기초과학연구원 의생명수학그룹
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 …
Presentor(s) Mentor Talk title Jaehun Jeong Gyuyoung Hwang Analyzing coupled SCN cell frequencies of mammals for multi-step transcriptional model Hyunsuk Choo, Yonghee Lee Seok Joo Chae Development of a data-driven causality detection method using Taken's Theorem Juhyeon Kim Dongju Lim Accurate initial condition for circadian pacemaker model estimating the circadian phase Kyeongtae Ko Dongju …
Abstract: A system of ordinary differential equations (ODEs) is one of the most widely used tools to describe a deterministic dynamical system. In general, such ODEs involve nonlinear equations, which make analysis of dynamical systems difficult. In this talk, we introduce Koopman theory, which offers a linear representation – not an approximation – of nonlinear dynamics. In particular, we present a data-driven algorithm to find such a linear representation
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 …
Abstract: Wearable biosensors measure physiological variables with high temporal resolution over multiple days and are increasingly employed in clinical settings, such as continuous glucose monitoring in diabetes care. Such datasets bring new opportunities and challenges, and patients, clinicians, and researchers are today faced with a common challenge: how to best summarize and capture relevant information …
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 …
Abstract: The realization that microbiomes, associated with virtually all multicellular organisms, have tremendous impact on their host health is considered as one of the most important scientific discoveries in the last decade. The host associated microbiomes, composed of tens to hundreds of co-existing microbial species, are highly heterogenous at multiple scales (e.g. between different hosts …
The talk will be hybrid, participants may join via Zoom with the following link: https://us06web.zoom.us/j/99567630778?pwd=N2ZrUWtqZzJ0YURVTzlZT3JJR3FUQT09
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 …
