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 …

In this talk, we discuss the paper "Self-supervised learning of accelerometer data provides new insights for sleep and its association with mortality" by H. Yuan et.al, npj digital medicine, 2024, at the Journal Club. Abstract  Sleep is essential to life. Accurate measurement and classification of sleep/wake and sleep stages is important in clinical studies for …

In this talk, we discuss the paper "A cell atlas foundation model for scalable search of similar human cells" by Graham Heimberg et.al., Nature, 2024 at the Journal Club. Abstract Single-cell RNA sequencing has profiled hundreds of millions of human cells across organs, diseases, development and perturbations to date. Mining these growing atlases could reveal …

In this talk, we discuss the paper "Method for cycle detection in sparse, irregularly sampled, long-term neuro-behavioral timeseries: Basis pursuit denoising with polynomial detrending of long-term, inter-ictal epileptiform activity" by Irena Balzekas et.al., Plos Com., 2024. Abstract Numerous physiological processes are cyclical, but sampling these processes densely enough to perform frequency decomposition and subsequent analyses …

In this talk, we discuss the paper "Constraining nonlinear time series modeling with the metabolic theory of ecology" by S.B. Munch et.al., PNAS, 2023. Abstract Forecasting the response of ecological systems to environmental change is a critical challenge for sustainable management. The metabolic theory of ecology (MTE) posits scaling of biological rates with temperature, but …

In this talk, we discuss the paper "Quantifying information accumulation encoded in the dynamics of biochemical signaling" by Y. Tang, et.al, Nature Communications, 2021. Abstract Cellular responses to environmental changes are encoded in the complex temporal patterns of signaling proteins. However, quantifying the accumulation of information over time to direct cellular decision-making remains an unsolved …

In this talk, we discuss the paper "The Large Language Models on Biomedical Data Analysis: A Survey" by Wei Lan et.al, IEEE J. Biomedical and Health Informatics, 2025, at the Journal Club. Abstract  With the rapid development of Large Language Model (LLM) technology, it has become an indispensable force in biomedical data analysis research. However, …

In this talk, we discuss the paper "A biological model of nonlinear dimensionality reduction" by K. Yoshida and T. Toyoizumi, Science Advances, 2025, at the Journal Club. Abstract Obtaining appropriate low-dimensional representations from high-dimensional sensory inputs in an unsupervised manner is essential for straightforward downstream processing. Although nonlinear dimensionality reduction methods such as t-distributed stochastic neighbor …

In this talk, we discuss the paper "Designing microplastic-binding peptides with a variational quantum circuit–based hybrid quantum-classical approach" by R.C. Vendrell et.al., Sci. Adv. 2024 at the Journal Club. Abstract De novo peptide design exhibits great potential in materials engineering, particularly for the use of plastic-binding peptides to help remediate microplastic pollution. There are no …