Using genome-scale models to predict biological capabilities
Constraint-based reconstruction and analysis (COBRA) methods at the genome scale have
been under development since the first whole-genome sequences appeared in the mid …
been under development since the first whole-genome sequences appeared in the mid …
Constraint-based models predict metabolic and associated cellular functions
The prediction of cellular function from a genotype is a fundamental goal in biology. For
metabolism, constraint-based modelling methods systematize biochemical, genetic and …
metabolism, constraint-based modelling methods systematize biochemical, genetic and …
Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase
Metabolic networks are interconnected and influence diverse cellular processes. The protein-
metabolite interactions that mediate these networks are frequently low affinity and …
metabolite interactions that mediate these networks are frequently low affinity and …
High-resolution 13C metabolic flux analysis
CP Long, MR Antoniewicz - Nature protocols, 2019 - nature.com
Precise quantification of metabolic pathway fluxes in biological systems is of major
importance in guiding efforts in metabolic engineering, biotechnology, microbiology, human …
importance in guiding efforts in metabolic engineering, biotechnology, microbiology, human …
A guide to 13C metabolic flux analysis for the cancer biologist
MR Antoniewicz - Experimental & molecular medicine, 2018 - nature.com
Cancer metabolism is significantly altered from normal cellular metabolism allowing cancer
cells to adapt to changing microenvironments and maintain high rates of proliferation. In the …
cells to adapt to changing microenvironments and maintain high rates of proliferation. In the …
A guide to metabolic flux analysis in metabolic engineering: Methods, tools and applications
MR Antoniewicz - Metabolic engineering, 2021 - Elsevier
The field of metabolic engineering is primarily concerned with improving the biological
production of value-added chemicals, fuels and pharmaceuticals through the design …
production of value-added chemicals, fuels and pharmaceuticals through the design …
LC‐MS data processing with MAVEN: a metabolomic analysis and visualization engine
MF Clasquin, E Melamud… - Current protocols in …, 2012 - Wiley Online Library
MAVEN is an open‐source software program for interactive processing of LC‐MS‐based
metabolomics data. MAVEN enables rapid and reliable metabolite quantitation from multiple …
metabolomics data. MAVEN enables rapid and reliable metabolite quantitation from multiple …
High-throughput generation, optimization and analysis of genome-scale metabolic models
Genome-scale metabolic models have proven to be valuable for predicting organism
phenotypes from genotypes. Yet efforts to develop new models are failing to keep pace with …
phenotypes from genotypes. Yet efforts to develop new models are failing to keep pace with …
Metabolic engineering of microorganisms for production of aromatic compounds
D Huccetogullari, ZW Luo, SY Lee - Microbial Cell Factories, 2019 - Springer
Metabolic engineering has been enabling development of high performance microbial
strains for the efficient production of natural and non-natural compounds from renewable …
strains for the efficient production of natural and non-natural compounds from renewable …
Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli
D McCloskey, BØ Palsson, AM Feist - Molecular systems biology, 2013 - embopress.org
The genome‐scale model (GEM) of metabolism in the bacterium Escherichia coli K‐12 has
been in development for over a decade and is now in wide use. GEM‐enabled studies of E …
been in development for over a decade and is now in wide use. GEM‐enabled studies of E …