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X-WR-CALNAME:Biomedical Mathematics Group
X-ORIGINAL-URL:https://www.ibs.re.kr/bimag
X-WR-CALDESC:Events for Biomedical Mathematics Group
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BEGIN:VTIMEZONE
TZID:Asia/Seoul
BEGIN:STANDARD
TZOFFSETFROM:+0900
TZOFFSETTO:+0900
TZNAME:KST
DTSTART:20220101T000000
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END:VTIMEZONE
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20250530T110000
DTEND;TZID=Asia/Seoul:20250530T120000
DTSTAMP:20260525T161809
CREATED:20250217T081212Z
LAST-MODIFIED:20250217T082031Z
UID:10780-1748602800-1748606400@www.ibs.re.kr
SUMMARY:Koopman operator approach to complex rhythmic systems - Hiroya Nakao
DESCRIPTION:Abstract \nSpontaneous rhythmic oscillations are widely observed in real-world systems. Synchronized rhythmic oscillations often provide important functions for biological or engineered systems. One of the useful theoretical methods for analyzing rhythmic oscillations is the phase reduction theory for weakly perturbed limit-cycle oscillators\, which systematically gives a low-dimensional description of the oscillatory dynamics using only the asymptotic phase of the oscillator. Recent advances in Koopman operator theory provide a new viewpoint on phase reduction\, yielding an operator-theoretic definition of the classical notion of the asymptotic phase and\, moreover\, of the amplitudes\, which characterize distances from the limit cycle. This led to the generalization of classical phase reduction to phase-amplitude reduction\, which can characterize amplitude deviations of the oscillator from the unperturbed limit cycle in addition to the phase along the cycle in a systematic manner. In the talk\, these theories are briefly reviewed and then applied to several examples of synchronizing rhythmic systems\, including biological oscillators\, networked dynamical systems\, and rhythmic spatiotemporal patterns.
URL:https://www.ibs.re.kr/bimag/event/koopman-operator-approach-to-complex-rhythmic-systems-hiroya-nakao/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2025/02/nakao-hiroya.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20250521T160000
DTEND;TZID=Asia/Seoul:20250521T170000
DTSTAMP:20260525T161809
CREATED:20250217T080703Z
LAST-MODIFIED:20250217T080703Z
UID:10775-1747843200-1747846800@www.ibs.re.kr
SUMMARY:Simplified descriptions of stochastic oscillators - Benjamin Lindner
DESCRIPTION:Abstract \nMany natural systems exhibit oscillations that show sizeable fluctuations in frequency and amplitude. This variability can arise from a wide variety of physical mechanisms. Phase descriptions that work for deterministic oscillators have a limited applicability for stochastic oscillators. In my talk I review attempts to generalize the phase concept to stochastic oscillations\, specifically\, the mean-return-time phase and the asymptotic phase.\nFor stochastic systems described by Fokker-Planck and Kolmogorov-backward equations\, I introduce a mapping of the system’s variables to a complex pointer (instead of a real-valued phase) that is based on the eigenfunction of the Kolmogorov equation. Under the new (complex-valued) description\, the statistics of the oscillator’s spontaneous activity\, of its response to external perturbations\, and of the coordinated activity of (weakly) coupled oscillators\, is brought into a universal and greatly simplified form. The theory is tested for three theoretical models of noisy oscillators arising from fundamentally different mechanisms: a damped harmonic oscillator with dynamical noise\, a fluctuation-perturbed limit-cycle system\, and an excitable system in which oscillations require noise to occur.
URL:https://www.ibs.re.kr/bimag/event/simplified-descriptions-of-stochastic-oscillators-benjamin-lindner/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2025/02/Benjamin-Lindner-e1739779616840.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20250404T110000
DTEND;TZID=Asia/Seoul:20250404T120000
DTSTAMP:20260525T161809
CREATED:20250217T080308Z
LAST-MODIFIED:20250217T080308Z
UID:10771-1743764400-1743768000@www.ibs.re.kr
SUMMARY:A lognormal Poisson model for single cell transcriptomic normalization - Fred Wright
DESCRIPTION:Abstract \nThe advent of single-cell transcriptomics has brought a greatly improved understanding of the heterogeneity of gene expression across cell types\, with important applications in developmental biology and cancer research. Single-cell RNA sequencing datasets\, which are based on tags called universal molecular identifiers\, typically include a large number of zeroes. For such datasets\, genes with even moderate expression may be poorly represented in sequencing count matrices. Standard pipelines often retain only a small subset of genes for further analysis\, but we address the problem of estimating relative expression across the entire transcriptome by adopting a multivariate lognormal Poisson count model. We propose empirical Bayes estimation procedures to estimate latent cell-cell correlations\, and to recover meaningful estimates for genes with low expression. For small groups of cells\, an important sampling procedure uses the full cell-cell correlation structure and is computationally feasible. For larger datasets\, we propose a gene-level shrinkage procedure that has favorable performance for datasets with approximately compound symmetric cell-cell correlation. A fast procedure that incorporates matrix approximations is also promising\, and extensible to very large datasets. We apply our approaches to simulated and real datasets\, and demonstrate favorable performance in comparisons to competing normalization approaches. We further illustrate the applications of our approach in downstream analyses\, including cell-type clustering and identification. \n 
URL:https://www.ibs.re.kr/bimag/event/a-lognormal-poisson-model-for-single-cell-transcriptomic-normalization-fred-wright/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2025/02/Fred_wright-e1739779380180.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20250328T110000
DTEND;TZID=Asia/Seoul:20250328T120000
DTSTAMP:20260525T161809
CREATED:20250217T075911Z
LAST-MODIFIED:20250217T081432Z
UID:10766-1743159600-1743163200@www.ibs.re.kr
SUMMARY:Dynamics and Decision Making in Single Cells - Galit Lahav
DESCRIPTION:Abstract \nIndividual human cancer cells often show different responses to the same treatment. In this talk I will share the quantitative experimental approaches my lab has developed for studying the fate and behavior of human cells at the single-cell level. I will focus on the tumor suppressor protein p53\, a transcription factor controlling genomic integrity and cell survival. In the last several years we have established the dynamics of p53 (changes in its levels over time) as an important mechanism controlling gene expression and guiding cellular outcomes. I will present recent studies from the lab demonstrating how studying p53 dynamics in response to radiation and chemotherapy in single cells can guide the design and schedule of combinatorial therapy\, and how the p53 oscillator can be used to study the principles and function of entertainment in Biology. I will also present new findings suggesting that p53’s post-translational modification state is altered between its first and second pulses of expression\, and the effects these have on gene expression programs over time.
