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X-ORIGINAL-URL:https://www.ibs.re.kr/bimag
X-WR-CALDESC:Events for Biomedical Mathematics Group
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TZID:Asia/Seoul
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TZOFFSETFROM:+0900
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DTSTART:20210101T000000
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BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220204T130000
DTEND;TZID=Asia/Seoul:20220204T140000
DTSTAMP:20260427T033521
CREATED:20220126T170000Z
LAST-MODIFIED:20220125T115800Z
UID:5397-1643979600-1643983200@www.ibs.re.kr
SUMMARY:Mechanisms for the generation of robust circadian oscillations through ultrasensitivity and differential binding affinity
DESCRIPTION:We will discuss about “Mechanisms for the generation of robust circadian oscillations through ultrasensitivity and differential binding affinity”\, Behera\, Junco\, and Vaikuntanathan\, The Journal of Physical Chemistry B\, 2021 \nBiochemical circadian rhythm oscillations play an important role in many signaling mechanisms. In this work\, we explore some of the biophysical mechanisms responsible for sustaining robust oscillations by constructing a minimal but analytically tractable model of the circadian oscillations in the KaiABC protein system found in the cyanobacteria S. elongatus. In particular\, our minimal model explicitly accounts for two experimentally characterized biophysical features of the KaiABC protein system\, namely\, a differential binding affinity and an ultrasensitive response. Our analytical work shows how these mechanisms might be crucial for promoting robust oscillations even in suboptimal nutrient conditions. Our analytical and numerical work also identifies mechanisms by which biological clocks can stably maintain a constant time period under a variety of nutrient conditions. Finally\, our work also explores the thermodynamic costs associated with the generation of robust sustained oscillations and shows that the net rate of entropy production alone might not be a good figure of merit to asses the quality of oscillations. \n 
URL:https://www.ibs.re.kr/bimag/event/2022-02-04/
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
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BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220211T130000
DTEND;TZID=Asia/Seoul:20220211T140000
DTSTAMP:20260427T033521
CREATED:20220210T190000Z
LAST-MODIFIED:20220208T054847Z
UID:5552-1644584400-1644588000@www.ibs.re.kr
SUMMARY:Phiclust: a clusterability measure for single-cell transcriptomics reveals phenotypic subpopulations
DESCRIPTION:We will discuss about “Phiclust: a clusterability measure for single-cell transcriptomics reveals phenotypic subpopulations”\, Mircea et al.\, 2022\, Genome Biology \nThe ability to discover new cell phenotypes by unsupervised clustering of single-cell transcriptomes has revolutionized biology. Currently\, there is no principled way to decide whether a cluster of cells contains meaningful subpopulations that should be further resolved. Here\, we present phiclust (ϕ_clust)\, a clusterability measure derived from random matrix theory that can be used to identify cell clusters with non-random substructure\, testably leading to the discovery of previously overlooked phenotypes.
URL:https://www.ibs.re.kr/bimag/event/2022-02-11/
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:20220218T130000
DTEND;TZID=Asia/Seoul:20220218T140000
DTSTAMP:20260427T033521
CREATED:20220130T031904Z
LAST-MODIFIED:20220130T031904Z
UID:5554-1645189200-1645192800@www.ibs.re.kr
SUMMARY:A Deficiency-Based Approach to Parametrizing Positive Equilibria of Biochemical Reaction Systems
DESCRIPTION:We will discuss about “A Deficiency-Based Approach to Parametrizing Positive Equilibria of Biochemical Reaction Systems”\, Johnston\, Müller\, and Pantea\, Bulletin of Mathematical Biology\, 2019 \nWe present conditions which guarantee a parametrization of the set of positive equilibria of a generalized mass-action system. Our main results state that (1) if the underlying generalized chemical reaction network has an effective deficiency of zero\, then the set of positive equilibria coincides with the parametrized set of complex-balanced equilibria and (2) if the network is weakly reversible and has a kinetic deficiency of zero\, then the equilibrium set is nonempty and has a positive\, typically rational\, parametrization. Via the method of network translation\, we apply our results to classical mass-action systems studied in the biochemical literature\, including the EnvZ–OmpR and shuttled WNT signaling pathways. A parametrization of the set of positive equilibria of a (generalized) mass-action system is often a prerequisite for the study of multistationarity and allows an easy check for the occurrence of absolute concentration robustness\, as we demonstrate for the EnvZ–OmpR pathway.
URL:https://www.ibs.re.kr/bimag/event/2022-02-18/
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
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