Approximating solutions of the chemical master equation using neural networks
Summary The Chemical Master Equation (CME) provides an accurate description of
stochastic biochemical reaction networks in well-mixed conditions, but it cannot be solved …
stochastic biochemical reaction networks in well-mixed conditions, but it cannot be solved …
Network switches and their role in circadian clocks
M Del Olmo, S Legewie, M Brunner, T Höfer… - Journal of Biological …, 2024 - ASBMB
Circadian rhythms are generated by complex interactions among genes and proteins. Self-
sustained∼ 24 h oscillations require negative feedback loops and sufficiently strong …
sustained∼ 24 h oscillations require negative feedback loops and sufficiently strong …
PRD-2 mediates clock-regulated perinuclear localization of clock gene RNAs within the circadian cycle of Neurospora
BM Bartholomai, AS Gladfelter… - Proceedings of the …, 2022 - National Acad Sciences
The transcription–translation negative feedback loops underlying animal and fungal
circadian clocks are remarkably similar in their molecular regulatory architecture and …
circadian clocks are remarkably similar in their molecular regulatory architecture and …
[HTML][HTML] Timely questions emerging in Chronobiology: the Circadian Clock keeps on ticking
Chronobiology investigations have revealed much about cellular and physiological
clockworks but we are far from having a complete mechanistic understanding of the …
clockworks but we are far from having a complete mechanistic understanding of the …
Inference and uncertainty quantification of stochastic gene expression via synthetic models
K Öcal, MU Gutmann… - Journal of The Royal …, 2022 - royalsocietypublishing.org
Estimating uncertainty in model predictions is a central task in quantitative biology.
Biological models at the single-cell level are intrinsically stochastic and nonlinear, creating …
Biological models at the single-cell level are intrinsically stochastic and nonlinear, creating …
An effective model of endogenous clocks and external stimuli determining circadian rhythms
T Breitenbach, C Helfrich-Förster, T Dandekar - Scientific Reports, 2021 - nature.com
Circadian endogenous clocks of eukaryotic organisms are an established and rapidly
developing research field. To investigate and simulate in an effective model the effect of …
developing research field. To investigate and simulate in an effective model the effect of …
Coupling allows robust mammalian redox circadian rhythms despite heterogeneity and noise
Circadian clocks are endogenous oscillators present in almost all cells that drive daily
rhythms in physiology and behavior. There are two mechanisms that have been proposed to …
rhythms in physiology and behavior. There are two mechanisms that have been proposed to …
An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells
Motivation Detecting oscillations in time series remains a challenging problem even after
decades of research. In chronobiology, rhythms (for instance in gene expression, eclosion …
decades of research. In chronobiology, rhythms (for instance in gene expression, eclosion …
Cell Biological Dissection of the Neurospora Circadian Oscillator: Tools, Approaches, and Fundamental Observations
BM Bartholomai - 2022 - search.proquest.com
The study of circadian behavior in living organisms has a long history dating back to the 18
th century AD. Over time, the scale at which the clock is studied has changed. Well into the …
th century AD. Over time, the scale at which the clock is studied has changed. Well into the …
Coupling allows robust redox circadian rhythms despite heterogeneity and noise
Circadian clocks are endogenous oscillators present in almost all cells that drive daily
rhythms in physiology and behavior. There are two mechanisms that have been proposed to …
rhythms in physiology and behavior. There are two mechanisms that have been proposed to …