기초과학연구원 의생명수학그룹
We will discuss about "Network design principle for robust oscillatory behaviors with respect to biological noise", Qiao et al, bioRxiv, 2021 Oscillatory behaviors, which are ubiquitous in transcriptional regulatory networks, are often subject to inevitable biological noise. Thus a natural question is how transcriptional regulatory networks can robustly achieve accurate oscillation in the presence of …
Abstract: Variable selection is an approach to identifying a set of covariates that are truly important to explain the feature of a response variable. It is closely connected or belongs to model selection approaches. This talk provides a gentle introduction to Bayesian variable selection methods. The basic notion of variable selection is introduced, followed by several Bayesian approaches with a simple application example.
We will discuss about "Mechanisms for the generation of robust circadian oscillations through ultrasensitivity and differential binding affinity", Behera, Junco, and Vaikuntanathan, The Journal of Physical Chemistry B, 2021 Biochemical circadian rhythm oscillations play an important role in many signaling mechanisms. In this work, we explore some of the biophysical mechanisms responsible for sustaining robust …
Abstract: TBA
Abstract: TBA
We will discuss about "Phiclust: a clusterability measure for single-cell transcriptomics reveals phenotypic subpopulations", Mircea et al., 2022, Genome Biology The ability to discover new cell phenotypes by unsupervised clustering of single-cell transcriptomes has revolutionized biology. Currently, there is no principled way to decide whether a cluster of cells contains meaningful subpopulations that should be …
We will discuss about "A Deficiency-Based Approach to Parametrizing Positive Equilibria of Biochemical Reaction Systems", Johnston, Müller, and Pantea, Bulletin of Mathematical Biology, 2019 We present conditions which guarantee a parametrization of the set of positive equilibria of a generalized mass-action system. Our main results state that (1) if the underlying generalized chemical reaction network …
This talk will be presented online. Zoom link: 997 8258 4700 (pw: 1234) Abstract: Cells make fate decisions in response to dynamic environments and multicellular structure emerges from interplays among cells in space and time. The recent single-cell genomics technology provides an unprecedented opportunity to profile cells. However, those measurements are taken as snapshots for …
We will discuss about "Modeling polypharmacy side effects with graph convolutional networks", Zitnik, Agrawal, and Leskovec, Bioinformatics, 2018 Motivation The use of drug combinations, termed polypharmacy, is common to treat patients with complex diseases or co-existing conditions. However, a major consequence of polypharmacy is a much higher risk of adverse side effects for the patient. …
Abstract: Genetic feedback loops can be used by cells as a means to regulate internal processes or keep track of time. It is often thought that, for a genetic circuit to display self-sustained oscillations, a degree of cooperativity is needed in the binding and unbinding of actor species. This cooperativity is usually modeled using a …
Abstract: The discovery of governing equations from scientific data has the potential to transform data-rich fields that lack well-characterized quantitative descriptions. Advances in sparse regression are currently enabling the tractable identification of both the structure and parameters of a nonlinear dynamical system from data. The resulting models have the fewest terms necessary to describe the …
This talk will be presented online. Zoom link: 997 8258 4700 (pw: 1234) Abstract: I will give an introduction to topological data analysis (TDA), in which one uses ideas from algebraic topology to study the "shape" of data. I will focus on persistent homology (PH), which is the most common approach in TDA.