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PRODID:-//Biomedical Mathematics Group - ECPv6.16.2//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:20190101T000000
END:STANDARD
END:VTIMEZONE
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210305T130000
DTEND;TZID=Asia/Seoul:20210305T140000
DTSTAMP:20260526T221124
CREATED:20210228T074756Z
LAST-MODIFIED:20210406T075234Z
UID:4157-1614949200-1614952800@www.ibs.re.kr
SUMMARY:Eui Min Jeong\, Pairing of segmentation clock genes drives robust pattern formation
DESCRIPTION:We will discuss about “Pairing of segmentation clock genes drives robust pattern formation”\, Zinani et al.\, Nature (2021) \nGene expression is an inherently stochastic process; however\, organismal development and homeostasis require cells to coordinate the spatiotemporal expression of large sets of genes. In metazoans\, pairs of co-expressed genes often reside in the same chromosomal neighbourhood\, with gene pairs representing 10 to 50% of all genes\, depending on the species. Because shared upstream regulators can ensure correlated gene expression\, the selective advantage of maintaining adjacent gene pairs remains unknown6. Here\, using two linked zebrafish segmentation clock genes\, her1 and her7\, and combining single-cell transcript counting\, genetic engineering\, real-time imaging and computational modelling\, we show that gene pairing boosts correlated transcription and provides phenotypic robustness for the formation of developmental patterns. Our results demonstrate that the prevention of gene pairing disrupts oscillations and segmentation\, and the linkage of her1 and her7 is essential for the development of the body axis in zebrafish embryos. We predict that gene pairing may be similarly advantageous in other organisms\, and our findings could lead to the engineering of precise synthetic clocks in embryos and organoids \n  \n 
URL:https://www.ibs.re.kr/bimag/event/2021-03-05/
LOCATION:Tea Room\, IBS\, Daejeon\, Daejeon\, 34141\, Korea\, Republic of
CATEGORIES:Journal Club,Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210205T100000
DTEND;TZID=Asia/Seoul:20210205T110000
DTSTAMP:20260526T221124
CREATED:20210228T071217Z
LAST-MODIFIED:20210406T075239Z
UID:4140-1612519200-1612522800@www.ibs.re.kr
SUMMARY:Jaewoo Park\, Introduction to RcppArmadillo for Statistical Programming
DESCRIPTION:The speaker presents how to use Rcpp (Seamless R and C++ Integration) and RcppArmadillo packages (‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra Library) for statistical programming. \n 
URL:https://www.ibs.re.kr/bimag/event/2021-02-05/
LOCATION:ZOOM ID: 709 120 4849 (ibsbimag)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Seminar,Seminar
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/02/JaewooPark_20210205_Rcpp.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210204T130000
DTEND;TZID=Asia/Seoul:20210204T150000
DTSTAMP:20260526T221124
CREATED:20210223T091012Z
LAST-MODIFIED:20210228T073227Z
UID:3968-1612443600-1612450800@www.ibs.re.kr
SUMMARY:Hyukpyo Hong\, Frequency Spectra and the Color of Cellular Noise
DESCRIPTION:We will discuss about “Frequency Spectra and the Color of Cellular Noise”\,  bioRxiv (2020). \nThe invention of the Fourier integral in the 19th century laid the foundation for modern spectral analysis methods. By decomposing a (time) signal into its essential frequency components\, these methods uncovered deep insights into the signal and its generating process\, precipitating tremendous inventions and discoveries in many fields of engineering\, technology\, and physical science. In systems and synthetic biology\, however\, the impact of frequency methods has been far more limited despite their huge promise. This is in large part due to the difficulty of gleaning spectral information from single-cell trajectories\, owing to their distinctive noisy character forged by the underlying discrete stochastic dynamics of the living cell\, typically modelled as a continuous-time Markov chain (CTMC). Here we draw on stochastic process theory to develop a spectral theory and computational methodologies tailored specifically to the computation and analysis of frequency spectra of noisy cellular networks. For linear networks we present exact expressions for the frequency spectrum and use them to decompose the variability of a signal into its sources. For nonlinear networks\, we develop methods to obtain accurate Padé approximants of the spectrum from a single Monte Carlo trajectory simulation. Our results provide new conceptual and practical methods for the analysis and design of noisy cellular networks based on their output frequency spectra. We illustrate this through diverse case studies in which we show that the single-cell frequency spectrum enables topology discrimination\, synthetic oscillator optimization\, cybergenetic controller design\, and systematic investigation of stochastic entrainment. \n 
URL:https://www.ibs.re.kr/bimag/event/2021-02-04/
LOCATION:KAIST E2-1 room 3221\, E2-1 building\, Daejeon\, Daejeon\, 34141\, Korea\, Republic of
CATEGORIES:Journal Club,Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210129T140000
