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 …
A linked organ-on-chip model of the human neurovascular unit reveals the metabolic coupling of endothelial and neuronal cells
The neurovascular unit (NVU) regulates metabolic homeostasis as well as drug
pharmacokinetics and pharmacodynamics in the central nervous system. Metabolic fluxes …
pharmacokinetics and pharmacodynamics in the central nervous system. Metabolic fluxes …
Metabolic network analysis reveals altered bile acid synthesis and metabolism in Alzheimer's disease
Increasing evidence suggests Alzheimer's disease (AD) pathophysiology is influenced by
primary and secondary bile acids, the end product of cholesterol metabolism. We analyze …
primary and secondary bile acids, the end product of cholesterol metabolism. We analyze …
Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
Reconstructed microbial metabolic networks facilitate a mechanistic description of the
genotype–phenotype relationship through the deployment of constraint-based …
genotype–phenotype relationship through the deployment of constraint-based …
Astrocyte immunometabolic regulation of the tumour microenvironment drives glioblastoma pathogenicity
R Perelroizen, B Philosof, N Budick-Harmelin… - Brain, 2022 - academic.oup.com
Malignant brain tumours are the cause of a disproportionate level of morbidity and mortality
among cancer patients, an unfortunate statistic that has remained constant for decades …
among cancer patients, an unfortunate statistic that has remained constant for decades …
Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT
Development of high throughput analytical methods has given physicians the potential
access to extensive and patient-specific data sets, such as gene sequences, gene …
access to extensive and patient-specific data sets, such as gene sequences, gene …
OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities
AR Zomorrodi, CD Maranas - PLoS computational biology, 2012 - journals.plos.org
Microorganisms rarely live isolated in their natural environments but rather function in
consolidated and socializing communities. Despite the growing availability of high …
consolidated and socializing communities. Despite the growing availability of high …
Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE
Background Human tissues perform diverse metabolic functions. Mapping out these tissue-
specific functions in genome-scale models will advance our understanding of the metabolic …
specific functions in genome-scale models will advance our understanding of the metabolic …
A systematic evaluation of methods for tailoring genome-scale metabolic models
Genome-scale models of metabolism can illuminate the molecular basis of cell phenotypes.
Since some enzymes are only active in specific cell types, several algorithms use omics data …
Since some enzymes are only active in specific cell types, several algorithms use omics data …