Kinetic Modeling of Saccharomyces cerevisiae Central Carbon Metabolism: Achievements, Limitations, and Opportunities
Central carbon metabolism comprises the metabolic pathways in the cell that process
nutrients into energy, building blocks and byproducts. To unravel the regulation of this …
nutrients into energy, building blocks and byproducts. To unravel the regulation of this …
Chemical reservoir computation in a self-organizing reaction network
Chemical reaction networks, such as those found in metabolism and signalling pathways,
enable cells to process information from their environment,. Current approaches to …
enable cells to process information from their environment,. Current approaches to …
pyPESTO: a modular and scalable tool for parameter estimation for dynamic models
Mechanistic models are important tools to describe and understand biological processes.
However, they typically rely on unknown parameters, the estimation of which can be …
However, they typically rely on unknown parameters, the estimation of which can be …
Benchmarking of numerical integration methods for ODE models of biological systems
Ordinary differential equation (ODE) models are a key tool to understand complex
mechanisms in systems biology. These models are studied using various approaches …
mechanisms in systems biology. These models are studied using various approaches …
Combining hypothesis-and data-driven neuroscience modeling in FAIR workflows
Modeling in neuroscience occurs at the intersection of different points of view and
approaches. Typically, hypothesis-driven modeling brings a question into focus so that a …
approaches. Typically, hypothesis-driven modeling brings a question into focus so that a …
A microfluidic optimal experimental design platform for forward design of cell-free genetic networks
B van Sluijs, RJM Maas, AJ van der Linden… - Nature …, 2022 - nature.com
Cell-free protein synthesis has been widely used as a “breadboard” for design of synthetic
genetic networks. However, due to a severe lack of modularity, forward engineering of …
genetic networks. However, due to a severe lack of modularity, forward engineering of …
Long-term monitoring of SARS-CoV-2 seroprevalence and variants in Ethiopia provides prediction for immunity and cross-immunity
Under-reporting of COVID-19 and the limited information about circulating SARS-CoV-2
variants remain major challenges for many African countries. We analyzed SARS-CoV-2 …
variants remain major challenges for many African countries. We analyzed SARS-CoV-2 …
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance
BRAF is prototypical of oncogenes that can be targeted therapeutically and the treatment of
BRAFV600E melanomas with RAF and MEK inhibitors results in rapid tumor regression …
BRAFV600E melanomas with RAF and MEK inhibitors results in rapid tumor regression …
Design and application of a kinetic model of lipid metabolism in Saccharomyces cerevisiae
Lipid biosynthesis plays a vital role in living cells and has been increasingly engineered to
overproduce various lipid-based chemicals. However, owing to the tightly constrained and …
overproduce various lipid-based chemicals. However, owing to the tightly constrained and …
Assessment of prediction uncertainty quantification methods in systems biology
Biological processes are often modelled using ordinary differential equations. The unknown
parameters of these models are estimated by optimizing the fit of model simulation and …
parameters of these models are estimated by optimizing the fit of model simulation and …