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METHOD:PUBLISH
X-ORIGINAL-URL:https://www.ibs.re.kr/bimag
X-WR-CALDESC:Events for Biomedical Mathematics Group
REFRESH-INTERVAL;VALUE=DURATION:PT1H
X-Robots-Tag:noindex
X-PUBLISHED-TTL:PT1H
BEGIN:VTIMEZONE
TZID:Asia/Seoul
BEGIN:STANDARD
TZOFFSETFROM:+0900
TZOFFSETTO:+0900
TZNAME:KST
DTSTART:20220101T000000
END:STANDARD
END:VTIMEZONE
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230922T140000
DTEND;TZID=Asia/Seoul:20230922T160000
DTSTAMP:20260423T181134
CREATED:20230901T091012Z
LAST-MODIFIED:20230906T083720Z
UID:8440-1695391200-1695398400@www.ibs.re.kr
SUMMARY:Yun Min Song\, A data-driven approach for timescale decomposition of biochemical reaction networks
DESCRIPTION:We will discuss about “A data-driven approach for timescale decomposition of biochemical reaction networks”\, Amir Akbari\, Zachary B. Haiman\, Bernhard O. Palsson\, bioRxiv (2023) \nAbstract \n\nUnderstanding the dynamics of biological systems in evolving environments is a challenge due to their scale and complexity. Here\, we present a computational framework for timescale decomposition of biochemical reaction networks to distill essential patterns from their intricate dynamics. This approach identifies timescale hierarchies\, concentration pools\, and coherent structures from time-series data\, providing a system-level description of reaction networks at physiologically important timescales. We apply this technique to kinetic models of hypothetical and biological pathways\, validating it by reproducing analytically characterized or previously known concentration pools of these pathways. Moreover\, by analyzing the timescale hierarchy of the glycolytic pathway\, we elucidate the connections between the stoichiometric and dissipative structures of reaction networks and the temporal organization of coherent structures. Specifically\, we show that glycolysis is a cofactor driven pathway\, the slowest dynamics of which are described by a balance between high-energy phosphate bond and redox trafficking. Overall\, this approach provides more biologically interpretable characterizations of network dynamics than large-scale kinetic models\, thus facilitating model reduction and personalized medicine applications. \n\n 
URL:https://www.ibs.re.kr/bimag/event/2023-09-22-jc/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
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:20260423T181134
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:20230918T160000
DTEND;TZID=Asia/Seoul:20230918T170000
DTSTAMP:20260423T181134
CREATED:20230918T080118Z
LAST-MODIFIED:20230918T080118Z
UID:8524-1695052800-1695056400@www.ibs.re.kr
SUMMARY:Balazs Erdos\, Quantifying the dynamics of postmeal metabolism: Inference from challenge test data
DESCRIPTION:
URL:https://www.ibs.re.kr/bimag/event/balazs-erdos-quantifying-the-dynamics-of-postmeal-metabolism-inference-from-challenge-test-data/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230915T140000
DTEND;TZID=Asia/Seoul:20230915T160000
DTSTAMP:20260423T181134
CREATED:20230829T100538Z
LAST-MODIFIED:20230914T051626Z
UID:8371-1694786400-1694793600@www.ibs.re.kr
SUMMARY:Eui Min Jung\, Antithetic proportional-integral feedback for reduced variance and improved control performance of stochastic reaction networks
DESCRIPTION:We will discuss about “Antithetic proportional-integral feedback for reduced variance and improved control performance of stochastic reaction networks\n”\,Briat\, Corentin\, Ankit Gupta\, and Mustafa Khammash.\, Journal of The Royal Society Interface 15.143 (2018): 20180079 \nAbstract \n\n\n\n\n\n\n\nThe ability of a cell to regulate and adapt its internal state in response to unpredictable environmental changes is called homeostasis and this ability is crucial for the cell’s survival and proper functioning. Understanding how cells can achieve homeostasis\, despite the intrinsic noise or randomness in their dynamics\, is fundamentally important for both systems and synthetic biology. In this context\, a significant development is the proposed antithetic integral feedback (AIF) motif\, which is found in natural systems\, and is known to ensure robust perfect adaptation for the mean dynamics of a given molecular species involved in a complex stochastic biomolecular reaction network. From the standpoint of applications\, one drawback of this motif is that it often leads to an increased cell-to-cell heterogeneity or variance when compared to a constitutive (i.e. open-loop) control strategy. Our goal in this paper is to show that this performance deterioration can be countered by combining the AIF motif and a negative feedback strategy. Using a tailored moment closure method\, we derive approximate expressions for the stationary variance for the controlled network that demonstrate that increasing the strength of the negative feedback can indeed decrease the variance\, sometimes even below its constitutive level. Numerical results verify the accuracy of these results and we illustrate them by considering three biomolecular networks with two types of negative feedback strategies. Our computational analysis indicates that there is a trade-off between the speed of the settling-time of the mean trajectories and the stationary variance of the controlled species; i.e. smaller variance is associated with larger settling-time.