URL:https://www.ibs.re.kr/bimag/event/dynamics-and-decision-making-in-single-cells-galit-lahav/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2025/02/Galit-Lahav-e1739779209180.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20250321T110000
DTEND;TZID=Asia/Seoul:20250321T120000
DTSTAMP:20260525T161809
CREATED:20250217T075507Z
LAST-MODIFIED:20250217T075934Z
UID:10756-1742554800-1742558400@www.ibs.re.kr
SUMMARY:Disrupting Heathcare Using Deep Data and Remote Monitoring - Michael Snyder
DESCRIPTION:Abstract \nOur present healthcare system focuses on treating people when they are ill rather than keeping them healthy. We have been using big data and remote monitoring approaches to monitor people while they are healthy to keep them that way and detect disease at its earliest moment presymptomatically. We use advanced multiomics technologies (genomics\, immunomics\, transcriptomics\, proteomics\, metabolomics\, microbiomics) as well as wearables and microsampling for actively monitoring health. Following a group of 109 individuals for over 13 years revealed numerous major health discoveries covering cardiovascular disease\, oncology\, metabolic health and infectious disease. We have also found that individuals have distinct aging patterns that can be measured in an actionable period of time. Finally\, we have used wearable devices for early detection of infectious disease\, including COVID-19 as well as microsampling for monitoring and improving lifestyle. We believe that advanced technologies have the potential to transform healthcare and keep people healthy.
URL:https://www.ibs.re.kr/bimag/event/disrupting-heathcare-using-deep-data-and-remote-monitoring-michael-snyder/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2025/02/mike-snyder-e1739778881131.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20250314T110000
DTEND;TZID=Asia/Seoul:20250314T120000
DTSTAMP:20260525T161809
CREATED:20250217T075146Z
LAST-MODIFIED:20250217T075146Z
UID:10749-1741950000-1741953600@www.ibs.re.kr
SUMMARY:COVID-19 and Challenges to the Classical Theory of Epidemics - Simon Levin
DESCRIPTION:Abstract \nThe standard theory of infectious diseases\, tracing back to the work of Kermack and McKendrick nearly a century ago\, has been a triumph of mathematical biology\, a rare marriage of theory and application. Yet the limitations of its most simple representations\, which has always been known\, have been laid bare in dealing with COVID-19\, sparking a spate of extensions of the basic theory to deal more effectively with aspects of viral evolution\, asymptotic stages\, heterogeneity of various kinds\, the ambiguities of notions of herd immunity\, the role of social behaviors and other features. This lecture will address some progress in addressing these\, and open challenges in expanding the mathematical theory.
URL:https://www.ibs.re.kr/bimag/event/covid-19-and-challenges-to-the-classical-theory-of-epidemics-simon-levin/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2025/02/simon-levin-e1739778689468.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20241211T160000
DTEND;TZID=Asia/Seoul:20241211T170000
DTSTAMP:20260525T161809
CREATED:20240829T004544Z
LAST-MODIFIED:20241204T022447Z
UID:10005-1733932800-1733936400@www.ibs.re.kr
SUMMARY:Circadian phase in cells and humans - Achim Kramer
DESCRIPTION:Abstract: \nCircadian clocks in cells and humans are heterogeneous in period and phase. This heterogeneity can be exploited not only to gain insight into the molecular basis of circadian rhythms\, but also to explore plasticity and robustness. In this talk\, I will report on two ongoing projects in the lab: (i) We are exploiting the heterogeneity of cells in both circadian period and a metabolic parameter – protein stability – to study their interdependence without the need for genetic manipulation. We have generated cells expressing key circadian proteins (CRYPTOCHROME1/2 (CRY1/2) and PERIOD1/2 (PER1/2)) as endogenous fusions with fluorescent proteins and are simultaneously monitoring circadian rhythm and degradation in thousands of single cells. (ii) We are developing molecular biomarkers of human circadian characteristics that will allow an objective description of the epidemiology of the human circadian clock and an assessment of its robustness and plasticity.
