In this talk, we discuss the paper "Holimap: an accurate and efficient method for solving stochastic gene network dynamics" by Chen Jia and Ramon Grima, bioRxiv, 2024. Abstract  Gene-gene interactions are crucial to the control of sub-cellular processes but our understanding of their stochastic dynamics is hindered by the lack of simulation methods that can accurately and efficiently …

In this talk, we discuss the paper "Stochastic representations of ion channel kinetics and exact stochastic simulation of neuronal dynamics" by D. F. Anderson, B. Ermentrout and P. J. Thomas, Journal of Computational Neuroscience, 2015. Abstract In this paper we provide two representations for stochastic ion channel kinetics, and compare the perfor- mance of exact …

In this talk, we discuss the paper "Temperature compensation through kinetic regulation in biochemical oscillators" by HaochenFu, Chenyi Fei, Qi Ouyang, and Yuhai Tu, to appear in PNAS.  Abstract  Although individual kinetic rates in biochemical reactions are sensitive to temperature, most circadian clocks exhibit a relatively constant period across a wide range of temperatures, a phenomenon called …

In this talk, we discuss the paper "RNA velocity of single sells" by Gioele La Manno et.al., Nature, 2018. Abstract RNA abundance is a powerful indicator of the state of individual cells. Single-cell RNA sequencing can reveal RNA abundance with high quantitative accuracy, sensitivity and throughput. However, this approach captures only a static snapshot at …

In this talk, we discuss the paper "A universal description of stochastic oscillators", by Alberto Perez-Cervera et. al., PNAS, 2023. Abstract  Many systems in physics, chemistry, and biology exhibit oscillations with a pronounced random component. Such stochastic oscillations can emerge via different mechanisms, for example, linear dynamics of a stable focus with fluctuations, limit-cycle systems …

In this talk, we discuss the paper, "SMSSVD : Submatrix selection singular value decomposition", by Rasmus Henningsson and Magnus Fontes, Bioinformatics, 2019. Abstract Motivation High throughput biomedical measurements normally capture multiple overlaid biologically relevant signals and often also signals representing different types of technical artefacts like e.g. batch effects. Signal identification and decomposition are accordingly …