URL:https://www.ibs.re.kr/bimag/event/2023-09-15-jc/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230914T160000
DTEND;TZID=Asia/Seoul:20230914T173000
DTSTAMP:20260423T181134
CREATED:20230913T040446Z
LAST-MODIFIED:20230913T040446Z
UID:8516-1694707200-1694712600@www.ibs.re.kr
SUMMARY:Jonathan Rubin\, Qualitative inverse problems: mapping from limited data to properties of dynamics and parameter values for ODE models
DESCRIPTION:
URL:https://www.ibs.re.kr/bimag/event/jonathan-rubin-qualitative-inverse-problems-mapping-from-limited-data-to-properties-of-dynamics-and-parameter-values-for-ode-models/
LOCATION:KAIST E6-1 1501 Auditorium\, 291 Daehak-ro\, Yuseong-gu\, Daejeon\, 34141\, Korea\, Republic of
CATEGORIES:Seminar
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2023/09/2023FallMathColloquium-scaled.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230908T140000
DTEND;TZID=Asia/Seoul:20230908T160000
DTSTAMP:20260423T181134
CREATED:20230829T100233Z
LAST-MODIFIED:20230907T044351Z
UID:8369-1694181600-1694188800@www.ibs.re.kr
SUMMARY:Dongju Lim\, Exact solution of a three-stage model of stochastic gene expression including cell-cycle dynamics
DESCRIPTION:We will discuss about “Exact solution of a three-stage model of stochastic gene expression including cell-cycle dynamics”\, Wang\, Yiling\, et al.\, bioRxiv (2023): 2023-08. \n  \nAbstract \n\n\n\n\n\n\nThe classical three-stage model of stochastic gene expression predicts the statistics of single cell mRNA and protein number fluctuations as a function of the rates of promoter switching\, transcription\, translation\, degradation and dilution. While this model is easily simulated\, its analytical solution remains an unsolved problem. Here we modify this model to explicitly include cell-cycle dynamics and then derive an exact solution for the time-dependent joint distribution of mRNA and protein numbers. We show large differences between this model and the classical model which captures cell-cycle effects implicitly via effective first-order dilution reactions. In particular we find that the Fano factor of protein numbers calculated from a population snapshot measurement are underestimated by the classical model whereas the correlation between mRNA and protein can be either over- or underestimated\, depending on the timescales of mRNA degradation and promoter switching relative to the mean cell-cycle duration time. \n 
URL:https://www.ibs.re.kr/bimag/event/2023-09-08-jc/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230906T160000
DTEND;TZID=Asia/Seoul:20230906T170000
DTSTAMP:20260423T181134
CREATED:20230904T132811Z
LAST-MODIFIED:20230904T132811Z
UID:8487-1694016000-1694019600@www.ibs.re.kr
SUMMARY:Jonathan Rubin\, Multiple timescale modeling for neural systems
DESCRIPTION:Abstract \nMathematical models of biological systems\, including neurons\, often feature components that evolve on very different timescales. Mathematical analysis of these multi-timescale systems can be greatly simplified by partitioning them into subsystems that evolve on different time scales. The subsystems are then analyzed semi-independently\, using a technique called fast-slow analysis. I will briefly describe the fast-slow analysis technique and its application to neuronal bursting oscillations and basic coupled neuron modeling. After this\, I will discuss fancier forms of dynamics such as canard oscillations\, mixed-mode oscillations\, and three-timescale dynamics. Although these examples all involve neural systems\, the methods can and have been applied to other biological\, chemical\, and physical systems.