DTEND;TZID=Asia/Seoul:20210129T160000
DTSTAMP:20260526T221124
CREATED:20210223T092935Z
LAST-MODIFIED:20210406T075248Z
UID:3978-1611928800-1611936000@www.ibs.re.kr
SUMMARY:Yun Min Song\, On the quasi-steady-state approximation in an open Michaelis-Menten reaction mechanism
DESCRIPTION:We will discuss about “On the quasi-steady-state approximation in an open Michaelis-Menten reaction mechanism”\, bioRxiv (2021). \nThe conditions for the validity of the standard quasi-steady-state approximation in the Michaelis–Menten mechanism in a closed reaction vessel have been well studied\, but much less so the conditions for the validity of this approximation for the system with substrate inflow. We analyze quasi-steady-state scenarios for the open system attributable to singular perturbations\, as well as less restrictive conditions. For both settings we obtain distinguished invariant slow manifolds and time scale estimates\, and we highlight the special role of singular perturbation parameters in higher order approximations of slow manifolds. We close the paper with a discussion of distinguished invariant manifolds in the global phase portrait. \n 
URL:https://www.ibs.re.kr/bimag/event/2021-01-29/
LOCATION:KAIST E2-1 room 3221\, E2-1 building\, Daejeon\, Daejeon\, 34141\, Korea\, Republic of
CATEGORIES:Journal Club,Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210125T160000
DTEND;TZID=Asia/Seoul:20210125T170000
DTSTAMP:20260526T221124
CREATED:20210223T120915Z
LAST-MODIFIED:20210406T075255Z
UID:4005-1611590400-1611594000@www.ibs.re.kr
SUMMARY:Eui Min Jeong\, Mathematical modeling of circadian clocks of mammal and Drosophila to reveal molecular mechanism for rhythm generation
DESCRIPTION:
URL:https://www.ibs.re.kr/bimag/event/2021-01-25_1/
LOCATION:KAIST E2-1 room 3221\, E2-1 building\, Daejeon\, Daejeon\, 34141\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar,Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210125T150000
DTEND;TZID=Asia/Seoul:20210125T160000
DTSTAMP:20260526T221124
CREATED:20210223T121036Z
LAST-MODIFIED:20210406T075132Z
UID:4010-1611586800-1611590400@www.ibs.re.kr
SUMMARY:Dae Wook Kim\, Development of mathematical models and theoretical frameworks to unravel mysteries of complex dynamics in biology
DESCRIPTION:
URL:https://www.ibs.re.kr/bimag/event/2021-01-25_2/
LOCATION:KAIST E2-1 room 3221\, E2-1 building\, Daejeon\, Daejeon\, 34141\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar,Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210121T140000
DTEND;TZID=Asia/Seoul:20210121T160000
DTSTAMP:20260526T221124
CREATED:20210223T094006Z
LAST-MODIFIED:20210406T075136Z
UID:3980-1611237600-1611244800@www.ibs.re.kr
SUMMARY:Seokjoo Chae\, Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression
DESCRIPTION:We will discuss about “Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression”\, Benzinger et al.\, bioRxiv (2021) \nCells live in constantly changing environments and employ dynamic signaling pathways to transduce information about the signals they encounter. However\, the mechanisms by which dynamic signals are decoded into appropriate gene expression patterns remain poorly understood. Here\, we devise networked optogenetic pathways that achieve novel dynamic signal processing functions that recapitulate cellular information processing. Exploiting light-responsive transcriptional regulators with differing response kinetics\, we build a falling-edge pulse-detector and show that this circuit can be employed to demultiplex dynamically encoded signals. We combine this demultiplexer with dCas9-based gene networks to construct pulsatile-signal filters and decoders. Applying information theory\, we show that dynamic multiplexing significantly increases the information transmission capacity from signal to gene expression state. Finally\, we use dynamic multiplexing for precise multidimensional regulation of a heterologous metabolic pathway. Our results elucidate design principles of dynamic information processing and provide original synthetic systems capable of decoding complex signals for biotechnological applications. \n 
URL:https://www.ibs.re.kr/bimag/event/2021-01-21_1/
LOCATION:KAIST E2-1 room 3221\, E2-1 building\, Daejeon\, Daejeon\, 34141\, Korea\, Republic of
CATEGORIES:Journal Club,Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210108T143000
DTEND;TZID=Asia/Seoul:20210108T160000
DTSTAMP:20260526T221124
CREATED:20210228T061102Z
LAST-MODIFIED:20210406T075128Z
UID:4114-1610116200-1610121600@www.ibs.re.kr
SUMMARY:Hyukpyo Hong\, Introduction to Git and GitHub
DESCRIPTION:In this talk\, the speaker introduces what Git and GitHub are and explains how to use them. \n 
URL:https://www.ibs.re.kr/bimag/event/2021-01-08/
CATEGORIES:Biomedical Mathematics Seminar,Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20201231T160000
DTEND;TZID=Asia/Seoul:20201231T170000
DTSTAMP:20260526T221124
CREATED:20210228T061941Z
LAST-MODIFIED:20210406T075352Z
UID:4116-1609430400-1609434000@www.ibs.re.kr
SUMMARY:Yun Min Song\, Exact upper and lower bounds of total quasi-steady-state approximation for reversible binding network.
