ReviewBriefings in bioinformatics2023
Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations.
Review in Briefings in bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Engineering cyanobacterial resilience for cadmium bioremediation: linking Cd speciation, cellular detoxification, and synthetic biology.RSC advances · 2026Review
- Thermo-flux: generation and analysis of thermodynamic-stoichiometric metabolic network models.Molecular systems biology · 2026Article
- Metabolic robustness is an emergent property of hierarchical network organization in yeast.mSystems · 2026Article
- Genome-Scale Metabolic Models Guided Improvement of Fermented Milk Quality and Flavor byFoods (Basel, Switzerland) · 2026Article
- NAViFluX: a visualization‑centric platform for interactive analysis, refinement and design of genome‑scale metabolic networks.Bioinformatics (Oxford, England) · 2026Article
- Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.NPJ biofilms and microbiomes · 2026Review
- Article
- Microbial and molecular approaches for PFAS transformation in soils: prospects and limitations.RSC advances · 2026Review
- Molecular adaptations and engineering of extremophiles for synthetic biology and biotechnological applications.Frontiers in microbiology · 2026Review
- Modelling reliable metabolic phenotypes by analysing the context-specific transcriptomics data.NPJ systems biology and applications · 2025Article
- Article
- Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.Briefings in bioinformatics · 2025Review
- A survey of computational approaches for characterizing microbial interactions in microbial mats.Genome biology · 2025Review
- Genomic and metabolic network properties in thermophiles and psychrophiles compared to mesophiles.Scientific reports · 2025Article
- Operationalizing Team Science at the Academic Cancer Center Network to Unveil the Structure and Function of the Gut Microbiome.Journal of clinical medicine · 2025Review
- Integration of metatranscriptomics data improves the predictive capacity of microbial community metabolic models.The ISME journal · 2025Article
- Article
- Preliminary Bioactivity Assessment ofJournal of fungi (Basel, Switzerland) · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Environmental perturbations are encountered by microorganisms regularly and will require metabolic adaptations to ensure an organism can survive in the newly presenting conditions. In order to study the mechanisms of metabolic adaptation in such conditions, various experimental and computational approaches have been used. Genome-scale metabolic models (GEMs) are one of the most powerful approaches to study metabolism, providing a platform to study the systems level adaptations of an organism to different environments which could otherwise be infeasible experimentally. In this review, we are describing the application of GEMs in understanding how microbes reprogram their metabolic system as a result of environmental variation. In particular, we provide the details of metabolic model reconstruction approaches, various algorithms and tools for model simulation, consequences of genetic perturbations, integration of '-omics' datasets for creating context-specific models and their application in studying metabolic adaptation due to the change in environmental conditions.
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Registered trials
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