URL:https://www.ibs.re.kr/bimag/event/jonathan-rubin-multiple-timescale-modeling-for-neural-systems/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230901T100000
DTEND;TZID=Asia/Seoul:20230901T120000
DTSTAMP:20260423T181134
CREATED:20230810T082738Z
LAST-MODIFIED:20230831T040832Z
UID:8236-1693562400-1693569600@www.ibs.re.kr
SUMMARY:Hyeongjun Jang\, Generalized Michaelis–Menten rate law with time-varying molecular concentrations
DESCRIPTION:We will discuss about “Generalized Michaelis–Menten rate law with time-varying molecular concentrations”\, Lim\, Roktaek\, et al.\,bioRxiv (2022): 2022-01 \n  \nAbstract \n\n\n\n\n\n\nThe Michaelis–Menten (MM) rate law has been the dominant paradigm of modeling biochemical rate processes for over a century with applications in biochemistry\, biophysics\, cell biology\, and chemical engineering. The MM rate law and its remedied form stand on the assumption that the concentration of the complex of interacting molecules\, at each moment\, approaches an equilibrium much faster than the molecular concentrations change. Yet\, this assumption is not always justified. Here\, we relax this quasi-steady state requirement and propose the generalized MM rate law for the interactions of molecules with active concentration changes over time. Our approach for time-varying molecular concentrations\, termed the effective time-delay scheme (ETS)\, is based on rigorously estimated time-delay effects in molecular complex formation. With particularly marked improvements in protein– protein and protein–DNA interaction modeling\, the ETS provides an analytical framework to interpret and predict rich transient or rhythmic dynamics (such as autogenously-regulated cellular adaptation and circadian protein turnover)\, which goes beyond the quasi-steady state assumption.
URL:https://www.ibs.re.kr/bimag/event/2023-09-01-jc/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230814T120000
DTEND;TZID=Asia/Seoul:20230814T130000
DTSTAMP:20260423T181134
CREATED:20230730T231426Z
LAST-MODIFIED:20230814T093131Z
UID:8144-1692014400-1692018000@www.ibs.re.kr
SUMMARY:Dongju Lim and Olive Cawiding
DESCRIPTION:Dongju Lim: Mood Prediction for Bipolar Disorder Patient with Sleep Pattern Information \nOlive Cawiding: Detecting causality between weather variables and dengue cases in the Philippines \n  \n 
URL:https://www.ibs.re.kr/bimag/event/2023-08-14-lls/
LOCATION:Tea Room\, IBS\, Daejeon\, Daejeon\, 34141\, Korea\, Republic of
CATEGORIES:Lunch Lab Meeting Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230811T150000
DTEND;TZID=Asia/Seoul:20230811T170000
DTSTAMP:20260423T181134
CREATED:20230730T230909Z
LAST-MODIFIED:20230809T124859Z
UID:8141-1691766000-1691773200@www.ibs.re.kr
SUMMARY:Olive Cawiding\, Decomposing predictability to identify dominant causal drivers in complex ecosystems
DESCRIPTION:We will discuss about “ Decomposing predictability to identify dominant causal drivers in complex ecosystems ”\,Suzuki\, Kenta\, Shin-ichiro S. Matsuzaki\, and Hiroshi Masuya.\, Proceedings of the National Academy of Sciences 119.42 (2022): e2204405119. \n  \nAbstract \n\nEcosystems are complex systems of various physical\, biological\, and chemical processes. Since ecosystem dynamics are composed of a mixture of different levels of stochasticity and nonlinearity\, handling these data is a challenge for existing methods of time series–based causal inferences. Here\, we show that\, by harnessing contemporary machine learning approaches\, the concept of Granger causality can be effectively extended to the analysis of complex ecosystem time series and bridge the gap between dynamical and statistical approaches. The central idea is to use an ensemble of fast and highly predictive artificial neural networks to select a minimal set of variables that maximizes the prediction of a given variable. It enables decomposition of the relationship among variables through quantifying the contribution of an individual variable to the overall predictive performance. We show how our approach\, EcohNet\, can improve interaction network inference for a mesocosm experiment and simulated ecosystems. The application of the method to a long-term lake monitoring dataset yielded interpretable results on the drivers causing cyanobacteria blooms\, which is a serious threat to ecological integrity and ecosystem services. Since performance of EcohNet is enhanced by its predictive capabilities\, it also provides an optimized forecasting of overall components in ecosystems. EcohNet could be used to analyze complex and hybrid multivariate time series in many scientific areas not limited to ecosystems.
