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PRODID:-//Biomedical Mathematics Group - ECPv6.15.20//NONSGML v1.0//EN
CALSCALE:GREGORIAN
METHOD:PUBLISH
X-WR-CALNAME:Biomedical Mathematics Group
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:20210101T000000
END:STANDARD
END:VTIMEZONE
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220104T111000
DTEND;TZID=Asia/Seoul:20220104T120000
DTSTAMP:20260509T220245
CREATED:20220103T002320Z
LAST-MODIFIED:20220103T002320Z
UID:5432-1641294600-1641297600@www.ibs.re.kr
SUMMARY:Stem cell dynamics in the intestine and stomach
DESCRIPTION:In adult tissues\, stem cells undergo clonal competition because they proliferate while the stem cell niche provides limited space. This clonal competition allows the selection of healthy stem cells over time as unfit stem cells tend to lose from the competition. It could also be a mechanism to select a supercompetitor with tumorigenic mutations\, which may lead to tumorigenesis. I am going to explain general concepts of clonal competition and how a simple model can explain the behaviour of adult stem cells. I will also show how geometric constraints affect the overall dynamics of stem cell competition.
URL:https://www.ibs.re.kr/bimag/event/2022-01-03/
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:20220105T160000
DTEND;TZID=Asia/Seoul:20220105T173000
DTSTAMP:20260509T220245
CREATED:20220104T220000Z
LAST-MODIFIED:20211224T001927Z
UID:5366-1641398400-1641403800@www.ibs.re.kr
SUMMARY:Structure-based analysis of chemical reaction networks 1/2
DESCRIPTION:Abstract: Inside living cells\, chemical reactions form a large web of networks. Understanding the behavior of those complex reaction networks is an important and challenging problem. In many situations\, it is hard to identify the details of the reactions\, such as the reaction kinetics and parameter values. It would be good if we can clarify what we can say about the behavior of reaction systems\, when we know the structure of reaction networks but reaction kinetics is unknown. In these talks\, I plan to introduce two approaches in this spirit. Firstly\, we will discuss the sensitivity analysis of reaction systems based on the structural information of reaction networks [1]. I will give an introduction to the method of identifying subnetworks inside which the effects of the perturbation of reaction parameters are confined. Secondly\, I will introduce the reduction method that we developed recently [2]. In those two methods\, an integer determined by the topology of a subnetwork\, which we call an influence index\, plays a crucial role. \nReferences \n[1] T. Okada\, A. Mochizuki\, “Law of Localization in Chemical Reaction Networks\,” Phys. Rev. Lett. 117\, 048101 (2016); T. Okada\, A. Mochizuki\, “Sensitivity and network topology in chemical reaction systems\,” Phys. Rev. E 96\, 022322 (2017). \n[2] Y. Hirono\, T. Okada\, H. Miyazaki\, Y. Hidaka\, “Structural reduction of chemical reaction networks based on topology”\, Phys. Rev. Research 3\, 043123 (2021).
URL:https://www.ibs.re.kr/bimag/event/2022-01-05/
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:20220106T160000
DTEND;TZID=Asia/Seoul:20220106T173000
DTSTAMP:20260509T220245
CREATED:20220105T220000Z
LAST-MODIFIED:20211224T001917Z
UID:5369-1641484800-1641490200@www.ibs.re.kr
SUMMARY:Structure-based analysis of chemical reaction networks 2/2
DESCRIPTION:Inside living cells\, chemical reactions form a large web of networks. Understanding the behavior of those complex reaction networks is an important and challenging problem. In many situations\, it is hard to identify the details of the reactions\, such as the reaction kinetics and parameter values. It would be good if we can clarify what we can say about the behavior of reaction systems\, when we know the structure of reaction networks but reaction kinetics is unknown. In these talks\, I plan to introduce two approaches in this spirit. Firstly\, we will discuss the sensitivity analysis of reaction systems based on the structural information of reaction networks [1]. I will give an introduction to the method of identifying subnetworks inside which the effects of the perturbation of reaction parameters are confined. Secondly\, I will introduce the reduction method that we developed recently [2]. In those two methods\, an integer determined by the topology of a subnetwork\, which we call an influence index\, plays a crucial role. \n[1] T. Okada\, A. Mochizuki\, “Law of Localization in Chemical Reaction Networks\,” Phys. Rev. Lett. 117\, 048101 (2016); T. Okada\, A. Mochizuki\, “Sensitivity and network topology in chemical reaction systems\,” Phys. Rev. E 96\, 022322 (2017). \n[2] Y. Hirono\, T. Okada\, H. Miyazaki\, Y. Hidaka\, “Structural reduction of chemical reaction networks based on topology”\, Phys. Rev. Research 3\, 043123 (2021).