URL:https://www.ibs.re.kr/bimag/event/circadian-phase-in-cells-and-humans-achim-kramer/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2024/08/achim-kramer-e1724986773749.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20241129T110000
DTEND;TZID=Asia/Seoul:20241129T120000
DTSTAMP:20260525T161809
CREATED:20240829T004146Z
LAST-MODIFIED:20241114T001353Z
UID:10001-1732878000-1732881600@www.ibs.re.kr
SUMMARY:Mathematical Modelling of Microtube Driven Invasion of Glioma - Thomas Hillen
DESCRIPTION:Abstract: Malignant gliomas are highly invasive brain tumors. Recent attention has focused on their capacity for network-driven invasion\, whereby mitotic events can be followed by the migration of nuclei along long thin cellular protrusions\, termed tumour microtubes (TM). Here I develop a mathematical model that describes this microtube-driven invasion of gliomas. I show that scaling limits lead to well known glioma models as special cases such as go-or-grow models\, the PI model of Swanson\, and the anisotropic model of Swan. I compute the invasion speed and I use the model to fit experiments of cancer resection and regrowth in the mouse brain.\n(Joint work with N. Loy\, K.J. Painter\, R. Thiessen\, A. Shyntar).
URL:https://www.ibs.re.kr/bimag/event/mathematical-modelling-of-microtube-driven-invasion-of-glioma-thomas-hillen/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2024/08/thillen.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20241113T160000
DTEND;TZID=Asia/Seoul:20241113T170000
DTSTAMP:20260525T161809
CREATED:20240829T003616Z
LAST-MODIFIED:20240829T005258Z
UID:9996-1731513600-1731517200@www.ibs.re.kr
SUMMARY:Mathematical models for malaria - Jennifer Flegg
DESCRIPTION:Abstract:  The effect of malaria on the developing world is devastating. Each year there are more than 200 million cases and over 400\,000 deaths\, with children under the age of five the most vulnerable. Ambitious malaria elimination targets have been set by the World Health Organization for 2030. These involve the elimination of the disease in at least 35 countries. However\, these malaria elimination targets rest precariously on being able to treat the disease appropriately; a difficult feat with the emergence and spread of antimalarial drug resistance\, along with many other challenges. In this talk\, I will introduce several statistical and mathematical models that can be used to monitor malaria transmission and to support malaria elimination. For example\, I’ll present mechanistic models of disease transmission\, statistical models that allow the emergence and spread of antimalarial drug resistance to be monitored\, mechanistic models that capture the role of bioclimatic factors on the risk of malaria and optimal geospatial sampling schemes for future malaria surveillance. I will discuss how the results of these models have been used to inform public health policy and support ongoing malaria elimination efforts.
URL:https://www.ibs.re.kr/bimag/event/mathematical-models-for-malaria/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2024/08/Jennifer-Flegg-e1724892764918.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20241030T150000
DTEND;TZID=Asia/Seoul:20241030T160000
DTSTAMP:20260525T161809
CREATED:20240829T003420Z
LAST-MODIFIED:20241023T052507Z
UID:9992-1730300400-1730304000@www.ibs.re.kr
SUMMARY:Latent space dynamics identification - Youngsoo Choi
DESCRIPTION:Abstravt: Latent space dynamics identification (LaSDI) is an interpretable data-driven framework that follows three distinct steps\, i.e.\, compression\, dynamics identification\, and prediction. Compression allows high-dimensional data to be reduced so that they can be easily fit into an interpretable model. Dynamics identification lets you derive the interpretable model\, usually some form of parameterized differential equations that fit the reduced latent space data. Then\, in the prediction phase\, the identified differential equations are solved in the reduced space for a new parameter point and its solution is projected back to the full space. The efficiency of the LaSDI framework comes from the fact that the solution process in the prediction phase does not involve any full order model size. For the identification\, various approaches are possible\, e.g.\, a fixed form as in dynamic mode decomposition and thermodynamics-based LaSDI\, a regression form as in sparse identification of nonlinear dynamics (SINDy) and weak SINDy\, and a physics-driven form as projection-based reduced order model. Various physics prob- lems were accurately accelerated by the family of LaSDIs\, achieving a speed-up of 1000x\, e.g.\, kinetic plasma simulations\, pore collapse\, and computational fluid problems.
URL:https://www.ibs.re.kr/bimag/event/latent-space-dynmaics-identification-youngsoo-choi/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2024/08/choi15_1-e1724991182393.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20241018T110000
DTEND;TZID=Asia/Seoul:20241018T120000
DTSTAMP:20260525T161809
CREATED:20240829T002853Z
LAST-MODIFIED:20240830T041457Z
UID:9987-1729249200-1729252800@www.ibs.re.kr
SUMMARY:Interpretable Machine Learning-Based Scoring System for Clinical Decision Making - Nan Liu
DESCRIPTION:Abstract: There has been an increased use of scoring systems in clinical settings for the purpose of assessing risks in a convenient manner that provides important evidence for decision making. Machine learning-based methods may be useful for identifying important predictors and building models; however\, their ‘black box’ nature limits their interpretability as well as clinical acceptability. This talk aims to introduce and demonstrate how interpretable machine learning can be used to create scoring systems for clinical decision making.