DESCRIPTION:
URL:https://www.ibs.re.kr/bimag/event/2020-12-31/
CATEGORIES:Biomedical Mathematics Seminar,Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20201224T130000
DTEND;TZID=Asia/Seoul:20201224T140000
DTSTAMP:20260526T221124
CREATED:20210223T094304Z
LAST-MODIFIED:20210406T075331Z
UID:3983-1608814800-1608818400@www.ibs.re.kr
SUMMARY:Seokjoo Chae\, Ligand-receptor promiscuity enables cellular addressing
DESCRIPTION:We will discuss about “Ligand-receptor promiscuity enables cellular addressing”\, Su et al.\, bioRxiv (2021) \nIn multicellular organisms\, secreted ligands selectively activate\, or “address\,” specific target cell populations to control cell fate decision-making and other processes. Key cell-cell communication pathways use multiple promiscuously interacting ligands and receptors\, provoking the question of how addressing specificity can emerge from molecular promiscuity. To investigate this issue\, we developed a general mathematical modeling framework based on the bone morphogenetic protein (BMP) pathway architecture. We find that promiscuously interacting ligand-receptor systems allow a small number of ligands\, acting in combinations\, to address a larger number of individual cell types\, each defined by its receptor expression profile. Promiscuous systems outperform seemingly more specific one-to-one signaling architectures in addressing capacity. Combinatorial addressing extends to groups of cell types\, is robust to receptor expression noise\, grows more powerful with increasing receptor multiplicity\, and is maximized by specific biochemical parameter relationships. Together\, these results identify fundamental design principles governing cell addressing by ligand combinations.
URL:https://www.ibs.re.kr/bimag/event/2020-12-24_1/
LOCATION:KAIST E2-1 room 3221\, E2-1 building\, Daejeon\, Daejeon\, 34141\, Korea\, Republic of
CATEGORIES:Journal Club,Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20201224T020000
DTEND;TZID=Asia/Seoul:20201224T150000
DTSTAMP:20260526T221124
CREATED:20210223T094556Z
LAST-MODIFIED:20210406T075337Z
UID:3985-1608775200-1608822000@www.ibs.re.kr
SUMMARY:Dae Wook Kim\, Neural network aided approximation and parameter inference of stochastic models of gene expression
DESCRIPTION:We will discuss about “Neural network aided approximation and parameter inference of stochastic models of gene expression”\, Jian et al.\, bioRxiv (2020). \nNon-Markov models of stochastic biochemical kinetics often incorporate explicit time delays to effectively model large numbers of intermediate biochemical processes. Analysis and simulation of these models\, as well as the inference of their parameters from data\, are fraught with difficulties because the dynamics depends on the system’s history. Here we use an artificial neural network to approximate the time-dependent distributions of non-Markov models by the solutions of much simpler time-inhomogeneous Markov models; the approximation does not increase the dimensionality of the model and simultaneously leads to inference of the kinetic parameters. The training of the neural network uses a relatively small set of noisy measurements generated by experimental data or stochastic simulations of the non-Markov model. We show using a variety of models\, where the delays stem from transcriptional processes and feedback control\, that the Markov models learnt by the neural network accurately reflect the stochastic dynamics across parameter space.
URL:https://www.ibs.re.kr/bimag/event/2020-12-24_2/
LOCATION:KAIST E2-1 room 3221\, E2-1 building\, Daejeon\, Daejeon\, 34141\, Korea\, Republic of
CATEGORIES:Journal Club,Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
END:VCALENDAR