ArticleBMC systems biology2013
Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti.
Article in BMC systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
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- Constraint based modeling of drug induced metabolic changes in a cancer cell line.NPJ systems biology and applications · 2025Article
- ThermOptCobra: Thermodynamically optimal construction and analysis of metabolic networks for reliable phenotype predictions.iScience · 2025Article
- Comparative Transcriptomics of Fat Bodies between Symbiotic and Quasi-Aposymbiotic Adult Females ofInternational journal of molecular sciences · 2024Article
- Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism.Nature communications · 2023Article
- Coevolution of Metabolic Pathways in Blattodea and TheirMicrobiology spectrum · 2022Article
- Architect: A tool for aiding the reconstruction of high-quality metabolic models through improved enzyme annotation.PLoS computational biology · 2022Article
- ModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions.BMC bioinformatics · 2019Article
- Insights into metabolic osmoadaptation of the ectoines-producer bacterium Chromohalobacter salexigens through a high-quality genome scale metabolic model.Microbial cell factories · 2018Article
- Genome analysis of new Blattabacterium spp., obligatory endosymbionts of Periplaneta fuliginosa and P. japonica.PloS one · 2018Article
- Determinism and Contingency Shape Metabolic Complementation in an Endosymbiotic Consortium.Frontiers in microbiology · 2017Article
- Metabolic Complementation in Bacterial Communities: Necessary Conditions and Optimality.Frontiers in microbiology · 2016Article
- Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach.PloS one · 2015Article
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3 authors.
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Abstract
backgroundMetabolic reconstruction is the computational-based process that aims to elucidate the network of metabolites interconnected through reactions catalyzed by activities assigned to one or more genes. Reconstructed models may contain inconsistencies that appear as gap metabolites and blocked reactions. Although automatic methods for solving this problem have been previously developed, there are many situations where manual curation is still needed.
resultsWe introduce a general definition of gap metabolite that allows its detection in a straightforward manner. Moreover, a method for the detection of Unconnected Modules, defined as isolated sets of blocked reactions connected through gap metabolites, is proposed. The method has been successfully applied to the curation of iCG238, the genome-scale metabolic model for the bacterium Blattabacterium cuenoti, obligate endosymbiont of cockroaches.
conclusionWe found the proposed approach to be a valuable tool for the curation of genome-scale metabolic models. The outcome of its application to the genome-scale model B. cuenoti iCG238 is a more accurate model version named as B. cuenoti iMP240.
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