URL:https://www.ibs.re.kr/bimag/event/2022-01-06/
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:20220107T130000
DTEND;TZID=Asia/Seoul:20220107T140000
DTSTAMP:20260509T220245
CREATED:20220106T190000Z
LAST-MODIFIED:20211224T001535Z
UID:5363-1641560400-1641564000@www.ibs.re.kr
SUMMARY:Fundamental limits on the suppression of molecular fluctuations
DESCRIPTION:We will discuss about “Fundamental limits on the suppression of molecular fluctuations”\, Lestas et al\, Nature\, 2010 \nAbstract: Negative feedback is common in biological processes and can increase a system’s stability to internal and external perturbations. But at the molecular level\, control loops always involve signalling steps with finite rates for random births and deaths of individual molecules. Here we show\, by developing mathematical tools that merge control and information theory with physical chemistry\, that seemingly mild constraints on these rates place severe limits on the ability to suppress molecular fluctuations. Specifically\, the minimum standard deviation in abundances decreases with the quartic root of the number of signalling events\, making it extremely expensive to increase accuracy. Our results are formulated in terms of experimental observables\, and existing data show that cells use brute force when noise suppression is essential; for example\, regulatory genes are transcribed tens of thousands of times per cell cycle. The theory challenges conventional beliefs about biochemical accuracy and presents an approach to the rigorous analysis of poorly characterized biological systems.
URL:https://www.ibs.re.kr/bimag/event/2022-01-07/
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:20220113T130000
DTEND;TZID=Asia/Seoul:20220113T140000
DTSTAMP:20260509T220245
CREATED:20220112T190000Z
LAST-MODIFIED:20220112T070151Z
UID:5395-1642078800-1642082400@www.ibs.re.kr
SUMMARY:Quasi-Entropy Closure: A Fast and Reliable Approach to Close the Moment Equations of the Chemical Master Equation
DESCRIPTION:We will discuss about “Quasi-Entropy Closure: A Fast and Reliable Approach to Close the Moment Equations of the Chemical Master Equation”\, Wagner et al\, bioRxiv\, 2021 \nMotivation: The Chemical Master Equation is the most comprehensive stochastic approach to describe the evolution of a (bio-)chemical reaction system. Its solution is a time-dependent probability distribution on all possible configurations of the system. As the number of possible configurations is typically very large\, the Master Equation is often practically unsolvable. The Method of Moments reduces the system to the evolution of a few moments of this distribution\, which are described by a system of ordinary differential equations. Those equations are not closed\, since lower order moments generally depend on higher order moments. Various closure schemes have been suggested to solve this problem\, with different advantages and limitations. Two major problems with these approaches are first that they are open loop systems\, which can diverge from the true solution\, and second\, some of them are computationally expensive. \nResults: Here we introduce Quasi-Entropy Closure\, a moment closure scheme for the Method of Moments which estimates higher order moments by reconstructing the distribution that minimizes the distance to a uniform distribution subject to lower order moment constraints. Quasi-Entropy closure is similar to Zero-Information closure\, which maximizes the information entropy. Results show that both approaches outperform truncation schemes. Moreover\, Quasi-Entropy Closure is computationally much faster than Zero-Information Closure. Finally\, our scheme includes a plausibility check for the existence of a distribution satisfying a given set of moments on the feasible set of configurations. Results are evaluated on different benchmark problems.
