ArticleSTAR protocols2021
PhenoMapping: a protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models.
Article in STAR protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Modeling tissue-specific Drosophila metabolism identifies high sugar diet-induced metabolic dysregulation in muscle at reaction and pathway levels.Nature communications · 2026Article
- Metabolic network reconstruction as a resource for analyzing Salmonella Typhimurium SL1344 growth in the mouse intestine.PLoS computational biology · 2025Article
- Identification of high sugar diet-induced dysregulated metabolic pathways in muscle using tissue-specific metabolic models inbioRxiv : the preprint server for biology · 2024Article
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2 authors.
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Abstract
Targeted identification of cellular processes responsible for a phenotype is of major importance in guiding efforts in bioengineering and medicine. Genome-scale metabolic models (GEMs) are widely used to integrate various types of omics data and study the cellular physiology under different conditions. Here, we present PhenoMapping, a protocol that uses GEMs, omics, and phenotypic data to map cellular processes and observed phenotypes. PhenoMapping also classifies genes as conditionally and unconditionally essential and guides a comprehensive curation of GEMs. For complete details on the use and execution of this protocol, please refer to Stanway et al. (2019) and Krishnan et al. (2020).
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