ArticlePLoS computational biology2014
Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- Constraint-Based Metabolic Modeling Approach for Microbial Communities.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Moving from genome-scale to community-scale metabolic models for the human gut microbiome.Nature microbiology · 2025Review
- Control Theory and Systems Biology: Potential Applications in Neurodegeneration and Search for Therapeutic Targets.International journal of molecular sciences · 2023Review
- Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations.Briefings in bioinformatics · 2023Review
- Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability.Materials today. Bio · 2023Article
- Reconciliation and evolution of Penicillium rubens genome-scale metabolic networks-What about specialised metabolism?PloS one · 2023Article
- Predictive evolution of metabolic phenotypes using model-designed environments.Molecular systems biology · 2022Article
- A Computational Toolbox to Investigate the Metabolic Potential and Resource Allocation in Fission Yeast.mSystems · 2022Article
- Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer.Frontiers in oncology · 2022Review
- Assessing the intracellular primary metabolic profile ofFrontiers in fungal biology · 2022Article
- Review
- Genome Scale Modeling to Study the Metabolic Competition between Cells in the Tumor Microenvironment.Cancers · 2021Review
- Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels.The ISME journal · 2021Article
- Addressing uncertainty in genome-scale metabolic model reconstruction and analysis.Genome biology · 2021Review
- Antibiotic resistance: Time of synthesis in a post-genomic age.Computational and structural biotechnology journal · 2021Review
- Ancestral state reconstruction of metabolic pathways across pangenome ensembles.Microbial genomics · 2020Article
- New Therapeutic Candidates for the Treatment of Malassezia pachydermatis -Associated Infections.Scientific reports · 2020Article
- OptFill: A Tool for Infeasible Cycle-Free Gapfilling of Stoichiometric Metabolic Models.iScience · 2020Article
- Article
- Succession of physiological stages hallmarks the transcriptomic response of the fungusBiotechnology for biofuels · 2020Article
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We introduce a novel computational approach, CoReCo, for comparative metabolic reconstruction and provide genome-scale metabolic network models for 49 important fungal species. Leveraging on the exponential growth in sequenced genome availability, our method reconstructs genome-scale gapless metabolic networks simultaneously for a large number of species by integrating sequence data in a probabilistic framework. High reconstruction accuracy is demonstrated by comparisons to the well-curated Saccharomyces cerevisiae consensus model and large-scale knock-out experiments. Our comparative approach is particularly useful in scenarios where the quality of available sequence data is lacking, and when reconstructing evolutionary distant species. Moreover, the reconstructed networks are fully carbon mapped, allowing their use in 13C flux analysis. We demonstrate the functionality and usability of the reconstructed fungal models with computational steady-state biomass production experiment, as these fungi include some of the most important production organisms in industrial biotechnology. In contrast to many existing reconstruction techniques, only minimal manual effort is required before the reconstructed models are usable in flux balance experiments. CoReCo is available at http://esaskar.github.io/CoReCo/.
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