URL:https://www.ibs.re.kr/bimag/event/interpretable-machine-learning-based-scoring-system-for-clinical-decision-making-nan-liu/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2024/08/liu-nan-e1724991287242.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20241002T160000
DTEND;TZID=Asia/Seoul:20241002T170000
DTSTAMP:20260525T161809
CREATED:20240829T001952Z
LAST-MODIFIED:20240830T030008Z
UID:9983-1727884800-1727888400@www.ibs.re.kr
SUMMARY:Novel approaches and technologies for the study of sleep and circadian rhythms in health and disease - Derk-Jan Dijk
DESCRIPTION:Abstract: The study of sleep and circadian rhythms at scale requires novel technologies and approaches that are valid\, cost effective and do not pose much of a burden to the participant. Here we will present our recent studies in which we have evaluated several classes of technologies and approaches including wearables\, nearables\, blood based biomarkers and combinations of data with mathematical models.
URL:https://www.ibs.re.kr/bimag/event/novel-approaches-and-technologies-for-the-study-of-sleep-and-circadian-rhythms-in-health-and-disease-derk-jan-dijk/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/webp:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2024/08/derk-jan-dijk-e1724986795436.webp
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20240904T160000
DTEND;TZID=Asia/Seoul:20240904T170000
DTSTAMP:20260525T161809
CREATED:20240829T001214Z
LAST-MODIFIED:20240830T025822Z
UID:9974-1725465600-1725469200@www.ibs.re.kr
SUMMARY:Quantitative Ecology of Host-associated Microbiomes - Lei Dai
DESCRIPTION: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 and within a host). In this talk\, I will share our recent works on understanding the heterogeneity of complex microbial communities\, and how these conceptual and technological advances in microbial ecology pave the way for precision microbiome engineering to prevent and treat diseases.
URL:https://www.ibs.re.kr/bimag/event/quantitative-ecology-of-host-associated-microbiomes/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2024/08/lei-dai-1-e1724986646267.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20240510T110000
DTEND;TZID=Asia/Seoul:20240510T120000
DTSTAMP:20260525T161809
CREATED:20240219T044117Z
LAST-MODIFIED:20240728T142006Z
UID:9242-1715338800-1715342400@www.ibs.re.kr
SUMMARY:Jingyi Jessica Li\, ClusterDE: a post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping
DESCRIPTION:Abstract: In typical single-cell RNA-seq (scRNA-seq) data analysis\, a clustering algorithm is applied to find discrete cell clusters as putative cell types\, and then a statistical test is employed to identify the differentially expressed (DE) genes between the cell clusters. However\, this common procedure suffers the “double dipping” issue: the same data are used twice to find discrete cell clusters as putative cell types and DE genes as potential cell-type marker genes\, leading to false-positive cell-type marker genes even when the cell clusters are spurious. To overcome this challenge\, we propose ClusterDE\, a post-clustering DE method for controlling the false discovery rate (FDR) of identified DE genes regardless of clustering quality\, which can work as an add-on to popular pipelines such as Seurat. The core idea of ClusterDE is to generate real-data-based synthetic null data containing only one cell type\, in contrast to the real data\, for evaluating the whole procedure of clustering followed by a DE test. Using comprehensive simulation and real data analysis\, we show that ClusterDE has solid FDR control and the ability to identify canonical cell-type marker genes as top DE genes\, distinguishing them from common housekeeping genes. Notably\, the DE genes identified by ClusterDE are informative markers for discrete cell types and can guide the merging of spurious clusters. ClusterDE is fast\, transparent\, and adaptive to a wide range of clustering algorithms and DE tests.
URL:https://www.ibs.re.kr/bimag/event/jingyi-jessica-li-clusterde-a-post-clustering-differential-expression-de-method-robust-to-false-positive-inflation-caused-by-double-dipping/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2024/02/Jessica-li-e1722176393718.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20240503T110000
DTEND;TZID=Asia/Seoul:20240503T120000
DTSTAMP:20260525T161809
CREATED:20240219T043810Z
LAST-MODIFIED:20240728T142252Z
UID:9239-1714734000-1714737600@www.ibs.re.kr
SUMMARY:Pedro Mendes\, Multiscale hybrid differential equation and agent-based models
DESCRIPTION:Abstract: Biological phenomena are notorious for crossing several temporal and spatial scales. While often it may be sufficient to focus on a single scale\, it is not rare that we have to consider several scales simultaneously. Computational modeling and simulation of biological systems thus frequently requires to include diverse temporal and spatial scales. A popular approach in systems biology is to combine differential equations and agent-based models\, where usually small sets of differential equations are used to represent the internal state of each cell\, with the cells being represented as interacting autonomous agents on a lattice. This type of hybrid models allows for parallel solution of smaller sets of differential equations rather than the solution of a single but very large set of differential equations. At certain discrete times\, the agents are allowed to communicate\, and only then are the different sets of differential equations able to influence each other. This time discretization of the cell-cell interactions carries an inherent approximation error compared to the continuous interaction of these cells in the single model of a large set of coupled differential equations. Here we study this approximation error and investigate the conditions in which it becomes negligible\, thus defining the domain where the multiscale approach is valid. The approach is illustrated with a classic model of Drosophila segment polarity network\, where a model based on a full set of differential equations (the original version of that model) is compared with a hybrid model combining differential equations and agent-based approach (implemented with the open source software simulators Vivarium and COPASI). This study is also relevant to other hybrid simulations\, such as those representing “whole-cell models”\, where partitions may be done at other organizational scales.
