기초과학연구원 의생명수학그룹
Cells make individual fate decisions through linear and nonlinear regulation of gene network, generating diverse dynamics from a single reaction pathway. In this colloquium, I will present two topics of our recent work on signaling dynamics at cellular and patient levels. The first example is about the initial value of the model, as a mechanism …
We will discuss about “PI-VAE: Physics-Informed Variational Auto-Encoder for stochastic differential equations”, Zhong, Weiheng, and Hadi Meidani, Computer Methods in Applied Mechanics and Engineering 403 (2023): 115664. Abstract We propose a new class of physics-informed neural networks, called the Physics-Informed Variational Auto-Encoder (PI-VAE), to solve stochastic differential equations (SDEs) or inverse problems involving SDEs. In …
The circadian clock orchestrates a vast array of behavioral and physiological processes with a 24-hour cycle, enabling nearly all organisms -- from bread mold to fruit-flies to humans -- to anticipate and adapt to the Earth's day. Entrainable by environmental cue, the rhythm itself is generated by a self-sustained molecular oscillator present in nearly every …
We will discuss about “Detecting critical state before phase transition of complex biological systems by hidden Markov model”, Chen, Pei, et al. Bioinformatics 32.14 (2016): 2143-2150. Abstract Motivation: Identifying the critical state or pre-transition state just before the occurrence of a phase transition is a challenging task, because the state of the system may …
Transmission of SARS-CoV-2 relies on interactions between humans. Heterogeneity and stochasticity both in human-human interactions and in the transmission of the virus give rise to non-linear infection networks that gain complexity with time. We assessed the limits of control and the effect of pharmaceutical and non-pharmaceutical measures against COVID‐19 outbreaks with a detailed community‐specific agent-based model …
Abstract: Circadian clocks control the timing and 24-hour periodicity of virtually all physiological rhythms including sleep, cognition, and metabolism. There are optimal times for most behaviours; e.g., the best sleep is achieved during low circadian activity (night), while meals and physical exercise are best placed during high circadian activity (day) when metabolic rates, stress hormone …
Abstract: The ability to reliably engineer the mammalian cell will impact a variety of applications in a disruptive way, including cell fate control and reprogramming, targeted drug delivery, and regenerative medicine. However, our current ability to engineer mammalian genetic circuits that behave as predicted remains limited. These circuits depend on the intra and extra cellular …
We will discuss about “Multiparameter persistent homology landscapes identify immune cell spatial patterns in tumors”, Vipond, Oliver, et al, Proceedings of the National Academy of Sciences 118.41 (2021): e2102166118. Abstract Highly resolved spatial data of complex systems encode rich and nonlinear information. Quantification of heterogeneous and noisy data—often with outliers, artifacts, and mislabeled points—such as …
Abstract: Since before the time of Aristotle and the natural philosophers, reductionism has played a foundational role in western scientific thought. The premise of reductionism is that systems can be broken down into constituent pieces and studied independently, then reassembled to understand the behavior of the system as a whole. It embodies the classical linear …
Absolute Concentration Robustness (ACR) was introduced by Shinar and Feinberg (Science 327:1389-1391, 2010) as robustness of equilibrium species concentration in a mass action dynamical system. Their aim was to devise a mathematical condition that will ensure robustness in the function of the biological system being modeled. The robustness of function rests on what we refer to as empirical robustness — the …
We will discuss about "Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators”, Karapetyan, Sargis, and Nicolas E. Buchler,Physical Review E 92.6 (2015): 062712. Abstract Genetic oscillators, such as circadian clocks, are constantly perturbed by molecular noise arising from the small number of molecules involved in gene regulation. One of the strongest …
IBS BIMAG will host a mini-workshop on Monday, 19 December 2022, that will feature some of the current trends in pure and applied mathematics. Several faculties from the Institute of Mathematics, University of the Philippines Diliman are invited to share their academic group’s ongoing research. Prof. Seunggyu Lee (Korea University), Dr. Dae Wook Kim (University …
