ArticleCell reports methods2021
Model-based assessment of mammalian cell metabolic functionalities using omics data.
Article in Cell reports methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- NeuroMetBench: patient-aware evidence bounds for transcript-derived metabolic representations across cancer proteogenomic contexts.Functional & integrative genomics · 2026Article
- hypeR-GEM: connecting metabolite signatures to enzyme-coding genes via genome-scale metabolic models.Bioinformatics (Oxford, England) · 2026Article
- Metabolic Task Analysis Reveals Distinct Metabotypes in End-Stage Dilated Cardiomyopathy.Circulation. Genomic and precision medicine · 2026Article
- A community reconstruction of Chinese hamster metabolism and structural systems biology elucidate metabolic rewiring in lactate-free CHO cells.Cell systems · 2026Article
- Systematic data-driven genome-scale metabolic model reduction for bioprocess modeling: CHO culture case study.NPJ systems biology and applications · 2026Article
- Modeling tissue-specific Drosophila metabolism identifies high sugar diet-induced metabolic dysregulation in muscle at reaction and pathway levels.Nature communications · 2026Article
- hypeR-GEM: connecting metabolite signatures to enzyme-coding genes via genome-scale metabolic models.bioRxiv : the preprint server for biology · 2025Article
- Spatial Immunometabolism: Integrating Technologies to Decode Cellular Metabolism in Tissues.European journal of immunology · 2025Review
- Deciphering the determinants of recombinant protein expression across the human secretome.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Constraint based modeling of drug induced metabolic changes in a cancer cell line.NPJ systems biology and applications · 2025Article
- Accurate prediction of gene deletion phenotypes with Flux Cone Learning.Nature communications · 2025Article
- Temporal analysis of doxorubicin-induced cardiac toxicity and hypertrophy.NPJ systems biology and applications · 2025Article
- Atlas-scale metabolic activities inferred from single-cell and spatial transcriptomics.bioRxiv : the preprint server for biology · 2025Article
- Article
- Metabolic Objectives and Trade-Offs: Inference and Applications.Metabolites · 2025Review
- Inferring metabolic objectives and trade-offs in single cells during embryogenesis.Cell systems · 2025Article
- Cell-cell communication: new insights and clinical implications.Signal transduction and targeted therapy · 2024Review
- Integrating Genome-Scale Metabolic Models with Patient Plasma Metabolome to Study Endothelial Metabolism In Situ.International journal of molecular sciences · 2024Article
- MDIC3: Matrix decomposition to infer cell-cell communication.Patterns (New York, N.Y.) · 2024Article
- Inferring secretory and metabolic pathway activity from omic data with secCellFie.Metabolic engineering · 2024Article
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Authors and funding
20 authors.
Funding
Abstract
Omics experiments are ubiquitous in biological studies, leading to a deluge of data. However, it is still challenging to connect changes in these data to changes in cell functions because of complex interdependencies between genes, proteins, and metabolites. Here, we present a framework allowing researchers to infer how metabolic functions change on the basis of omics data. To enable this, we curated and standardized lists of metabolic tasks that mammalian cells can accomplish. Genome-scale metabolic networks were used to define gene sets associated with each metabolic task. We further developed a framework to overlay omics data on these sets and predict pathway usage for each metabolic task. We demonstrated how this approach can be used to quantify metabolic functions of diverse biological samples from the single cell to whole tissues and organs by using multiple transcriptomic datasets. To facilitate its adoption, we integrated the approach into GenePattern (www.genepattern.org-CellFie).
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