BEGIN:VCALENDAR
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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:20221202T110000
DTEND;TZID=Asia/Seoul:20221202T120000
DTSTAMP:20260425T112736
CREATED:20220825T011607Z
LAST-MODIFIED:20220828T060439Z
UID:6474-1669978800-1669982400@www.ibs.re.kr
SUMMARY:Mammalian synthetic biology by controller design
DESCRIPTION:Abstract: The ability to reliably engineer the mammalian cell will impact a variety of applications in a disruptive way\, including cell fate control and reprogramming\, targeted drug delivery\, and regenerative medicine. However\, our current ability to engineer mammalian genetic circuits that behave as predicted remains limited. These circuits depend on the intra and extra cellular environment in ways that are difficult to anticipate\, and this fact often hampers genetic circuit performance. This lack of robustness to poorly known and often variable cellular environment is the subject of this talk. Specifically\, I will describe control engineering approaches that make the performance of genetic devices robust to context. I will show a feedforward controller that makes gene expression robust to variability in cellular resources and\, more generally\, to changes in intra-cellular context linked to differences in cell type. I will then show a feedback controller that uses bacterial two component signaling systems to create a quasi-integral controller that makes the input/output response of a genetic device robust to a variety of perturbations that affect gene expression. These solutions support rational and modular design of sophisticated genetic circuits and can serve for engineering biological circuits that are more robust and predictable across changing contexts.
URL:https://www.ibs.re.kr/bimag/event/2022-12-02-colloquium/
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/2022/08/Domitilla-Del-Vecchio-250x250-1.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20221202T150000
DTEND;TZID=Asia/Seoul:20221202T170000
DTSTAMP:20260425T112736
CREATED:20221128T010402Z
LAST-MODIFIED:20221128T010402Z
UID:6906-1669993200-1670000400@www.ibs.re.kr
SUMMARY:Multiparameter persistent homology landscapes identify immune cell spatial patterns in tumors
DESCRIPTION:We will discuss about “Multiparameter persistent homology landscapes identify immune cell spatial patterns in tumors”\, Vipond\, Oliver\, et al\, Proceedings of the National Academy of Sciences 118.41 (2021): e2102166118. \nAbstract\nHighly resolved spatial data of complex systems encode rich and nonlinear information. Quantification of heterogeneous and noisy data—often with outliers\, artifacts\, and mislabeled points—such as those from tissues\, remains a challenge. The mathematical field that extracts information from the shape of data\, topological data analysis (TDA)\, has expanded its capability for analyzing real-world datasets in recent years by extending theory\, statistics\, and computation. An extension to the standard theory to handle heterogeneous data is multiparameter persistent homology (MPH). Here we provide an application of MPH landscapes\, a statistical tool with theoretical underpinnings. MPH landscapes\, computed for (noisy) data from agent-basedMultiparameter persistent homology landscapes identify immune cell spatial patterns in tumors model simulations of immune cells infiltrating into a spheroid\, are shown to surpass existing spatial statistics and one-parameter persistent homology. We then apply MPH landscapes to study immune cell location in digital histology images from head and neck cancer. We quantify intratumoral immune cells and find that infiltrating regulatory T cells have more prominent voids in their spatial patterns than macrophages. Finally\, we consider how TDA can integrate and interrogate data of different types and scales\, e.g.\, immune cell locations and regions with differing levels of oxygenation. This work highlights the power of MPH landscapes for quantifying\, characterizing\, and comparing features within the tumor microenvironment in synthetic and real datasets.
