ArticleGenome biology2012
FOCAL: an experimental design tool for systematizing metabolic discoveries and model development.
Article in Genome biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Metabolite coupling analysis and metabolite-flux coupling analysis of genome-scale metabolic models.Frontiers in bioinformatics · 2026Article
- Metabolic growth-coupling strategies forMetabolic engineering communications · 2025Article
- Dissimilar gene repertoires ofFrontiers in plant science · 2023Article
- StrainDesign: a comprehensive Python package for computational design of metabolic networks.Bioinformatics (Oxford, England) · 2022Article
- Examining organic acid production potential and growth-coupled strategies in Issatchenkia orientalis using constraint-based modeling.Biotechnology progress · 2022Article
- An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets.PLoS computational biology · 2020Article
- Integrating proteomic or transcriptomic data into metabolic models using linear bound flux balance analysis.Bioinformatics (Oxford, England) · 2018Article
- Model-enabled gene search (MEGS) allows fast and direct discovery of enzymatic and transport gene functions in the marine bacteriumThe Journal of biological chemistry · 2017Article
- MapMaker and PathTracer for tracking carbon in genome-scale metabolic models.Biotechnology journal · 2016Article
- Expanding Metabolic Engineering Algorithms Using Feasible Space and Shadow Price Constraint Modules.Metabolic engineering communications · 2014Article
- BioMog: a computational framework for the de novo generation or modification of essential biomass components.PloS one · 2013Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Current computational tools can generate and improve genome-scale models based on existing data; however, for many organisms, the data needed to test and refine such models are not available. To facilitate model development, we created the forced coupling algorithm, FOCAL, to identify genetic and environmental conditions such that a reaction becomes essential for an experimentally measurable phenotype. This reaction's conditional essentiality can then be tested experimentally to evaluate whether network connections occur or to create strains with desirable phenotypes. FOCAL allows network connections to be queried, which improves our understanding of metabolism and accuracy of developed models.
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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.