Systematic inference identifies a major source of heterogeneity in cell signaling dynamics: The rate-limiting step number
Identifying the sources of cell-to-cell variability in signaling dynamics is essential to
understand drug response variability and develop effective therapeutics. However, it is …
understand drug response variability and develop effective therapeutics. However, it is …
Nonmodular oscillator and switch based on RNA decay drive regeneration of multimodal gene expression
Periodic gene expression dynamics are key to cell and organism physiology. Studies of
oscillatory expression have focused on networks with intuitive regulatory negative feedback …
oscillatory expression have focused on networks with intuitive regulatory negative feedback …
Spatially coordinated collective phosphorylation filters spatiotemporal noises for precise circadian timekeeping
The circadian (∼ 24h) clock is based on a negative-feedback loop centered around the
PERIOD protein (PER), translated in the cytoplasm and then enters the nucleus to repress its …
PERIOD protein (PER), translated in the cytoplasm and then enters the nucleus to repress its …
Combined multiple transcriptional repression mechanisms generate ultrasensitivity and oscillations
Transcriptional repression can occur via various mechanisms, such as blocking,
sequestration and displacement. For instance, the repressors can hold the activators to …
sequestration and displacement. For instance, the repressors can hold the activators to …
Computational translation framework identifies biochemical reaction networks with special topologies and their long-term dynamics
Long-term behaviors of biochemical systems are described by steady states in deterministic
models and stationary distributions in stochastic models. Obtaining their analytic solutions …
models and stationary distributions in stochastic models. Obtaining their analytic solutions …
[HTML][HTML] Efficient and scalable prediction of stochastic reaction–diffusion processes using graph neural networks
The dynamics of locally interacting particles that are distributed in space give rise to a
multitude of complex behaviours. However the simulation of reaction–diffusion processes …
multitude of complex behaviours. However the simulation of reaction–diffusion processes …
[HTML][HTML] Model reduction for the chemical master equation: an information-theoretic approach
The complexity of mathematical models in biology has rendered model reduction an
essential tool in the quantitative biologist's toolkit. For stochastic reaction networks described …
essential tool in the quantitative biologist's toolkit. For stochastic reaction networks described …
Beyond homogeneity: Assessing the validity of the Michaelis–Menten rate law in spatially heterogeneous environments
The Michaelis–Menten (MM) rate law has been a fundamental tool in describing enzyme-
catalyzed reactions for over a century. When substrates and enzymes are homogeneously …
catalyzed reactions for over a century. When substrates and enzymes are homogeneously …
Coupled oscillator cooperativity as a control mechanism in chronobiology
MS Heltberg, Y Jiang, Y Fan, Z Zhang, MS Nordentoft… - Cell Systems, 2023 - cell.com
Control of dynamical processes is vital for maintaining correct cell regulation and cell-fate
decisions. Numerous regulatory networks show oscillatory behavior; however, our …
decisions. Numerous regulatory networks show oscillatory behavior; however, our …
Validity conditions of approximations for a target-mediated drug disposition model: A novel first-order approximation and its comparison to other approximations
Target-mediated drug disposition (TMDD) is a phenomenon characterized by a drug's high-
affinity binding to a target molecule, which significantly influences its pharmacokinetic profile …
affinity binding to a target molecule, which significantly influences its pharmacokinetic profile …