URL:https://www.ibs.re.kr/bimag/event/2022-01-13/
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:20220118T160000
DTEND;TZID=Asia/Seoul:20220118T170000
DTSTAMP:20260509T220245
CREATED:20220117T220000Z
LAST-MODIFIED:20220115T115221Z
UID:5466-1642521600-1642525200@www.ibs.re.kr
SUMMARY:다중 오믹스 분야의 현황 및 유전자-환경 상호 모델링의 필요성 (Current status of multi-omics research field and necessity of gene-by-environment (GxE) interaction modeling)
DESCRIPTION:본 발표에서는 다양한 기초 생명-의학 분야에서 생성되고 있는 오믹스 자료의 연구 개발 현황에 대해서 다룰 예정이다. 보다 큰 규모로\, 보다 빠르게\, 보다 정확하게\, 보다 정밀하게 라는 궁극적인 목표하에 이뤄지고 있는 오믹스 자료의 진화에 발맞춰\, 이를 분석하는 수리통계적 모형 역시 진화하고 있다. 그 중\, 이번 발표에서는 미국의 초 대형 정밀의료 프로젝트인 TopMed에서 진행하고 있는 COPD에 관한 다중 오믹스 자료의 통합 분석 방법 및 결과에 대해서 자세히 다룰 예정이다. 아울러 정밀의료라는 목표를 달성하기 위해 반드시 모형에서 고려해야 하는 “환경 특이적 효과”에 대해 강연할 예정이다. \n 
URL:https://www.ibs.re.kr/bimag/event/2022-01-18/
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:20220119T110000
DTEND;TZID=Asia/Seoul:20220119T120000
DTSTAMP:20260509T220245
CREATED:20220118T170000Z
LAST-MODIFIED:20220115T115214Z
UID:5400-1642590000-1642593600@www.ibs.re.kr
SUMMARY:Network design principle for robust oscillatory behaviors with respect to biological noise
DESCRIPTION:We will discuss about “Network design principle for robust oscillatory behaviors with respect to biological noise”\, Qiao et al\, bioRxiv\, 2021 \nOscillatory behaviors\, which are ubiquitous in transcriptional regulatory networks\, are often subject to inevitable biological noise. Thus a natural question is how transcriptional regulatory networks can robustly achieve accurate oscillation in the presence of biological noise. Here\, we search all two- and three-node transcriptional regulatory network topologies for those robustly capable of accurate oscillation against the parameter variability (extrinsic noise) or stochasticity of chemical reactions (intrinsic noise). We find that\, no matter what source of the noise is applied\, the topologies containing the repressilator with positive auto-regulation show higher robustness of accurate oscillation than those containing the activator-inhibitor oscillator\, and additional positive auto-regulation enhances the robustness against noise. Nevertheless\, the attenuation of different sources of noise is governed by distinct mechanisms: the parameter variability is buffered by the long period\, while the stochasticity of chemical reactions is filtered by the high amplitude. Furthermore\, we analyze the noise of a synthetic human nuclear factor κB (NF-κB) signaling network by varying three different topologies\, and verify that the addition of a repressilator to the activator-inhibitor oscillator\, which leads to the emergence of high-robustness motif—the repressilator with positive auto-regulation\, improves the oscillation accuracy in comparison to the topology with only an activator-inhibitor oscillator. These design principles may be applicable to other oscillatory circuits.
URL:https://www.ibs.re.kr/bimag/event/2022-01-19/
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:20220127T110000
DTEND;TZID=Asia/Seoul:20220127T130000
DTSTAMP:20260509T220245
CREATED:20220126T170000Z
LAST-MODIFIED:20220125T115708Z
UID:5507-1643281200-1643288400@www.ibs.re.kr
SUMMARY:Introduction to Bayesian Variable Selection.  
DESCRIPTION:Abstract:\nVariable selection is an approach to identifying a set of covariates that are truly important to explain the feature of a response variable. It is closely connected or belongs to model selection approaches. This talk provides a gentle introduction to Bayesian variable selection methods. The basic notion of variable selection is introduced\, followed by several Bayesian approaches with a simple application example.
URL:https://www.ibs.re.kr/bimag/event/2022-01-27-2/
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
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