Journal Club

In this talk, we discuss the paper, "MultiK: an automated tool to determine optimal cluster numbers in single-cell RNA sequencing data" by Siyao Liu et.al.  Genome Biology, 2024. Abstract  Single-cell RNA sequencing (scRNA-seq) provides new opportunities to characterize cell populations, typically accomplished through some type of clustering analysis. Estimation of the optimal cluster number (K) …

In this talk, we will discuss the paper, "A modified shuffled frog leaping algorithm with inertia weight", by Zhuanzhe Zhao et.al. , Scientific Reports, 2024. Abstract  The shuffled frog leaping algorithm (SFLA) is a promising metaheuristic bionics algorithm, which has been designed by the shuffled complex evolution and the particle swarm optimization (PSO) framework. However, …

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 …

In this talk, we discuss the paper, "Predicting multiple observations in complex systems through low-dimensional embeddings", by Tao Wu et. al., Nature Communications, 2024. Zoom : https://us06web.zoom.us/j/99567630778?pwd=N2ZrUWtqZzJ0YURVTzlZT3JJR3FUQT09 Abstract Forecasting all components in complex systems is an open and challenging task, possibly due to high dimensionality and undesirable predictors. We bridge this gap by proposing a data-driven …

In this talk, we discuss the paper "Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage" by Zhiwei Huang, et. al., bioRxiv, 2024. Zoom : https://us06web.zoom.us/j/99567630778?pwd=N2ZrUWtqZzJ0YURVTzlZT3JJR3FUQT09 Abstract Cells must adopt flexible regulatory strategies to make decisions regarding their fate, including differentiation, apoptosis, or survival in the face of …

In this talk, we discuss the paper "Achieving Occam’s razor: Deep learning for optimal model reduction" by Botond B. Antal et.al., PLOS Computational Biology, 2024. Abstract  All fields of science depend on mathematical models. Occam’s razor refers to the principle that good models should exclude parameters beyond those minimally required to describe the systems they represent. This …

In this talk we discuss the paper "Mathematical model for the distribution of DNA replication origins" by Alessandro de Moura and Jens Karschau, Physical Review E, 2024. Abstract  DNAreplication in yeast and in many other organisms starts from well-defined locations on the DNA known as replication origins. The spatial distribution of these origins in the genome is particularly …