기초과학연구원 의생명수학그룹
We will discuss about "Cell clustering for spatial transcriptomics data with graph neural networks", Li, J., Chen, S., Pan, X. et al., Nat Comput Sci 2, 399–408 (2022) Abstract: Spatial transcriptomics data can provide high-throughput gene expression profiling and the spatial structure of tissues simultaneously. Most studies have relied on only the gene expression information but …
Abstract: In real world, people are interested in causality rather than association. For example, pharmaceutical companies want to know effectiveness of their new drugs against diseases. South Korea Government officials are concerned about the effects of recent regulation with respect to an electric car subsidy from United States. Due to this reason, causal inference has …
We will discuss about "Absolute concentration robustness in networks with low-dimensional stoichiometric subspace", Meshkat, Nicolette, Anne Shiu, and Angelica Torres., Vietnam Journal of Mathematics 50.3 (2022): 623-651. Abstract: A reaction system exhibits “absolute concentration robustness” (ACR) in some species if the positive steady-state value of that species does not depend on initial conditions. Mathematically, this …
Abstract: The driving passion of molecular cell biologists is to understand the molecular mechanisms that control important aspects of cell physiology, but this ambition is - paradoxically - limited by the very wealth of molecular details currently known about these mechanisms. Their complexity overwhelms our intuitive notions of how molecular regulatory networks might respond under …
Abstract: Cell growth, DNA replication, mitosis and division are the fundamental processes by which life is passed on from one generation of eukaryotic cells to the next. The eukaryotic cell cycle is intrinsically a periodic process but not so much a ‘clock’ as a ‘copy machine’, making new daughter cells as warranted. Cells growing under …
Abstract: TBA
Abstract: Cellular, chemical, and population processes are all often represented via networks that describe the interactions between the different population types (typically called the "species"). If the counts of the species are low, then these systems are often modeled as continuous-time Markov chains on the d-dimensional integer lattice (with d being the number of species), …
We will discuss about "Rhythmicity is linked to expression cost at the protein level but to expression precision at the mRNA level", David Laloum, and Marc Robinson-Rechavi, PLoS computational biology 18.9 (2022): e1010399. Abstract: Many genes have nycthemeral rhythms of expression, i.e. a 24-hours periodic variation, at either mRNA or protein level or both, and …
Abstract: We’re all familiar with sleep, but how can we mathematically model it? And what determines how long and when we sleep? In this talk I’ll introduce the nonsmooth coupled oscillator systems that form the basis of current models of sleep-wake regulation and discuss their dynamical behaviour. I will describe how we are using models …
We will discuss about "Inferring microenvironmental regulation of gene expression from single-cell RNA sequencing data using scMLnet with an application to COVID-19", Cheng, Jinyu, et al., Briefings in bioinformatics 22.2 (2021): 988-1005. Abstract: Inferring how gene expression in a cell is influenced by cellular microenvironment is of great importance yet challenging. In this study, we …
We will discuss about "Model Reduction for the Chemical Master Equation: an Information-Theoretic Approach", Öcal, Kaan, Guido Sanguinetti, and Ramon Grima., arXiv preprint arXiv:2210.05329 (2022). Abstract: The complexity of mathematical models in biology has rendered model reduction an essential tool in the quantitative biologist's toolkit. For stochastic reaction networks described using the Chemical Master Equation, commonly …
Shift workers experience profound circadian disruption due to the nature of their work, which often has them working at times when their internal clock is sending a strong signal for sleep. Mathematical models can be used to generate recommendations for shift workers that shift their body's clock to better align with their work schedules, to …