URL:https://www.ibs.re.kr/bimag/event/2022-12-02-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:20221209T110000
DTEND;TZID=Asia/Seoul:20221209T120000
DTSTAMP:20260425T112736
CREATED:20220825T013528Z
LAST-MODIFIED:20221207T064542Z
UID:6504-1670583600-1670587200@www.ibs.re.kr
SUMMARY:Taming Complexity in Data-Limited Nonlinear Nonequilibrium Settings
DESCRIPTION:Abstract: \nSince before the time of Aristotle and the natural philosophers\, reductionism has played a foundational role in western scientific thought. The premise of reductionism is that systems can be broken down into constituent pieces and studied independently\, then reassembled to understand the behavior of the system as a whole. It embodies the classical linear perspective. This approach has been successful in developing basic physical laws and especially in engineering where linear analysis dominates and systems are purposefully designed that way. However\, reductionism is not universally applicable for natural complex systems where behavior is driven\, not by a few factors acting independently\, but by complex interactions between many components acting together and changing in time. \nNonlinearity in living systems means that its parts are interdependent – variables do not act in a mutually independent manner; rather they interact\, and as a consequence associations (correlations) between them will change as the overall system context (state) changes.  This problem is highlighted when extrapolating the results of single-factor experiments to nature\, and surely contributes to the frustrating disconnect between experimental findings and clinical outcomes in drug trials. Indeed\, while everyone knows Berkeley’s 1710 dictum “correlation does not imply causation” few realize that for nonlinear systems the converse “causation does not imply correlation” is also true. This conundrum runs counter to deeply ingrained heuristic thinking that is at the basis of modern science. Biological systems (esp. ecosystems) are particularly perverse on this issue by exhibiting mirage correlations that can continually cause us to rethink relationships we thought we understood. \nHere we examine a minimalist paradigm\, empirical dynamics (EDM)\, for studying non-linear systems and a method (CCM) that can detect causality when there is no correlation among variables. It is a data-driven approach that uses time series to study a system holistically by reconstructing its attractor – a geometric object that embodies the rules of a full set of equations for the system.  The ideas are intuitive and will be illustrated with examples from genetics\, ecology and epidemiology. \nA python version of EDM tools can be found at https://pepy.tech/project/pyEDM
URL:https://www.ibs.re.kr/bimag/event/2022-12-09-colloquium/
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/2022/08/Sugihara_George_250x250.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20221213T160000
DTEND;TZID=Asia/Seoul:20221213T170000
DTSTAMP:20260425T112736
CREATED:20221209T045119Z
LAST-MODIFIED:20221211T121541Z
UID:6984-1670947200-1670950800@www.ibs.re.kr
SUMMARY:Static and Dynamic Absolute Concentration Robustness
DESCRIPTION:Absolute Concentration Robustness (ACR) was introduced by Shinar and Feinberg (Science 327:1389-1391\, 2010) as robustness of equilibrium species concentration in a mass action dynamical system. Their aim was to devise a mathematical condition that will ensure robustness in the function of the biological system being modeled. The robustness of function rests on what we refer to as empirical robustness — the concentration of a species remains unvarying\, when measured in the long run\, across arbitrary initial conditions. Even simple examples show that the ACR notion introduced in Shinar and Feinberg (here referred to as static ACR) is neither necessary nor sufficient for empirical robustness. To make a stronger connection with empirical robustness\, we define dynamic ACR\, a property related to long-term\, global dynamics\, rather than only to equilibrium behavior. We discuss general dynamical systems with dynamic ACR properties as well as parametrized families of dynamical systems related to reaction networks. In particular\, we find necessary and sufficient conditions for dynamic ACR in complex balanced reaction networks\, a class of networks that is central to the theory of reaction networks.This is joint work with Badal Joshi (CSUSM)
URL:https://www.ibs.re.kr/bimag/event/static-and-dynamic-absolute-concentration-robustness/
LOCATION:B232 Seminar Room\, 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:20221216T130000
DTEND;TZID=Asia/Seoul:20221216T150000
DTSTAMP:20260425T112736
CREATED:20221214T122407Z
LAST-MODIFIED:20221214T122407Z
UID:7022-1671195600-1671202800@www.ibs.re.kr
SUMMARY:Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators
DESCRIPTION:We will discuss about “Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators”\, Karapetyan\, Sargis\, and Nicolas E. Buchler\,Physical Review E 92.6 (2015): 062712. \nAbstract \n\n\n\nGenetic oscillators\, such as circadian clocks\, are constantly perturbed by molecular noise arising from the small number of molecules involved in gene regulation. One of the strongest sources of stochasticity is the binary noise that arises from the binding of a regulatory protein to a promoter in the chromosomal DNA. In this study\, we focus on two minimal oscillators based on activator titration and repressor titration to understand the key parameters that are important for oscillations and for overcoming binary noise. We show that the rate of unbinding from the DNA\, despite traditionally being considered a fast parameter\, needs to be slow to broaden the space of oscillatory solutions. The addition of multiple\, independent DNA binding sites further expands the oscillatory parameter space for the repressor-titration oscillator and lengthens the period of both oscillators. This effect is a combination of increased effective delay of the unbinding kinetics due to multiple binding sites and increased promoter ultrasensitivity that is specific for repression. We then use stochastic simulation to show that multiple binding sites increase the coherence of oscillations by mitigating the binary noise. Slow values of DNA unbinding rate are also effective in alleviating molecular noise due to the increased distance from the bifurcation point. Our work demonstrates how the number of DNA binding sites and slow unbinding kinetics\, which are often omitted in biophysical models of gene circuits\, can have a significant impact on the temporal and stochastic dynamics of genetic oscillators.
