A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)
Genome-scale stoichiometric modeling of metabolism has become a standard systems
biology tool for modeling cellular physiology and growth. Extensions of this approach are …
biology tool for modeling cellular physiology and growth. Extensions of this approach are …
Recent advances in systems and synthetic biology approaches for developing novel cell-factories in non-conventional yeasts
Microbial bioproduction of chemicals, proteins, and primary metabolites from cheap carbon
sources is currently an advancing area in industrial research. The model yeast …
sources is currently an advancing area in industrial research. The model yeast …
[HTML][HTML] Metabolic modeling of single Th17 cells reveals regulators of autoimmunity
Metabolism is a major regulator of immune cell function, but it remains difficult to study the
metabolic status of individual cells. Here, we present Compass, an algorithm to characterize …
metabolic status of individual cells. Here, we present Compass, an algorithm to characterize …
Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism
Through advanced mechanistic modeling and the generation of large high-quality datasets,
machine learning is becoming an integral part of understanding and engineering living …
machine learning is becoming an integral part of understanding and engineering living …
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0
Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic
framework for integrative analysis of experimental molecular systems biology data and …
framework for integrative analysis of experimental molecular systems biology data and …
Metabolic interaction models recapitulate leaf microbiota ecology
Resource allocation affects the structure of microbiomes, including those associated with
living hosts. Understanding the degree to which this dependency determines interspecies …
living hosts. Understanding the degree to which this dependency determines interspecies …
An atlas of human metabolism
Genome-scale metabolic models (GEMs) are valuable tools to study metabolism and
provide a scaffold for the integrative analysis of omics data. Researchers have developed …
provide a scaffold for the integrative analysis of omics data. Researchers have developed …
Rewriting yeast central carbon metabolism for industrial isoprenoid production
AL Meadows, KM Hawkins, Y Tsegaye, E Antipov… - Nature, 2016 - nature.com
A bio-based economy has the potential to provide sustainable substitutes for petroleum-
based products and new chemical building blocks for advanced materials. We previously …
based products and new chemical building blocks for advanced materials. We previously …
Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints
Genome‐scale metabolic models (GEM s) are widely used to calculate metabolic
phenotypes. They rely on defining a set of constraints, the most common of which is that the …
phenotypes. They rely on defining a set of constraints, the most common of which is that the …
[HTML][HTML] Metabolic functions of gut microbes associate with efficacy of tumor necrosis factor antagonists in patients with inflammatory bowel diseases
Background & Aims Altered interactions between the mucosal immune system and intestinal
microbiota contribute to pathogenesis of inflammatory bowel diseases (IBD). It is not clear …
microbiota contribute to pathogenesis of inflammatory bowel diseases (IBD). It is not clear …