URL:https://www.ibs.re.kr/bimag/event/2023-08-11-jc/
LOCATION:B232 Seminar Room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230804T140000
DTEND;TZID=Asia/Seoul:20230804T160000
DTSTAMP:20260423T181134
CREATED:20230729T064450Z
LAST-MODIFIED:20230730T231258Z
UID:8131-1691157600-1691164800@www.ibs.re.kr
SUMMARY:Seokhwan Moon\, The Internal Model Principle for Biomolecular Control Theory
DESCRIPTION:We will discuss about “ The Internal Model Principle for Biomolecular Control Theory ”\, Gupta\, Ankit\, and Mustafa Khammash.\, IEEE Open Journal of Control Systems 2 (2023): 63-69. \n  \nAbstract \nThe well-known Internal Model Principle (IMP) is a cornerstone of modern control theory. It stipulates the necessary conditions for asymptotic robustness of disturbance-prone dynamical systems by asserting that such a system must embed a subsystem in a feedback loop\, and this subsystem must be able to reduplicate the dynamic disturbance using only the regulated variable as the input. The insights provided by IMP can help in both designing suitable controllers and also in analysing the regulatory mechanisms in complex systems. So far the application of IMP in biology has been case-specific and ad hoc\, primarily due to the lack of generic versions of the IMP for biomolecular reaction networks that model biological processes. In this short article we highlight the need for an IMP in biology and discuss a recently developed version of it for biomolecular networks that exhibit maximal Robust Perfect Adaptation (maxRPA) by being robust to the maximum number of disturbance sources.
URL:https://www.ibs.re.kr/bimag/event/2023-08-04-jc/
LOCATION:B232 Seminar Room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230731T120000
DTEND;TZID=Asia/Seoul:20230731T130000
DTSTAMP:20260423T181134
CREATED:20230629T055843Z
LAST-MODIFIED:20230731T143536Z
UID:7966-1690804800-1690808400@www.ibs.re.kr
SUMMARY:Yun Min Song and Seokjoo Chae
DESCRIPTION:Yun Min Song: Noisy delay denoises biochemical oscillators \nSeokjoo Chae: Reduction of spatiotemporal model and its validity condition
URL:https://www.ibs.re.kr/bimag/event/2023-07-31-lls/
LOCATION:Tea Room\, IBS\, Daejeon\, Daejeon\, 34141\, Korea\, Republic of
CATEGORIES:Lunch Lab Meeting Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230728T100000
DTEND;TZID=Asia/Seoul:20230728T110000
DTSTAMP:20260423T181134
CREATED:20230619T074840Z
LAST-MODIFIED:20230726T042649Z
UID:7948-1690538400-1690542000@www.ibs.re.kr
SUMMARY:Yun Min Song\, The singularity response reveals entrainment properties of the plant circadian clock
DESCRIPTION:We will discuss about “The singularity response reveals entrainment properties of the plant circadian clock”\, Masuda\, Kosaku\, et al.\, Nature Communications 12.1 (2021): 864. \nAbstract \n\n\n\n\n\n\nCircadian clocks allow organisms to synchronize their physiological processes to diurnal variations. A phase response curve allows researchers to understand clock entrainment by revealing how signals adjust clock genes differently according to the phase in which they are applied. Comprehensively investigating these curves is difficult\, however\, because of the cost of measuring them experimentally. Here we demonstrate that fundamental properties of the curve are recoverable from the singularity response\, which is easily measured by applying a single stimulus to a cellular network in a desynchronized state (i.e. singularity). We show that the singularity response of Arabidopsis to light/dark and temperature stimuli depends on the properties of the phase response curve for these stimuli. The measured singularity responses not only allow the curves to be precisely reconstructed but also reveal organ-specific properties of the plant circadian clock. The method is not only simple and accurate\, but also general and applicable to other coupled oscillator systems as long as the oscillators can be desynchronized. This simplified method may allow the entrainment properties of the circadian clock of both plants and other species in nature.
