Current status and applications of genome-scale metabolic models
Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction
associations for entire metabolic genes in an organism, and can be simulated to predict …
associations for entire metabolic genes in an organism, and can be simulated to predict …
Recent advances in metabolic engineering of Saccharomyces cerevisiae: new tools and their applications
Metabolic engineering aims to develop efficient cell factories by rewiring cellular
metabolism. As one of the most commonly used cell factories, Saccharomyces cerevisiae …
metabolism. As one of the most commonly used cell factories, Saccharomyces cerevisiae …
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2. 0
Over the past decade, a growing community of researchers has emerged around the use of
constraint-based reconstruction and analysis (COBRA) methods to simulate, analyze and …
constraint-based reconstruction and analysis (COBRA) methods to simulate, analyze and …
Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy
WB Dunn, DI Broadhurst, HJ Atherton… - Chemical society …, 2011 - pubs.rsc.org
The study of biological systems in a holistic manner (systems biology) is increasingly being
viewed as a necessity to provide qualitative and quantitative descriptions of the emergent …
viewed as a necessity to provide qualitative and quantitative descriptions of the emergent …
Applications of genome‐scale metabolic reconstructions
The availability and utility of genome‐scale metabolic reconstructions have exploded since
the first genome‐scale reconstruction was published a decade ago. Reconstructions have …
the first genome‐scale reconstruction was published a decade ago. Reconstructions have …
The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum
We present the RAVEN (R econstruction, A nalysis and V isualization of M e tabolic N
etworks) Toolbox: a software suite that allows for semi-automated reconstruction of genome …
etworks) Toolbox: a software suite that allows for semi-automated reconstruction of genome …
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
Genomic data allow the large-scale manual or semi-automated assembly of metabolic
network reconstructions, which provide highly curated organism-specific knowledge bases …
network reconstructions, which provide highly curated organism-specific knowledge bases …
Connecting extracellular metabolomic measurements to intracellular flux states in yeast
ML Mo, BØ Palsson, MJ Herrgård - BMC systems biology, 2009 - Springer
Background Metabolomics has emerged as a powerful tool in the quantitative identification
of physiological and disease-induced biological states. Extracellular metabolome or …
of physiological and disease-induced biological states. Extracellular metabolome or …
Addressing uncertainty in genome-scale metabolic model reconstruction and analysis
The reconstruction and analysis of genome-scale metabolic models constitutes a powerful
systems biology approach, with applications ranging from basic understanding of genotype …
systems biology approach, with applications ranging from basic understanding of genotype …
Genome-scale modeling of yeast metabolism: retrospectives and perspectives
Yeasts have been widely used for production of bread, beer and wine, as well as for
production of bioethanol, but they have also been designed as cell factories to produce …
production of bioethanol, but they have also been designed as cell factories to produce …