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Integration of graph neural networks and genome-scale metabolic models for predicting gene essentiality
Genome-scale metabolic models are powerful tools for understanding cellular physiology. Flux balance analysis (FBA), in particular, is an...
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Genome Scale Modeling for Novel Drug Targets
System-level metabolic research can make use of computational simulations of genome-scale modeling (GSM), this depict the relationships between genes...
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Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models
Genome-scale metabolic models (GEMs) are extensively used to simulate cell metabolism and predict cell phenotypes. GEMs can also be tailored to...
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ICON-GEMs: integration of co-expression network in genome-scale metabolic models, shedding light through systems biology
BackgroundFlux Balance Analysis (FBA) is a key metabolic modeling method used to simulate cellular metabolism under steady-state conditions. Its...
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Prediction of metabolites associated with somatic mutations in cancers by using genome-scale metabolic models and mutation data
BackgroundOncometabolites, often generated as a result of a gene mutation, show pro-oncogenic function when abnormally accumulated in cancer cells....
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Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts
BackgroundUse of alternative non- Saccharomyces yeasts in wine and beer brewing has gained more attention the recent years. This is both due to the...
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Genome-scale metabolic network models: from first-generation to next-generation
AbstractOver the last two decades, thousands of genome-scale metabolic network models (GSMMs) have been constructed. These GSMMs have been widely...
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Advances and applications of machine learning and intelligent optimization algorithms in genome-scale metabolic network models
Due to the increasing demand for microbially manufactured products in various industries, it has become important to find optimal designs for...
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In silico cell factory design driven by comprehensive genome-scale metabolic models: development and challenges
Genome-scale metabolic models (GEMs) have been widely used to design cell factories in silico. However, initial flux balance analysis only considers...
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Flux sampling in genome-scale metabolic modeling of microbial communities
BackgroundMicrobial communities play a crucial role in ecosystem function through metabolic interactions. Genome-scale modeling is a promising method...
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Chromosome-scale genome assembly of the ‘Munstead’ cultivar of Lavandula angustifolia
ObjectivesLavandula angustifolia (English lavender) is commercially important not only as an ornamental species but also as a major source of...
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The chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus uncovers patterns of genome evolution in mosquitoes
BackgroundUnderstanding genome organization and evolution is important for species involved in transmission of human diseases, such as mosquitoes....
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Metabolic Modeling of Wine Fermentation at Genome Scale
Wine fermentation is an ancient biotechnological process mediated by different microorganisms such as yeast and bacteria. Understanding of the...
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Characterization of large-scale genomic differences in the first complete human genome
BackgroundThe first telomere-to-telomere (T2T) human genome assembly (T2T-CHM13) release is a milestone in human genomics. The T2T-CHM13 genome...
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A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes
Quinoa ( Chenopodium quinoa Willd.) is an allotetraploid seed crop with the potential to help address global food security concerns. Genomes have been...
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Chromosome-scale assembly and annotation of the perennial ryegrass genome
BackgroundThe availability of chromosome-scale genome assemblies is fundamentally important to advance genetics and breeding in crops, as well as for...
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Genome-Scale Modeling and Systems Metabolic Engineering of Vibrio natriegens for the Production of 1,3-Propanediol
The fastest-growing bacterium Vibrio natriegens is a highly promising next-generation workhorse for molecular biology and industrial biotechnology....
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Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control
Algal cultivations are strongly influenced by light and dark cycles. In this study, genome-scale metabolic models were applied to optimize nutrient...
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A genome catalogue of lake bacterial diversity and its drivers at continental scale
Lakes are heterogeneous ecosystems inhabited by a rich microbiome whose genomic diversity is poorly defined. We present a continental-scale study of...
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Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine
The human microbiome influences the efficacy and safety of a wide variety of commonly prescribed drugs. Designing precision medicine approaches that...