URL:https://www.ibs.re.kr/bimag/event/2023-07-28/
LOCATION:B232 Seminar Room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230707T140000
DTEND;TZID=Asia/Seoul:20230707T160000
DTSTAMP:20260423T181134
CREATED:20230529T032440Z
LAST-MODIFIED:20230707T034944Z
UID:7807-1688738400-1688745600@www.ibs.re.kr
SUMMARY:Hyun Kim\, scPrisma infers\, filters and enhances topological signals in single-cell data using spectral template matching
DESCRIPTION:We will discuss about “scPrisma infers\, filters and enhances topological signals in single-cell data using spectral template matching”\, Karin\, Jonathan\, Yonathan Bornfeld\, and Mor Nitzan.\, Nature Biotechnology (2023): 1-10. \nAbstract \n\n\n\nSingle-cell RNA sequencing has been instrumental in uncovering cellular spatiotemporal context. This task is challenging as cells simultaneously encode multiple\, potentially cross-interfering\, biological signals. Here we propose scPrisma\, a spectral computational method that uses topological priors to decouple\, enhance and filter different classes of biological processes in single-cell data\, such as periodic and linear signals. We apply scPrisma to the analysis of the cell cycle in HeLa cells\, circadian rhythm and spatial zonation in liver lobules\, diurnal cycle in Chlamydomonas and circadian rhythm in the suprachiasmatic nucleus in the brain. scPrisma can be used to distinguish mixed cellular populations by specific characteristics such as cell type and uncover regulatory networks and cell–cell interactions specific to predefined biological signals\, such as the circadian rhythm. We show scPrisma’s flexibility in incorporating prior knowledge\, inference of topologically informative genes and generalization to additional diverse templates and systems. scPrisma can be used as a stand-alone workflow for signal analysis and as a prior step for downstream single-cell analysis.
URL:https://www.ibs.re.kr/bimag/event/2023-07-07-jc/
LOCATION:B232 Seminar Room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230705T120000
DTEND;TZID=Asia/Seoul:20230705T130000
DTSTAMP:20260423T181134
CREATED:20230629T055533Z
LAST-MODIFIED:20230704T011831Z
UID:7964-1688558400-1688562000@www.ibs.re.kr
SUMMARY:Hyukpyo Hong and Seokmin Ha
DESCRIPTION:Hyukpyo Hong: Advancing Infectious Disease Modeling: Estimating Reproduction Number with Realistic Latent and Infectious Periods \nSeokmin Ha: Systematic inference-driven experiments reveal a fundamental mechanism governing clock protein interactions in plants
URL:https://www.ibs.re.kr/bimag/event/2023-07-05-lls/
LOCATION:Tea Room\, IBS\, Daejeon\, Daejeon\, 34141\, Korea\, Republic of
CATEGORIES:Lunch Lab Meeting Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230622T140000
DTEND;TZID=Asia/Seoul:20230622T160000
DTSTAMP:20260423T181134
CREATED:20230615T052932Z
LAST-MODIFIED:20230615T052932Z
UID:7932-1687442400-1687449600@www.ibs.re.kr
SUMMARY:Dae Wook kim\, "Wearable data science for personalized digital medicine"
DESCRIPTION:We will discuss about “Wearable data science for personalized digital medicine” \nAbstract \nMillions of people currently use wearables such as the Apple Watch to monitor their physical activity\, heart rate\, and other physiological signals\, generating an unprecedented amount of wearable data. This presents an opportunity for digital medicine to advance precision medicine. However\, the noisy nature of this wearable data makes it appear unusable without new mathematical techniques to extract key signals from it. In this talk\, I will discuss several techniques we have developed for analyzing this noisy time-series data\, including the level-set Kalman filter-based data assimilation technique – a new state space estimation method that can estimate the phase of circadian rhythms. Additionally\, I will introduce a Kalman filter-assisted autoencoder used for anomaly detection in time-series data\, as well as feature engineering based on persistent homology and mathematical modeling. These techniques have practical applications\, such as sleep scoring\, detection of physiological changes related to COVID-19\, and daily mood prediction.
