Search results for "Genome-scale metabolic model"
showing 5 items of 5 documents
Boosting Biomass Quantity and Quality by Improved Mixotrophic Culture of the Diatom Phaeodactylum tricornutum
2021
Diatoms are photoautotrophic unicellular algae and are among the most abundant, adaptable, and diverse marine phytoplankton. They are extremely interesting not only for their ecological role but also as potential feedstocks for sustainable biofuels and high-value commodities such as omega fatty acids, because of their capacity to accumulate lipids. However, the cultivation of microalgae on an industrial scale requires higher cell densities and lipid accumulation than those found in nature to make the process economically viable. One of the known ways to induce lipid accumulation in Phaeodactylum tricornutum is nitrogen deprivation, which comes at the expense of growth inhibition and lower c…
EFMviz
2020
Elementary Flux Modes (EFMs) are a tool for constraint-based modeling and metabolic network analysis. However, systematic and automated visualization of EFMs, capable of integrating various data types is still a challenge. In this study, we developed an extension for the widely adopted COBRA Toolbox, EFMviz, for analysis and graphical visualization of EFMs as networks of reactions, metabolites and genes. The analysis workflow offers a platform for EFM visualization to improve EFM interpretability by connecting COBRA toolbox with the network analysis and visualization software Cytoscape. The biological applicability of EFMviz is demonstrated in two use cases on medium (Escherichia coli, iAF1…
In silico exploration of Mycobacterium tuberculosis metabolic networks shows host-associated convergent fluxomic phenotypes
2022
This article belongs to the Special Issue Computational Approaches for the Study of Biomolecular Networks
Sustainable metabolic engineering for sustainability optimisation of industrial biotechnology
2021
Industrial biotechnology represents one of the most innovating and labour-productive industries with an estimated stable economic growth, thus giving space for improvement of the existing and setting up new value chains. In addition, biotechnology has clear environmental advantages over the chemical industry. Still, biotechnology’s environmental contribution is sometimes valued with controversy and societal aspects are frequently ignored. Environmental, economic and societal sustainability of various bioprocesses becomes increasingly important due to the growing understanding about complex and interlinked consequences of different human activities. Neglecting the sustainability issues in th…
Integrative Gene Expression and Metabolic Analysis Tool IgemRNA
2022
ABSTRACTGenome scale metabolic modelling is widely used technique to research metabolism impacts on organism’s properties. Additional omics data integration enables a more precise genotype-phenotype analysis for biotechnology, medicine and life sciences. Transcriptome data amounts rapidly increase each year. Many transcriptome analysis tools with integrated genome scale metabolic modelling are proposed. But these tools have own restrictions, compatibility issues and the necessity of previous experience and advanced user skills. We have analysed and classified published tools, summarized possible transcriptome pre-processing, and analysis methods and implemented them in the new transcriptome…