxford, England) · 2024Article
- Predicting pathways for old and new metabolites through clustering.Journal of theoretical biology · 2024Article
- Metabolic Connectome and Its Role in the Prediction, Diagnosis, and Treatment of Complex Diseases.Metabolites · 2024Review
- Computer-aided design and implementation of efficient biosynthetic pathways to produce high added-value products derived from tyrosine inFrontiers in bioengineering and biotechnology · 2024Article
- Plants and endophytes interaction: a "secret wedlock" for sustainable biosynthesis of pharmaceutically important secondary metabolites.Microbial cell factories · 2023Review
- Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook.PLoS computational biology · 2023Review
- COVRECON: automated integration of genome- and metabolome-scale network reconstruction and data-driven inverse modeling of metabolic interaction networks.Bioinformatics (Oxford, England) · 2023Article
- From degrader to producer: reversing the gallic acid metabolism of Pseudomonas putida KT2440.International microbiology : the official journal of the Spanish Society for Microbiology · 2023Article
- Biomanufacturing by In Vitro Biotransformation (ivBT) Using Purified Cascade Multi-enzymes.Advances in biochemical engineering/biotechnology · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metabolic pathways reflect an organism's chemical repertoire and hence their elucidation and design have been a primary goal in metabolic engineering. Various computational methods have been developed to design novel metabolic pathways while taking into account several prerequisites such as pathway stoichiometry, thermodynamics, host compatibility, and enzyme availability. The choice of the method is often determined by the nature of the metabolites of interest and preferred host organism, along with computational complexity and availability of software tools. In this paper, we review different computational approaches used to design metabolic pathways based on the reaction network representation of the database (i.e., graph or stoichiometric matrix) and the search algorithm (i.e., graph search, flux balance analysis, or retrosynthetic search). We also put forth a systematic workflow that can be implemented in projects requiring pathway design and highlight current limitations and obstacles in computational pathway design.
Identifiers
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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.