URL:https://www.ibs.re.kr/bimag/event/2023-06-22-jc/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230619T120000
DTEND;TZID=Asia/Seoul:20230619T130000
DTSTAMP:20260423T181134
CREATED:20230529T074802Z
LAST-MODIFIED:20230619T031311Z
UID:7837-1687176000-1687179600@www.ibs.re.kr
SUMMARY:Abbas Abbasli and Hyeongjun Jang
DESCRIPTION:Abbas Abbasli: Accurate prediction of in-vivo drug interaction mediated by cytochrome P450 inhibition \nHyeongjun Jang: Comparison of the inhibition constant approximation methods
URL:https://www.ibs.re.kr/bimag/event/2023-06-19-lls/
LOCATION:Tea Room\, IBS\, Daejeon\, Daejeon\, 34141\, Korea\, Republic of
CATEGORIES:Lunch Lab Meeting Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230612T120000
DTEND;TZID=Asia/Seoul:20230612T130000
DTSTAMP:20260423T181134
CREATED:20230529T074201Z
LAST-MODIFIED:20230529T110236Z
UID:7834-1686571200-1686574800@www.ibs.re.kr
SUMMARY:Hyun Kim
DESCRIPTION:TBD
URL:https://www.ibs.re.kr/bimag/event/2023-06-12-llb/
LOCATION:Tea Room\, IBS\, Daejeon\, Daejeon\, 34141\, Korea\, Republic of
CATEGORIES:Lunch Lab Meeting Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230609T140000
DTEND;TZID=Asia/Seoul:20230609T160000
DTSTAMP:20260423T181134
CREATED:20230529T032327Z
LAST-MODIFIED:20230608T050231Z
UID:7805-1686319200-1686326400@www.ibs.re.kr
SUMMARY:Seokjoo Chae\, The energy cost and optimal design of networks for biological discrimination
DESCRIPTION:We will discuss about “The energy cost and optimal design of networks for biological discrimination”\, Yu\, Qiwei\, Anatoly B. Kolomeisky\, and Oleg A. Igoshin.\, Journal of the Royal Society Interface 19.188 (2022): 20210883. \nAbstract \n\n\nMany biological processes discriminate between correct and incorrect substrates through the kinetic proofreading mechanism that enables lower error at the cost of higher energy dissipation. Elucidating physico-chemical constraints for global minimization of dissipation and error is important for understanding enzyme evolution. Here\, we identify theoretically a fundamental error–cost bound that tightly constrains the performance of proofreading networks under any parameter variations preserving the rate discrimination between substrates. The bound is kinetically controlled\, i.e. completely determined by the difference between the transition state energies on the underlying free energy landscape. The importance of the bound is analysed for three biological processes. DNA replication by T7 DNA polymerase is shown to be nearly optimized\, i.e. its kinetic parameters place it in the immediate proximity of the error–cost bound. The isoleucyl-tRNA synthetase (IleRS) of E. coli also operates close to the bound\, but further optimization is prevented by the need for reaction speed. In contrast\, E. coli ribosome operates in a high-dissipation regime\, potentially in order to speed up protein production. Together\, these findings establish a fundamental error–dissipation relation in biological proofreading networks and provide a theoretical framework for studying error–dissipation trade-off in other systems with biological discrimination.
URL:https://www.ibs.re.kr/bimag/event/2023-06-09-jc/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
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:20260423T181134
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:20230608T110000
DTEND;TZID=Asia/Seoul:20230608T120000
DTSTAMP:20260423T181134
CREATED:20230601T080809Z
LAST-MODIFIED:20230605T043518Z
UID:7870-1686222000-1686225600@www.ibs.re.kr
SUMMARY:Seonjin Kim\, Nonparametric vs Parametric Regression
DESCRIPTION:To understand nonparametric regression\, we should know first what the parametric model is. Simply speaking\, the parametric regression model consists of many assumptions and the nonparametric regression model eases the assumptions. I will introduce what assumptions the parametric regression model has and how the nonparametric regression model relieves them. In addition\, their pros and cons will be also presented.