URL:https://www.ibs.re.kr/bimag/event/pedro-mendes-multiscale-hybrid-differential-equation-and-agent-based-models/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2024/02/Pedro-Mendes-e1722176551946.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20240412T110000
DTEND;TZID=Asia/Seoul:20240412T120000
DTSTAMP:20260525T161809
CREATED:20240219T043247Z
LAST-MODIFIED:20240728T142452Z
UID:9233-1712919600-1712923200@www.ibs.re.kr
SUMMARY:Michael Chee\, How Data from Sleep Trackers Can Transform Our Understanding of Sleep
DESCRIPTION:Abstract: Wearable health trackers have shifted from gadgets for sports enthusiasts to valuable health sentinels over the last few years and that transformation is gathering pace. What do these devices really measure about sleep? What types of devices are there\, and which can we trust? Which of the many sleep measures reported\, contribute to a better understanding of sleep\, sleep habits and sleep health? How can sleep data improve personal and public health? What new uses of sensor data can we look forward to in coming years? I seek to shed light on these issues in a presentation that will focus on distinguishing scientific and health-oriented perspectives from consumer-facing ones.
URL:https://www.ibs.re.kr/bimag/event/michael-chee-how-data-from-sleep-trackers-can-transform-our-understanding-of-sleep-2/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2024/02/Michael-Chee-e1722176681984.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20240405T110000
DTEND;TZID=Asia/Seoul:20240405T120000
DTSTAMP:20260525T161809
CREATED:20240219T043532Z
LAST-MODIFIED:20240728T142635Z
UID:9236-1712314800-1712318400@www.ibs.re.kr
SUMMARY:Brian P. Delisle\, Circadian Regulation of Cardiac Electrophysiology
DESCRIPTION:Abstract: Circadian rhythms in physiology and behavior are regulated by circadian clocks\, ubiquitous molecular transcriptional-translational feedback loops that cycle with a periodicity of ~24 hours. Circadian clocks serve as cellular timekeepers regulating important cell-type specific functions. The phase of circadian rhythms and circadian clocks throughout the body are entrained to the light cycle by signals originating in the suprachiasmatic nucleus of the hypothalamus. The functional importance of circadian clocks in cardiomyocytes is underscored by the observation that genetic disruption of the circadian clock mechanism in mouse hearts alters the electrocardiogram (ECG)\, cardiac action potential\, and size of individual ionic currents. This presentation discusses recent basic science studies showing how daily environmental\, behavioral\, and circadian rhythms impact cardiac electrophysiology and cardiac arrhythmogenesis at the systems\, tissue\, and molecular levels. These studies provide new insights into how daily environmental\, behavioral\, and circadian rhythms affect the timing of cardiovascular events\, and they are starting to identify chronotherapeutic strategies that may mitigate the risk for cardiac arrhythmias.
URL:https://www.ibs.re.kr/bimag/event/brian-p-delisle-circadian-regulation-of-cardiac-electrophysiology/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2024/02/Brian-Delisle-e1722176786315.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20240308T110000
DTEND;TZID=Asia/Seoul:20240308T120000
DTSTAMP:20260525T161809
CREATED:20240219T042938Z
LAST-MODIFIED:20240728T142756Z
UID:9230-1709895600-1709899200@www.ibs.re.kr
SUMMARY:Mark Alber\, Combined multiscale mathematical modeling and experimental study of regulation mechanisms of shape formation during tissue development
DESCRIPTION:Abstract: The regulation and maintenance of an organ’s shape and structure is a major outstanding question in developmental biology. The Drosophila wing imaginal disc serves as a powerful system for elucidating design principles of the shape formation in epithelial morphogenesis.
URL:https://www.ibs.re.kr/bimag/event/mark-alber-combined-multiscale-mathematical-modeling-and-experimental-study-of-regulation-mechanisms-of-shape-formation-during-tissue-development/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2024/02/Mark-Alber-e1722176863895.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20231208T110000
DTEND;TZID=Asia/Seoul:20231208T120000
DTSTAMP:20260525T161809
CREATED:20230831T142407Z
LAST-MODIFIED:20240728T143005Z
UID:8394-1702033200-1702036800@www.ibs.re.kr
SUMMARY:Robyn P. Araujo\, Cellular cognition and the simple complexity of the networks of life
DESCRIPTION:Abstract: TBD
URL:https://www.ibs.re.kr/bimag/event/robyn-p-araujo-cellular-cognition-and-the-simple-complexity-of-the-networks-of-life/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2023/08/Robyn-Araujo-e1722176950408.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20231122T160000
DTEND;TZID=Asia/Seoul:20231122T170000
DTSTAMP:20260525T161809
CREATED:20230831T143538Z
LAST-MODIFIED:20240728T143214Z
UID:8405-1700668800-1700672400@www.ibs.re.kr
SUMMARY:Alfio Quarteroni\, Physics-based and data-driven numerical models for computational medicine
DESCRIPTION:Abstract: I will report on some recent results on modelling the heart\, the external circulation\, and their application to problems of clinical relevance. I will show that a proper integration between PDE-based and machine-learning algorithms can improve the computational efficiency and enhance the generality of our iHEART simulator.
