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Metabolic engineering in methanotrophic bacteria
Methane, as natural gas or biogas, is the least expensive source of carbon for (bio) chemical
synthesis. Scalable biological upgrading of this simple alkane to chemicals and fuels can …
synthesis. Scalable biological upgrading of this simple alkane to chemicals and fuels can …
Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis
Because they mainly do not involve chemical changes, membrane transporters have been a
Cinderella subject in the biotechnology of small molecule production, but this is a serious …
Cinderella subject in the biotechnology of small molecule production, but this is a serious …
Metabolic landscape of the tumor microenvironment at single cell resolution
The tumor milieu consists of numerous cell types each existing in a different environment.
However, a characterization of metabolic heterogeneity at single-cell resolution is not …
However, a characterization of metabolic heterogeneity at single-cell resolution is not …
Acetate metabolism and the inhibition of bacterial growth by acetate
During aerobic growth on glucose, Escherichia coli excretes acetate, a mechanism called
“overflow metabolism.” At high concentrations, the secreted acetate inhibits growth. Several …
“overflow metabolism.” At high concentrations, the secreted acetate inhibits growth. Several …
Recon 2.2: from reconstruction to model of human metabolism
Introduction The human genome-scale metabolic reconstruction details all known metabolic
reactions occurring in humans, and thereby holds substantial promise for studying complex …
reactions occurring in humans, and thereby holds substantial promise for studying complex …
Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
Constraint-based models of metabolism are a widely used framework for predicting flux
distributions in genome-scale biochemical networks. The number of published methods for …
distributions in genome-scale biochemical networks. The number of published methods for …
A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data
The metabolic heterogeneity and metabolic interplay between cells are known as significant
contributors to disease treatment resistance. However, with the lack of a mature high …
contributors to disease treatment resistance. However, with the lack of a mature high …
Modeling cancer metabolism on a genome scale
Cancer cells have fundamentally altered cellular metabolism that is associated with their
tumorigenicity and malignancy. In addition to the widely studied Warburg effect, several new …
tumorigenicity and malignancy. In addition to the widely studied Warburg effect, several new …
Path2Models: large-scale generation of computational models from biochemical pathway maps
Background Systems biology projects and omics technologies have led to a growing
number of biochemical pathway models and reconstructions. However, the majority of these …
number of biochemical pathway models and reconstructions. However, the majority of these …
Integration of single-cell RNA-seq data into population models to characterize cancer metabolism
Metabolic reprogramming is a general feature of cancer cells. Regrettably, the
comprehensive quantification of metabolites in biological specimens does not promptly …
comprehensive quantification of metabolites in biological specimens does not promptly …