ArticleMolecular systems biology2020
Modeling tissue-relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels.
Article in Molecular systems biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Neuropeptides NLP-10 and FLP-18 stimulate lipid catabolism in chronically diet-restrictedbioRxiv : the preprint server for biology · 2026Article
- Glycolytic Specialization Shapes Neuronal Physiology and FunctionbioRxiv : the preprint server for biology · 2026Article
- LumbriCyc: towards metabolic modelling of earthworms.NPJ systems biology and applications · 2026Article
- Flux sampling and context-specific genome-scale metabolic models for biotechnological applications.Trends in biotechnology · 2026Review
- Modeling tissue-specific Drosophila metabolism identifies high sugar diet-induced metabolic dysregulation in muscle at reaction and pathway levels.Nature communications · 2026Article
- Caenorhabditis elegans as an experimental model for resilience-boosting microbiota interventions in nonmodel ectotherms.FEMS microbiology reviews · 2026Review
- Resolving tissue and cellular functions of parasitic nematodes.Trends in parasitology · 2025Review
- Polyketide synthase-derived sphingolipids mediate microbiota protection against a bacterial pathogen in C. elegans.Nature communications · 2025Article
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- Eukaryotic Elongation Factor 2 Kinase EFK-1/eEF2K promotes starvation resistance by preventing oxidative damage in C. elegans.Nature communications · 2025Article
- Host-microbe interactions rewire metabolism in a C. elegans model of leucine breakdown deficiency.Nature metabolism · 2024Article
- Genome-scale metabolic models applied for human health and biopharmaceutical engineering.Quantitative biology (Beijing, China) · 2023Review
- A genome-scale metabolic model of parasitic whipworm.Nature communications · 2023Article
- Integrated Analysis of Transcriptome and Metabolome Provides Insight intoInternational journal of molecular sciences · 2023Article
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- A transcriptional cofactor regulatory network for the C. elegans intestine.G3 (Bethesda, Md.) · 2023Article
- Taurine deficiency as a driver of aging.Science (New York, N.Y.) · 2023Article
- Systems-level transcriptional regulation of Caenorhabditis elegans metabolism.Molecular systems biology · 2023Article
- A D-2-hydroxyglutarate dehydrogenase mutant reveals a critical role for ketone body metabolism in Caenorhabditis elegans development.PLoS biology · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Metabolism is a highly compartmentalized process that provides building blocks for biomass generation during development, homeostasis, and wound healing, and energy to support cellular and organismal processes. In metazoans, different cells and tissues specialize in different aspects of metabolism. However, studying the compartmentalization of metabolism in different cell types in a whole animal and for a particular stage of life is difficult. Here, we present MEtabolic models Reconciled with Gene Expression (MERGE), a computational pipeline that we used to predict tissue-relevant metabolic function at the network, pathway, reaction, and metabolite levels based on single-cell RNA-sequencing (scRNA-seq) data from the nematode Caenorhabditis elegans. Our analysis recapitulated known tissue functions in C. elegans, captured metabolic properties that are shared with similar tissues in human, and provided predictions for novel metabolic functions. MERGE is versatile and applicable to other systems. We envision this work as a starting point for the development of metabolic network models for individual cells as scRNA-seq continues to provide higher-resolution gene expression data.
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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.