URL:https://www.ibs.re.kr/bimag/event/alfio-quarteroni-physics-based-and-data-driven-numerical-models-for-computational-medicine/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2023/08/Alfio-Quarteroni-e1722177125537.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20231117T110000
DTEND;TZID=Asia/Seoul:20231117T120000
DTSTAMP:20260525T161809
CREATED:20230831T143713Z
LAST-MODIFIED:20240728T143844Z
UID:8408-1700218800-1700222400@www.ibs.re.kr
SUMMARY:Samuel Isaacson\, Spatial Particle Modeling of Immune Processes
DESCRIPTION:Abstract: \nSurface Plasmon Resonance (SPR) assays are a standard approach for quantifying kinetic parameters in antibody-antigen binding reactions. Classical SPR approaches ignore the bivalent structure of antibodies\, and use simplified ODE models to estimate effective reaction rates for such interactions. In this work we develop a new SPR protocol\, coupling a model that explicitly accounts for the bivalent nature of such interactions and the limited spatial distance over which such interactions can occur\, to a SPR assay that provides more features in the generated data. Our approach allows the estimation of bivalent binding kinetics and the spatial extent over which antibodies and antigens can interact\, while also providing substantially more robust fits to experimental data compared to classical ODE models. I will present our new modeling and parameter estimation approach\, and demonstrate how it is being used to study interactions between antibodies and spike protein. I will also explain how we make the overall parameter estimation problem computationally feasible via the construction of a surrogate approximation to the (computationally-expensive) particle model. The latter enables fitting of model parameters via standard optimization approaches. \nTime-permitting\, I will also give an introduction to our Catalyst.jl symbolic chemical reaction modeling library\, which we have recently demonstrated outperforms a number of popular systems biology simulation packages in solving ODE and stochastic reaction models. A distinguishing feature of Catalyst is the ease with which it integrates with other Julia libraries to enable sensitivity analysis\, parameter estimation studies\, structural identifiability analysis\, bifurcation analysis\, solution of the chemical master equation\, and a variety of higher-level functionality.
URL:https://www.ibs.re.kr/bimag/event/samuel-isaacson-spatial-particle-modeling-of-immune-processes/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2023/08/Samuel-Isaacson-scaled-e1722177501809.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20231110T110000
DTEND;TZID=Asia/Seoul:20231110T120000
DTSTAMP:20260525T161809
CREATED:20230831T142922Z
LAST-MODIFIED:20240728T144105Z
UID:8399-1699614000-1699617600@www.ibs.re.kr
SUMMARY:Matthew Simpson\, Efficient prediction\, estimation and identifiability analysis with mechanistic mathematical models
DESCRIPTION:Abstract: Interpreting data using mechanistic mathematical models provides a foundation for discovery and decision-making in all areas of science and engineering. Key steps in using mechanistic mathematical models to interpret data include: (i) identifiability analysis; (ii) parameter estimation; and (iii) model prediction. Here we present a systematic\, computationally efficient likelihood-based workflow that addresses all three steps in a unified way. Recently developed methods for constructing profile-wise prediction intervals enable this workflow and provide the central linkage between different workflow components. These methods propagate profile-likelihood-based confidence sets for model parameters to predictions in a way that isolates how different parameter combinations affect model predictions. We show how to extend these profile-wise prediction intervals to two-dimensional interest parameters\, and then combine profile-wise prediction confidence sets to give an overall prediction confidence set that approximates the full likelihood-based prediction confidence set well. We apply our methods to a range of synthetic data and real-world ecological data describing re-growth of coral reefs on the Great Barrier Reef after some external disturbance\, such as a tropical cyclone or coral bleaching event.
URL:https://www.ibs.re.kr/bimag/event/matthew-simpson-efficient-prediction-estimation-and-identifiability-analysis-with-mechanistic-mathematical-models/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2023/08/Matthew-Simpson-e1722177652995.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20231101T160000
DTEND;TZID=Asia/Seoul:20231101T170000
DTSTAMP:20260525T161809
CREATED:20230831T143129Z
LAST-MODIFIED:20240728T144218Z
UID:8402-1698854400-1698858000@www.ibs.re.kr
SUMMARY:Eder Zavala\, Quantitative analysis of high-resolution daily profiles of HPA axis hormones
DESCRIPTION:Abstract: The Hypothalamic-Pituitary-Adrenal (HPA) axis is the key regulatory pathway responsible for maintaining homeostasis under conditions of real or perceived stress. Endocrine responses to stressors are mediated by adrenocorticotrophic hormone (ACTH) and corticosteroid (CORT) hormones. In healthy\, non-stressed conditions\, ACTH and CORT exhibit highly correlated ultradian pulsatility with an amplitude modulated by circadian processes. Disruption of these hormonal rhythms can occur as a result of stressors or in the very early stages of disease. Despite the fact that misaligned endocrine rhythms are associated with increased morbidity\, a quantitative understanding of their mechanistic origin and pathogenicity is missing. Mathematically\, the HPA axis can be understood as a dynamical system that is optimised to respond and adapt to perturbations. Normally\, the body copes well with minor disruptions\, but finds it difficult to withstand severe\, repeated or long-lasting perturbations. Whilst a healthy HPA axis maintains a certain degree of robustness to stressors\, its fragility in diseased states is largely unknown\, and this understanding constitutes a critical step toward the development of digital tools to support clinical decision-making. This talk will explore how these challenges are being addressed by combining high-resolution biosampling techniques with mathematical and computational analysis methods. This interdisciplinary approach is helping us quantify the inter-individual variability of daily hormone profiles and develop novel “dynamic biomarkers” that serve as a normative reference and to signal endocrine dysfunction. By shifting from a qualitative to a quantitative description of the HPA axis\, these insights bring us a step closer to personalised clinical interventions for which timing is key.
