ReviewComputational and structural biotechnology journal2014
Methods for integration of transcriptomic data in genome-scale metabolic models.
Review in Computational and structural biotechnology journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- A fusion-based multiomics classification approach for enhanced gene discovery in non-small cell lung cancer.Bioinformatics advances · 2026Article
- In vivo and in silico models of Drosophila for Parkinson's disease.The FEBS journal · 2025Review
- MitoMAMMAL: a genome scale model of mammalian mitochondria predicts cardiac and BAT metabolism.Bioinformatics advances · 2025Article
- Review
- Biocontrol in built environments to reduce pathogen exposure and infection risk.The ISME journal · 2024Review
- A multi-organ maize metabolic model connects temperature stress with energy production and reducing power generation.iScience · 2023Article
- Genome-scale modeling predicts metabolic differences between macrophage subtypes in colorectal cancer.iScience · 2023Article
- Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook.PLoS computational biology · 2023Review
- Ensemble-based genome-scale modeling predicts metabolic differences between macrophage subtypes in colorectal cancer.bioRxiv : the preprint server for biology · 2023Article
- Computational Approaches to Assess Abnormal Metabolism in Alzheimer's Disease Using Transcriptomics.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Tuning a high performing multiplexed-CRISPRiMetabolic engineering communications · 2022Article
- Fuzzy optimization for identifying anti-cancer targets with few side effects in constraint-based models of head and neck cancer.Royal Society open science · 2022Article
- What are housekeeping genes?PLoS computational biology · 2022Article
- Article
- Dual RNA Sequencing ofInternational journal of molecular sciences · 2022Article
- Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism.BMC bioinformatics · 2021Article
- Path to improving the life cycle and quality of genome-scale models of metabolism.Cell systems · 2021Review
- Resolving trained immunity with systems biology.European journal of immunology · 2021Review
- Guided extraction of genome-scale metabolic models for the integration and analysis of omics data.Computational and structural biotechnology journal · 2021Article
- Advances in flux balance analysis by integrating machine learning and mechanism-based models.Computational and structural biotechnology journal · 2021Review
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2 authors.
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Abstract
Several computational methods have been developed that integrate transcriptomic data with genome-scale metabolic reconstructions to infer condition-specific system-wide intracellular metabolic flux distributions. In this mini-review, we describe each of these methods published to date with categorizing them based on four different grouping criteria (requirement for multiple gene expression datasets as input, requirement for a threshold to define a gene's high and low expression, requirement for a priori assumption of an appropriate objective function, and validation of predicted fluxes directly against measured intracellular fluxes). Then, we recommend which group of methods would be more suitable from a practical perspective.
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