URL:https://www.ibs.re.kr/bimag/event/2022-12-16-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:20221223T150000
DTEND;TZID=Asia/Seoul:20221223T170000
DTSTAMP:20260425T112736
CREATED:20221222T082248Z
LAST-MODIFIED:20221222T082248Z
UID:7075-1671807600-1671814800@www.ibs.re.kr
SUMMARY:Olive Cawiding\, Optimal control of aging in complex networks
DESCRIPTION:We will discuss about “Optimal control of aging in complex networks”\,\nSun\, Eric D.\, Thomas CT Michaels\, and L. Mahadevan\, Proceedings of the National Academy of Sciences 117.34 (2020): 20404-20410. \nAbstract \n\n\n\nMany complex systems experience damage accumulation\, which leads to aging\, manifest as an increasing probability of system collapse with time. This naturally raises the question of how to maximize health and longevity in an aging system at minimal cost of maintenance and intervention. Here\, we pose this question in the context of a simple interdependent network model of aging in complex systems and show that it exhibits cascading failures. We then use both optimal control theory and reinforcement learning alongside a combination of analysis and simulation to determine optimal maintenance protocols. These protocols may motivate the rational design of strategies for promoting longevity in aging complex systems with potential applications in therapeutic schedules and engineered system maintenance.
URL:https://www.ibs.re.kr/bimag/event/2022-12-23-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:20221226T100000
DTEND;TZID=Asia/Seoul:20221226T120000
DTSTAMP:20260425T112736
CREATED:20221226T004917Z
LAST-MODIFIED:20260404T011224Z
UID:7164-1672048800-1672056000@www.ibs.re.kr
SUMMARY:IBS BIMAG 2022 Winter Internship Workshop
DESCRIPTION:IBS BIMAG will host a kick-off workshop for the winter internships on Monday\, 26 December 2022. The internship participants from Pusan National University and Postech will give 8 minutes presentations on their research topics. \nPresentation List:\n\n김미지 (Miji Kim) – A Comparison Study of Dropout to Prevent Overfitting Problem in CNN Image Data Classification\n김지현 (Jihyeon Kim)- Study of Ensemble Kalman Filter\n이시은 (Sieun Lee) – Early Detection using Epidemic Data\n이유진 (Youjin Lee) – On Parameter Estimation Approaches for Biomathematical Models through Physics-Informed Neural Networks\n장근수 (Geunsoo Jang) – Development of mathematical model for impact evaluation of Radioactive Water Discharge in Fukushima\n김진영 (Jinyoung Kim) – Stochastic aggregation models in 2D and 3D spaces to describe Liquid-Liquid Phase Separation (LLPS)\n김민준 (Minjoon Kim) –  Stability of Chemical reaction networks
URL:https://www.ibs.re.kr/bimag/event/ibs-bimag-winter-internship-workshop/
LOCATION:IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, Daejeon\, 34126\, 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:20221228T140000
DTEND;TZID=Asia/Seoul:20221228T150000
DTSTAMP:20260425T112736
CREATED:20221215T221715Z
LAST-MODIFIED:20221222T082709Z
UID:7043-1672236000-1672239600@www.ibs.re.kr
SUMMARY:Ji Won Oh\, From Grave to Cradle: Human Somatic Mosaicism and Unsolved Questions
