Research Articles
CarveMe vs gapseq vs KBase: A 2024 Researcher's Guide to Metabolic Network Reconstruction
This article provides a comprehensive, evidence-based comparison of three leading automated tools for genome-scale metabolic model (GEM) reconstruction: CarveMe, gapseq, and KBase.
Consensus Reconstruction for Microbial Community Models: A Framework for Enhanced Metabolic Prediction and Clinical Application
This article provides a comprehensive guide to consensus reconstruction for genome-scale metabolic models (GEMs) of microbial communities, a method that synthesizes outputs from multiple automated tools to create more accurate...
Dead-End Metabolites: A Comprehensive Guide for Researchers from Detection to Clinical Impact
This guide provides a systematic overview of dead-end metabolites (DEMs) in metabolic networks, crucial yet often overlooked components that signify gaps in metabolic knowledge.
Complete fastGapFill Tutorial: Efficient Gap Filling for Compartmentalized Metabolic Models in Biomedical Research
This comprehensive tutorial provides researchers and drug development professionals with practical guidance for using fastGapFill to resolve metabolic gaps in compartmentalized genome-scale metabolic reconstructions.
Stoichiometric Inconsistency and Network Gaps: From Detection to Resolution in Metabolic Models
This article explores the critical challenge of stoichiometric inconsistencies in genome-scale metabolic models (GEMs) and their role in creating network gaps that impair predictive accuracy.
Flux Consistency in Metabolic Models: A Guide to Reliable Predictions for Biomedical Research
This article provides a comprehensive overview of flux consistency in genome-scale metabolic models (GEMs), a critical factor for generating reliable predictions in biomedical and biotechnological applications.
Compartmentalization in Metabolic Networks: Uncovering and Addressing Gaps for Drug Discovery and Systems Biology
This article explores the critical yet underexplored role of cellular compartmentalization in creating and complicating gaps within genome-scale metabolic models (GEMs).
Identifying Blocked Reactions in Metabolic Networks: Methods, Tools, and Clinical Applications
This article provides a comprehensive guide for researchers and drug development professionals on identifying and resolving blocked reactions in genome-scale metabolic models (GEMs).
Bridging Knowledge Gaps: How KEGG and Universal Databases Power Metabolic Network Reconstruction
This article explores the critical role of universal biochemical databases, with a focus on the Kyoto Encyclopedia of Genes and Genomes (KEGG), in addressing knowledge gaps in genome-scale metabolic models...
Bridging the Gaps: A Comprehensive Guide to Network Gaps in Genome-Scale Metabolic Reconstructions
Genome-scale metabolic reconstructions (GENREs) are powerful computational tools that map an organism's metabolism from its genome.