URL:https://www.ibs.re.kr/bimag/event/eder-zavala-quantitative-analysis-of-high-resolution-daily-profiles-of-hpa-axis-hormones/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2023/08/Eder-Zavala-e1722177727704.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20231020T110000
DTEND;TZID=Asia/Seoul:20231020T120000
DTSTAMP:20260525T161809
CREATED:20230831T143835Z
LAST-MODIFIED:20231124T001740Z
UID:8411-1697799600-1697803200@www.ibs.re.kr
SUMMARY:Tetsuya J. Kobayashi\, Optimality of Biological Information Processing
DESCRIPTION:Abstract: \nAlmost all biological systems possess the ability to gather environmental information and modulate their behaviors to adaptively respond to changing environments. While animals excel at sensing odors\, even simple bacteria can detect faint chemicals using stochastic receptors. They then navigate towards or away from the chemical source by processing this sensed information through intracellular reaction systems. \nIn the first half of our talk\, we demonstrate that the E. coli chemotactic system is optimally structured for sensing noisy signals and controlling taxis. We utilize filtering theory and optimal control theory to theoretically derive this optimal structure and compare it to the quantitatively verified biochemical model of chemotaxis. \nIn the latter half\, we discuss the limitations of traditional information theory\, filtering theory\, and optimal control theory in analyzing biological systems. Notably\, all biological systems\, especially simpler ones\, have constrained computational resources like memory size and energy\, which influence optimal behaviors. Conventional theories don’t directly address these resource constraints\, likely because they emerged during a period when computational resources were continually expanding. To address this gap\, we introduce the “memory-limited partially observable optimal control\,” a new theoretical framework developed by our group\, and explore its relevance to biological problems.
URL:https://www.ibs.re.kr/bimag/event/tetsuya-j-kobayashi-optimality-of-biological-information-processing/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2023/08/Tetsuya-Kobayashi-1.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230920T160000
DTEND;TZID=Asia/Seoul:20230920T170000
DTSTAMP:20260525T161810
CREATED:20230831T142706Z
LAST-MODIFIED:20240728T144517Z
UID:8397-1695225600-1695229200@www.ibs.re.kr
SUMMARY:Sebastian Walcher\, Reaction networks: Reduction of dimension and critical parameters
DESCRIPTION:Abstract: Typically\, the mathematical description of reaction networks involves a system of parameter-dependent ordinary differential equations. Generally\, one is interested in the qualitative and quantitative behavior of solutions in various parameter regions. In applications\, identifying the reaction parameters is a fundamental task. Reduction of dimension is desirable from a practical perspective\, and even necessary when different timescales are present. For biochemical reaction networks\, a classical reduction technique assumes quasi-steady state (QSS) of certain species. From a general mathematical perspective\, singular perturbation theory – involving a small parameter – is often invoked. The talk is mathematically oriented. The following points will be discussed: Singular perturbation reduction in general coordinates. (“How does one compute reductions?”) Critical parameters for singular perturbations. (“How does one find small parameters?”) Quasi-steady state and singular perturbations. (“What is applicable\, what is correct?”)
URL:https://www.ibs.re.kr/bimag/event/sebastian-walcher-reaction-networks-reduction-of-dimension-and-critical-parameters/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2023/08/Sebastian-Walcher-1-e1722177866528.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230609T110000
DTEND;TZID=Asia/Seoul:20230609T120000
DTSTAMP:20260525T161810
CREATED:20230218T033305Z
LAST-MODIFIED:20230529T011204Z
UID:7356-1686308400-1686312000@www.ibs.re.kr
SUMMARY:Sushmita Roy\, Deciphering gene regulatory networks underlying cell-fate specification
DESCRIPTION:Abstract: Cell fate specification is a dynamic process during which gene regulatory networks (GRNs) transition between different states and define cell type-specific patterns of gene expression. Identifying such cell type-specific gene regulatory networks is important for understanding how cells differentiate to diverse lineages from a progenitor state\, how differentiated cells can be reprogrammed\, and how these networks get disrupted in diseases such as cancer and developmental disorders. The advent of single cell omics has enabled us to perform high-throughput molecular phenotyping of individual cells at different omic levels. These technologies have revolutionized our understanding of cell type composition across diverse normal and disease conditions; however inferring cell type-specific networks and their dynamics from single cell omic datasets is an open challenge. I will present some of our recent efforts for inference and analysis of cell type-specific regulatory networks from single cell omic datasets. Application of our approach to hematopoietic differentiation and mouse cellular reprogramming predicted key regulatory nodes likely important for establishing different cell-type specific expression programs.
