Journal Club

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 …

In this talk, we discuss the paper, “A frequency-amplitude coordinator and its optimal energy consumption for biological oscillators”, by Bo-Wei Qin et. al., Nature Communications, 2021. Zoom : https://us06web.zoom.us/j/99567630778?pwd=N2ZrUWtqZzJ0YURVTzlZT3JJR3FUQT09 Abstract  Biorhythm including neuron firing and protein-mRNA interaction are fundamental activities with diffusive effect. Their well-balanced spatiotemporal dynamics are beneficial for healthy sustainability. Therefore, calibrating both anomalous …

In this talk, we discuss the paper : "Noise robustness and metabolic load determine the principles of central dogma regulation" by Teresa W. Lo et al, Sci. Adv, https://doi.org/10.1126/sciadv.ado3095. Zoom: https://us06web.zoom.us/j/99567630778?pwd=N2ZrUWtqZzJ0YURVTzlZT3JJR3FUQT09 Abstract The processes of gene expression are inherently stochastic, even for essential genes required for growth. How does the cell maximize fitness in light …

In this talk, we discuss the paper : "Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment" by Leech et al, nature biotechnology, https://doi.org/10.1371/journal.pcbi.1011879. Zoom: https://us06web.zoom.us/j/99567630778?pwd=N2ZrUWtqZzJ0YURVTzlZT3JJR3FUQT09 Abstract Collective alignment of cell populations is a commonly observed phenomena in biology. An important example …

Abstract: We propose a universal method for data-driven modeling of complex nonlinear dynamics from time-resolved snapshot data without prior knowledge. Complex nonlinear dynamics govern many fields of science and engineering. Data-driven dynamic modeling often assumes a low-dimensional subspace or manifold for the state. We liberate ourselves from this assumption by proposing cluster-based network modeling (CNM) …

In this talk, we discuss the paper "Next generation reservoir computing", by Gauthier, et.al, Nat. Comm., 2021. Abstract : Reservoir computing is a best-in-class machine learning algorithm for processing information generated by dynamical systems using observed time-series data. Importantly, it requires very small training data sets, uses linear optimization, and thus requires minimal computing resources. …

In this talk, we discuss the paper "SVD-AE: An asymmetric autoencoder with SVD regularization for multivariate time series anomaly detection" by Yueyue Yao, et.al., Neural Networks, 2024.  Abstract  Anomaly detection in multivariate time series is of critical importance in many real-world applications, such as system maintenance and Internet monitoring. In this article, we propose a novel …

In this talk, we study and discuss the paper "Laplacian renormalization group for heterogeneous networks" by Pablo Villegas et.al, Nature Physics, 2023. Abstract  The renormalization group is the cornerstone of the modern theory of universality and phase transitions and it is a powerful tool to scrutinize symmetries and organizational scales in dynamical systems. However, its …

In this talk, we discuss the paper "cellFlow: a generative flow-based model for single-cell count data" by A. Palma et.al, ICLR, 2024. Abstract Generative modeling for single-cell RNA-seq has proven transformative in crucial fields such as learning single-cell representations and perturbation responses. However, despite their appeal in relevant applications involving data augmentation and unseen cell …

In this talk, we discuss the paper "Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model" by F. W. Townes et.al., Genome Biology, 2019. Abstract  Single-cell RNA-Seq (scRNA-Seq) profiles gene expression of individual cells. Recent scRNA-Seq datasets have incorporated unique molecular identifiers (UMIs). Using negative controls, we show UMI counts follow …

In this talk, we discuss the paper "CARE as a wearable derived feature linking circadian amplitude to human cognitive functions" by Shuya Cui et.al., npj Digital Medicine, 2023. Abstract Circadian rhythms are crucial for regulating physiological and behavioral processes. Pineal hormone melatonin is often used to measure circadian amplitude but its collection is costly and …

In this talk, we discuss the paper "Plausible, robust biological oscillations through allelic buffering" by F-S. Hsieh et.al, Cell Systems, 2024. at the Journal Club.  Abstract Biological oscillators can specify time- and dose-dependent functions via dedicated control of their oscillatory dynamics. However, how biological oscillators, which recurrently activate noisy biochemical processes, achieve robust oscillations remains …