URL:https://www.ibs.re.kr/bimag/event/nonparametric-vs-parametric-regression/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230602T140000
DTEND;TZID=Asia/Seoul:20230602T160000
DTSTAMP:20260423T181134
CREATED:20230529T032114Z
LAST-MODIFIED:20230529T032114Z
UID:7803-1685714400-1685721600@www.ibs.re.kr
SUMMARY:Eui Min Jung\, Uncovering specific mechanisms across cell types in dynamical models
DESCRIPTION:We will discuss about “Uncovering specific mechanisms across cell types in dynamical models”\, Hauber\, Adrian Lukas\, Marcus Rosenblatt\, and Jens Timmer.\, bioRxiv (2023): 2023-01. \nAbstract \nOrdinary differential equations are frequently employed for mathematical modeling of biological systems. The identification of mechanisms that are specific to certain cell types is crucial for building useful models and to gain insights into the underlying biological processes. Regularization techniques have been proposed and applied to identify mechanisms specific to two cell types\, e.g.\, healthy and cancer cells\, including the LASSO (least absolute shrinkage and selection operator). However\, when analyzing more than two cell types\, these approaches are not consistent\, and require the selection of a reference cell type\, which can affect the results. \nTo make the regularization approach applicable to identifying cell-type specific mechanisms in any number of cell types\, we propose to incorporate the clustered LASSO into the framework of ordinary differential equation modeling by penalizing the pairwise differences of the logarithmized fold-change parameters encoding a specific mechanism in different cell types. The symmetry introduced by this approach renders the results independent of the reference cell type. We discuss the necessary adaptations of state-of-the-art numerical optimization techniques and the process of model selection for this method. We assess the performance with realistic biological models and synthetic data\, and demonstrate that it outperforms existing approaches. Finally\, we also exemplify its application to published biological models including experimental data\, and link the results to independent biological measurements.
URL:https://www.ibs.re.kr/bimag/event/2023-06-02-jc/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230531T120000
DTEND;TZID=Asia/Seoul:20230531T130000
DTSTAMP:20260423T181134
CREATED:20230529T035221Z
LAST-MODIFIED:20230529T102040Z
UID:7809-1685534400-1685538000@www.ibs.re.kr
SUMMARY:Dongju Lim\, Eui Min Jeong\, Hyeontae Jo
DESCRIPTION:Dongju Lim: Mood Prediction for Bipolar Disorder Patient with Sleep Pattern Information \n  \nEui Min Jeong:Noise attenuation through the multiple repression mechanism in transcription \n  \nHyeontae Jo: Parameter estimation with discontinuously switching system
URL:https://www.ibs.re.kr/bimag/event/2023-05-31-lls/
LOCATION:Tea Room\, IBS\, Daejeon\, Daejeon\, 34141\, Korea\, Republic of
CATEGORIES:Lunch Lab Meeting Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230530T160000
DTEND;TZID=Asia/Seoul:20230530T170000
DTSTAMP:20260423T181134
CREATED:20230524T125426Z
LAST-MODIFIED:20230524T125651Z
UID:7788-1685462400-1685466000@www.ibs.re.kr
SUMMARY:Trivial but not trivial things in data science: From a statistical perspective
DESCRIPTION:TBA
URL:https://www.ibs.re.kr/bimag/event/t/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230526T140000
DTEND;TZID=Asia/Seoul:20230526T160000
DTSTAMP:20260423T181134
CREATED:20230430T034034Z
LAST-MODIFIED:20230524T094243Z
UID:7650-1685109600-1685116800@www.ibs.re.kr
SUMMARY:Hyeontae Jo\,Parameter Estimation of Power Electronic Converters With Physics-Informed Machine Learning
DESCRIPTION:We will discuss about “Parameter Estimation of Power Electronic Converters With Physics-Informed Machine Learning”\, Zhao\, Shuai\, et al.\, IEEE Transactions on Power Electronics 37.10 (2022): 11567-11578. \nAbstract \nPhysics-informed machine learning (PIML) has been emerging as a promising tool for applications with domain knowledge and physical models. To uncover its potentials in power electronics\, this article proposes a PIML-based parameter estimation method demonstrated by a case study of dc–dc Buck converter. A deep neural network and the dynamic models of the converter are seamlessly coupled. It overcomes the challenges related to training data\, accuracy\, and robustness which a typical data-driven approach has. This exemplary application envisions to provide a new perspective for tailoring existing machine learning tools for power electronics.