URL:https://www.ibs.re.kr/bimag/event/tbd-2/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2023/02/srpic-1.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230524T160000
DTEND;TZID=Asia/Seoul:20230524T170000
DTSTAMP:20260525T161810
CREATED:20230213T110844Z
LAST-MODIFIED:20230308T101313Z
UID:7342-1684944000-1684947600@www.ibs.re.kr
SUMMARY:Thomas Philipp\, Stochastic gene expression in lineage trees
DESCRIPTION:Abstract: Stochasticity in gene expression is an important source of cell-to-cell variability (or noise) in clonal cell populations. So far\, this phenomenon has been studied using the Gillespie Algorithm\, or the Chemical Master Equation\, which implicitly assumes that cells are independent and do neither grow nor divide. This talk will discuss recent developments in modelling populations of growing and dividing cells through agent-based approaches. I will show how the lineage structure affects gene expression noise over time\, which leads to a straightforward interpretation of cell-to-cell variability in population snapshots. I will also illustrate how cell cycle variability shapes extrinsic noise across lineage trees. Finally\, I outline how to construct effective chemical master equation models based on dilution reactions and extrinsic variability that provide surprisingly accurate approximations of the noise statistics across growing populations. The results highlight that it is crucial to consider cell growth and division when quantifying cellular noise.
URL:https://www.ibs.re.kr/bimag/event/stochastic-gene-expression-in-lineage-trees/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2023/02/PThomastojpeg_1587640386131_x2.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230510T160000
DTEND;TZID=Asia/Seoul:20230510T170000
DTSTAMP:20260525T161810
CREATED:20230213T110735Z
LAST-MODIFIED:20230308T101512Z
UID:7339-1683734400-1683738000@www.ibs.re.kr
SUMMARY:Mogens Jensen\, Droplet formation\, DNA repair and chaos in CellsBD
DESCRIPTION:Abstract: TBD
URL:https://www.ibs.re.kr/bimag/event/tbd/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2023/02/Mogens_Hogh_Jensen.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230428T110000
DTEND;TZID=Asia/Seoul:20230428T120000
DTSTAMP:20260525T161810
CREATED:20230213T110626Z
LAST-MODIFIED:20230308T101702Z
UID:7336-1682679600-1682683200@www.ibs.re.kr
SUMMARY:Hans P.A. Van Dongen\, Modeling the temporal dynamics of neurobehavioral performance impairment due to sleep loss and circadian misalignment
DESCRIPTION:Abstract: The well-known two-process model of sleep regulation makes accurate predictions of sleep timing and duration\, as well as neurobehavioral performance\, for a variety of acute sleep deprivation and nap sleep scenarios\, but it fails to predict the effects of chronic sleep restriction on neurobehavioral performance. The two-process model belongs to a broader class of coupled\, non-homogeneous\, first-order\, ordinary differential equations (ODEs)\, which can capture the effects of chronic sleep restriction. These equations exhibit a bifurcation\, which appears to be an essential feature of performance impairment due to sleep loss. The equations implicate a biological system analogous to two connected compartments containing interacting compounds with time-varying concentrations\, such as the adenosinergic neuromodulator/receptor system\, as a key mechanism for the regulation of neurobehavioral functioning under conditions of sleep loss. The equations account for dynamic interaction with circadian rhythmicity\, and also provide a new approach to dynamically tracking the magnitude of sleep inertia upon awakening from restricted sleep. This presentation will describe the development of the ODE system and its experimental calibration and validation\, and will discuss some novel predictions.
URL:https://www.ibs.re.kr/bimag/event/modeling-the-temporal-dynamics-of-neurobehavioral-performance-impairment-due-to-sleep-loss-and-circadian-misalignment/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2023/02/HANS-VAN-DONGEN-396x293-1.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230407T110000
DTEND;TZID=Asia/Seoul:20230407T120000
DTSTAMP:20260525T161810
CREATED:20230213T110215Z
LAST-MODIFIED:20230308T100617Z
UID:7328-1680865200-1680868800@www.ibs.re.kr
SUMMARY:George Karniadakis\, BINNS: Biophysics-Informed Neural Networks
DESCRIPTION:Abstract: We will present a new approach to develop a data-driven\, learning-based framework for predicting outcomes of biophysical systems and for discovering hidden mechanisms and pathways from noisy data. We will introduce a deep learning approach based on neural networks (NNs) and on generative adversarial networks (GANs). Unlike other approaches that rely on big data\, here we “learn” from small data by exploiting the information provided by the mathematical physics\, e.g..\, conservation laws\, reaction kinetics\, etc\,. which are used to obtain informative priors or regularize the neural networks. We will demonstrate how we can train BINNs from multifidelity/multimodality data\, and we will present several examples of inverse problems\, e.g.\, in systems biology for diabetes and in biomechanics for non-invasive inference of thrombus material properties. We will also discuss how operator regression in the form of DeepOnet can be used to accelerate inference based on historical data and only a few new data\, as well its generalization and transfer learning capacity.
URL:https://www.ibs.re.kr/bimag/event/binns-biophysics-informed-neural-networks/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2023/02/GeorgeKarniadakis.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
END:VCALENDAR