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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:20210101T000000
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BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20221202T150000
DTEND;TZID=Asia/Seoul:20221202T170000
DTSTAMP:20260426T043819
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:20221216T130000
DTEND;TZID=Asia/Seoul:20221216T150000
DTSTAMP:20260426T043819
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:20260426T043819
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:20221230T150000
DTEND;TZID=Asia/Seoul:20221230T170000
DTSTAMP:20260426T043819
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
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