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X-WR-CALDESC:Events for Biomedical Mathematics Group
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TZID:Asia/Seoul
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DTSTART:20200101T000000
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BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210806T130000
DTEND;TZID=Asia/Seoul:20210806T140000
DTSTAMP:20260427T122842
CREATED:20210801T140652Z
LAST-MODIFIED:20210801T140652Z
UID:4835-1628254800-1628258400@www.ibs.re.kr
SUMMARY:Frequency Modulation of Transcriptional Bursting Enables Sensitive and Rapid Gene Regulation
DESCRIPTION:We will discuss about “Frequency Modulation of Transcriptional Bursting Enables Sensitive and Rapid Gene Regulation”\, Li et. al.\, Cell Systems\, 2018 \nAbstract \nGene regulation is a complex non-equilibrium process. Here\, we show that quantitating the temporal regulation of key gene states (transcriptionally inactive\, active\, and refractory) provides a parsimonious framework for analyzing gene regulation. Our theory makes two non-intuitive predictions. First\, for transcription factors (TFs) that regulate transcription burst frequency\, as opposed to amplitude or duration\, weak TF binding is sufficient to elicit strong transcriptional responses. Second\, refractoriness of a gene after a transcription burst enables rapid responses to stimuli. We validate both predictions experimentally by exploiting the natural\, optogenetic-like responsiveness of the Neurospora GATA-type TF White Collar Complex (WCC) to blue light. Further\, we demonstrate that differential regulation of WCC target genes is caused by different gene activation rates\, not different TF occupancy\, and that these rates are tuned by both the core promoter and the distance between TF-binding site and core promoter. In total\, our work demonstrates the relevance of a kinetic\, non-equilibrium framework for understanding transcriptional regulation.
URL:https://www.ibs.re.kr/bimag/event/2021-08-06/
LOCATION:B305 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:20210813T090000
DTEND;TZID=Asia/Seoul:20210813T100000
DTSTAMP:20260427T122842
CREATED:20210810T220000Z
LAST-MODIFIED:20210811T064522Z
UID:4837-1628845200-1628848800@www.ibs.re.kr
SUMMARY:TimeCycle: Topology Inspired MEthod for the Detection of Cycling Transcripts in Circadian Time-Series Data
DESCRIPTION:We will discuss about “TimeCycle: Topology Inspired MEthod for the Detection of Cycling Transcripts in Circadian Time-Series Data”\, Ness-Cohn and Braun\, Bioinformatics\, 2021 \nAbstract \nMotivation: The circadian rhythm drives the oscillatory expression of thousands of genes across all tissues. The recent revolution in high-throughput transcriptomics\, coupled with the significant implicatins of the circadian clock for human health\, has sparked an interest in circadian profiling studies to discover genes under circadian control.\nResult: We present TimeCycle: a topology-based rhythm detection method designed to identify cycling transcripts. For a given time-series\, the method reconstructs the state space using time-delay embedding\, a data transformation technique from dynamical systems theory. In the embedded space\, Takens’ theorem proves that the dynamics of a rhythmic signal will exhibit circular patterns. The degree of circularity of the embedding is calculated as a persistence score using persistent homology\, an algebraic method for discerning the topological features of data. By comparing the persistence scores to a bootstrapped null distribution\, cycling genes are identified. Results in both synthetic and biological data highlight TimeCycle’s ability to identify cycling genes across a range of sampling schemes\, number of replicates\, and missing data. Comparison to competing methods highlights their relative strengths\, providing guidance as to the optimal choice of cycling detection method.\nAvailability: A fully documented open-source R package implementing TimeCycle is available at: https://nesscoder.github.io/TimeCycle/ .
URL:https://www.ibs.re.kr/bimag/event/2021-08-13-2/
LOCATION:B305 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:20210819T130000
DTEND;TZID=Asia/Seoul:20210819T140000
DTSTAMP:20260427T122842
CREATED:20210819T190000Z
LAST-MODIFIED:20210812T095509Z
UID:4839-1629378000-1629381600@www.ibs.re.kr
SUMMARY:Cellular signaling beyond the Wiener-Kolmogorov limit
DESCRIPTION:We will discuss about “Cellular signaling beyond the Wiener-Kolmogorov limit”\, Weisenberger et al.\, bioRxiv\, 2021 \nAbstract: \nAccurate propagation of signals through stochastic biochemical networks involves significant expenditure of cellular resources. The same is true for regulatory mechanisms that suppress fluctuations in biomolecular populations. Wiener-Kolmogorov (WK) optimal noise filter theory\, originally developed for engineering problems\, has recently emerged as a valuable tool to estimate the maximum performance achievable in such biological systems for a given metabolic cost. However\, WK theory has one assumption that potentially limits its applicability: it relies on a linear\, continuum description of the reaction dynamics. Despite this\, up to now no explicit test of the theory in nonlinear signaling systems with discrete molecular populations has ever seen performance beyond the WK bound. Here we report the first direct evidence the bound being broken. To accomplish this\, we develop a theoretical framework for multi-level signaling cascades\, including the possibility of feedback interactions between input and output. In the absence of feedback\, we introduce an analytical approach that allows us to calculate exact moments of the stationary distribution for a nonlinear system. With feedback\, we rely on numerical solutions of the system’s master equation. The results show WK violations in two common network motifs: a two-level signaling cascade and a negative feedback loop. However the magnitude of the violation is biologically negligible\, particularly in the parameter regime where signaling is most effective. The results demonstrate that while WK theory does not provide strict bounds\, its predictions for performance limits are excellent approximations\, even for nonlinear systems. \n  \n 
URL:https://www.ibs.re.kr/bimag/event/2021-08-19/
LOCATION:B305 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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