DESCRIPTION:사람이 어떻게 만들어지고 각 기관이 어떻게 발달하는지에 대한 질문은 아주 오래전부터 있었습니다. 체외수정(IVF)의 고유의 장점으로 인해 과학자들이 수정란을 외부에서 관찰할 수 있게 되었습니다. 하지만\, 1979년도에 제정된 14일 규정(the 14-day rule)으로 인해\, 수정 후 최대 14일까지의 배아 만의 연구가 가능합니다. 따라서\, 이 14일 규정은 발생 생물학자들이 사람 발생학 연구에 있어서 수정 후 2주 이상(신경계 발달\, 기관 형성 등)에 나타나는 현상을 연구하고자 할 경우 다른 방향을 모색할 수밖에 없게 되었습니다. 본 연구는 이 지점에서부터 시작합니다. 연구진들은 세포 분열 때 우연히 발생하는 생리학적 체세포 변이(Post-zygotic Variants)를 추적하여 각 세포들의 운명을 재구성하였습니다. 특히 사망 후 기증된 시신에서 단일 세포를 배양하고\, 최근 개발된 차세대 염기서열 분석 기술을 사용하여 인간 발생 연구의 후향적 혈통 추적(Retrospective Lineage Tracing)을 수행하는 과정을 발표하고자 합니다. 이번 발표를 통해서 이런 방법론이 어떻게 가능했는지에 대한 생물학적 및 과학적 배경과 인간 발생학의 미래에서 해결해야 할 과제와 가설을 강조할 예정입니다. 추가로\, 이 과정에서 필요한 수학적인 해석이 필요한 질문들에 대해서도 논의할 예정입니다. 여러분들의 참신한 시각과 질문을 크게 환영합니다. \n\n\n\n\n1) Park\, S.\, Mali\, N.M.\, Kim\, R. et al. Clonal dynamics in early human embryogenesis inferred from somatic mutation. Nature 597\, 393–397 (2021). https://doi.org/10.1038/s41586-021-03786-8 \n2) Kwon\, S.G.\, Bae\, G.H.\, Choi\, J.H. et al. Asymmetric Contribution of Blastomere Lineages of First Division of the Zygote to Entire Human Body Using Post-Zygotic Variants. Tissue Eng Regen Med 19\, 809–821 (2022). https://doi.org/10.1007/s13770-022-00443-7
URL:https://www.ibs.re.kr/bimag/event/from-grave-to-cradle-human-somatic-mosaicism-and-unsolved-questions/
LOCATION:B232 Seminar Room\, 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:20221230T150000
DTEND;TZID=Asia/Seoul:20221230T170000
DTSTAMP:20260425T112736
CREATED:20221222T082525Z
LAST-MODIFIED:20221230T060020Z
UID:7080-1672412400-1672419600@www.ibs.re.kr
SUMMARY:Candan Celik\, Analytical time-dependent distributions for gene expression models with complex promoter switching mechanisms
DESCRIPTION:We will discuss about “Analytical time-dependent distributions for gene expression models with complex promoter switching mechanisms”\,Jia\, Chen\, and Youming Li\, BioRxiv (2022). \nAbstract \n\n\n\nClassical gene expression models assume exponential switching time distributions between the active and inactive promoter states. However\, recent experiments have shown that many genes in mammalian cells may produce non-exponential switching time distributions\, implying the existence of multiple promoter states and molecular memory in the promoter switching dynamics. Here we analytically solve a gene expression model with random bursting and complex promoter switching\, and derive the time-dependent distributions of the mRNA and protein copy numbers\, generalizing the steady-state solution obtained in [SIAM J. Appl. Math. 72\, 789-818 (2012)] and [SIAM J. Appl. Math. 79\, 1007-1029 (2019)]. Using multiscale simplification techniques\, we find that molecular memory has no influence on the time-dependent distribution when promoter switching is very fast or very slow\, while it significantly affects the distribution when promoter switching is neither too fast nor too slow. By analyzing the dynamical phase diagram of the system\, we also find that molecular memory in the inactive gene state weakens transient and stationary bimodality of the copy number distribution\, while molecular memory in the active gene state enhances such bimodality.
URL:https://www.ibs.re.kr/bimag/event/2022-12-30-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
END:VCALENDAR