URL:https://www.ibs.re.kr/bimag/event/2023-05-26-jc/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230525T110000
DTEND;TZID=Asia/Seoul:20230525T120000
DTSTAMP:20260423T181134
CREATED:20230522T134427Z
LAST-MODIFIED:20230522T134449Z
UID:7767-1685012400-1685016000@www.ibs.re.kr
SUMMARY:Nonparametric predictive model for sparse and irregular longitudinal data
DESCRIPTION:We propose a kernel-based estimator to predict the mean response trajectory for sparse and irregularly measured longitudinal data. The kernel estimator is constructed by imposing weights based on the subject-wise similarity on L2 metric space between predictor trajectories\, where we assume that an analogous fashion in predictor trajectories over time would result in a similar trend in the response trajectory among subjects. In order to deal with the curse of dimensionality caused by the multiple predictors\, we propose an appealing multiplicative model with multivariate Gaussian kernels. This model is capable of achieving dimension reduction as well as selecting functional covariates with predictive significance. The asymptotic properties of the proposed nonparametric estimator are investigated under mild regularity conditions. We illustrate the robustness and flexibility of our proposed method via the simulation study and an application to Framingham Heart Study
URL:https://www.ibs.re.kr/bimag/event/2023-05-25-seminar/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
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:20260423T181134
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:20230522T120000
DTEND;TZID=Asia/Seoul:20230522T130000
DTSTAMP:20260423T181134
CREATED:20230509T062709Z
LAST-MODIFIED:20230509T062709Z
UID:7730-1684756800-1684760400@www.ibs.re.kr
SUMMARY:Pan Li\, Modeling the circadian control of cardiac function
DESCRIPTION:Abstract: TBA
URL:https://www.ibs.re.kr/bimag/event/pan-li-modeling-the-circadian-control-of-cardiac-function/
LOCATION:IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230519T140000
DTEND;TZID=Asia/Seoul:20230519T160000
DTSTAMP:20260423T181134
CREATED:20230430T033701Z
LAST-MODIFIED:20230515T040214Z
UID:7648-1684504800-1684512000@www.ibs.re.kr
SUMMARY:Dongju Lim\, A multi-scale model explains oscillatory slowing and neuronal hyperactivity in Alzheimer’s disease
DESCRIPTION:We will discuss about “A multi-scale model explains oscillatory slowing and neuronal hyperactivity in Alzheimer’s disease”\, Alexandersen\, Christoffer G.\, et al.\, Journal of the Royal Society Interface 20.198 (2023): 20220607. \nAbstract \n\n\n\n\n\n\nAlzheimer’s disease is the most common cause of dementia and is linked to the spreading of pathological amyloid-β and tau proteins throughout the brain. Recent studies have highlighted stark differences in how amyloid-β and tau affect neurons at the cellular scale. On a larger scale\, Alzheimer’s patients are observed to undergo a period of early-stage neuronal hyperactivation followed by neurodegeneration and frequency slowing of neuronal oscillations. Herein\, we model the spreading of both amyloid-β and tau across a human connectome and investigate how the neuronal dynamics are affected by disease progression. By including the effects of both amyloid-β and tau pathology\, we find that our model explains AD-related frequency slowing\, early-stage hyperactivation and late-stage hypoactivation. By testing different hypotheses\, we show that hyperactivation and frequency slowing are not due to the topological interactions between different regions but are mostly the result of local neurotoxicity induced by amyloid-β and tau protein.
URL:https://www.ibs.re.kr/bimag/event/2023-05-19-jc/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230512T110000
DTEND;TZID=Asia/Seoul:20230512T130000
DTSTAMP:20260423T181134
CREATED:20230430T155858Z
LAST-MODIFIED:20230508T134254Z
UID:7653-1683889200-1683896400@www.ibs.re.kr
SUMMARY:Hyukpyo Hong\, Inference and uncertainty quantification of stochastic gene expression via synthetic models
DESCRIPTION:We will discuss about “Inference and uncertainty quantification of stochastic gene expression via synthetic models”\, Öcal et al.\, J. R. Soc. Interface. \nAbstract \n\n\n\n\nEstimating uncertainty in model predictions is a central task in quantitativebiology. Biological models at the single-cell level are intrinsically stochastic and nonlinear\, creating formidable challenges for their statistical estimation which inevitably has to rely on approximations that trade accuracy for tractability. Despite intensive interest\, a sweet spot in this trade-off has not been found yet. We propose a flexible procedure for uncertainty quantification in a wide class of reaction networks describing stochastic gene expression including those with feedback. The method is based on creating a tractable coarse-graining of the model that is learned from simulations\, a synthetic model\, to approximate the likelihood function. We demonstrate that synthetic models can substantially outperform state-of-the-art approaches on a number of non-trivial systems and datasets\, yielding an accurate and computationally viable solution to uncertainty quantification in stochastic models of gene expression.
URL:https://www.ibs.re.kr/bimag/event/2023-05-12-jc/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
END:VCALENDAR