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PRODID:-//Biomedical Mathematics Group - ECPv6.15.20//NONSGML v1.0//EN
CALSCALE:GREGORIAN
METHOD:PUBLISH
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:20210611T123000
DTEND;TZID=Asia/Seoul:20210611T133000
DTSTAMP:20260425T044852
CREATED:20210507T123416Z
LAST-MODIFIED:20210601T035036Z
UID:4545-1623414600-1623418200@www.ibs.re.kr
SUMMARY:DNA as a universal substrate for chemical kinetics
DESCRIPTION:We will discuss about “DNA as a universal substrate for chemical kinetics “\, Soloveichik et al.\, PNAS (2009) \nMolecular programming aims to systematically engineer molecular and chemical systems of autonomous function and ever-increasing complexity. A key goal is to develop embedded control circuitry within a chemical system to direct molecular events. Here we show that systems of DNA molecules can be constructed that closely approximate the dynamic behavior of arbitrary systems of coupled chemical reactions. By using strand displacement reactions as a primitive\, we construct reaction cascades with effectively unimolecular and bimolecular kinetics. Our construction allows individual reactions to be coupled in arbitrary ways such that reactants can participate in multiple reactions simultaneously\, reproducing the desired dynamical properties. Thus arbitrary systems of chemical equations can be compiled into real chemical systems. We illustrate our method on the Lotka–Volterra oscillator\, a limit-cycle oscillator\, a chaotic system\, and systems implementing feedback digital logic and algorithmic behavior.
URL:https://www.ibs.re.kr/bimag/event/2021-05-27/
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:20210610T110000
DTEND;TZID=Asia/Seoul:20210610T120000
DTSTAMP:20260425T044852
CREATED:20210406T074242Z
LAST-MODIFIED:20210607T080017Z
UID:4364-1623322800-1623326400@www.ibs.re.kr
SUMMARY:Towards individualized predictions of human sleep and circadian timing
DESCRIPTION:This talk will be presented online. Zoom link: 709 120 4849 (pw: 1234) \nAbstract: Accurate assessment of circadian timing is critical to many applications\, including timing of drug delivery\, prediction of neurobehavioral performance\, and optimized scheduling of sleep. Current methods for measuring circadian timing are onerous and do not produce results in real time. Mathematical models have been developed for predicting circadian timing from an individual’s light exposure patterns\, which can be applied to passively collected data. These models are now well validated in the field at the group-average level\, but tend to perform poorly at the individual level. One potential solution to this problem is the estimation of model parameters at an individual level. We explored whether this approach could be applied to parameters relating to an individual’s light sensitivity. We found that these parameters can account for inter-individual and intra-individual variation in circadian timing. These findings demonstrate that model parametrization based on physiological measurements of light sensitivity could lead to more accurate individual-level circadian phase prediction.
URL:https://www.ibs.re.kr/bimag/event/2021-06-10/
LOCATION:ZOOM ID: 709 120 4849 (ibsbimag)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/04/AndrewPhillips_profile_crop-e1617768455279.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210526T170000
DTEND;TZID=Asia/Seoul:20210526T180000
DTSTAMP:20260425T044852
CREATED:20210311T114629Z
LAST-MODIFIED:20210407T040940Z
UID:4248-1622048400-1622052000@www.ibs.re.kr
SUMMARY:Neural network aided approximation and parameter inference of stochastic models of gene expression
DESCRIPTION:This talk will be presented online. Zoom link: 709 120 4849 (pw: 1234) \nAbstract: Non-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/2021-05-26/
LOCATION:ZOOM ID: 709 120 4849 (ibsbimag)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/03/DjvWsbfJ-e1617756286824.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210520T123000
DTEND;TZID=Asia/Seoul:20210520T133000
DTSTAMP:20260425T044852
CREATED:20210507T123654Z
LAST-MODIFIED:20210507T123746Z
UID:4547-1621513800-1621517400@www.ibs.re.kr
SUMMARY:Independent Markov Decomposition: Towards modeling kinetics of biomolecular complexes
DESCRIPTION:We will discuss about “Independent Markov Decomposition: Towards modeling kinetics of biomolecular complexes”\, Hempel et. al.\, bioRxiv\, 2021 \nIn order to advance the mission of in silico cell biology\, modeling the interactions of large and complex biological systems becomes increasingly relevant. The combination of molecular dynamics (MD) and Markov state models (MSMs) have enabled the construction of simplified models of molecular kinetics on long timescales. Despite its success\, this approach is inherently limited by the size of the molecular system. With increasing size of macromolecular complexes\, the number of independent or weakly coupled subsystems increases\, and the number of global system states increase exponentially\, making the sampling of all distinct global states unfeasible. In this work\, we present a technique called Independent Markov Decomposition (IMD) that leverages weak coupling between subsystems in order to compute a global kinetic model without requiring to sample all combinatorial states of subsystems. We give a theoretical basis for IMD and propose an approach for finding and validating such a decomposition. Using empirical few-state MSMs of ion channel models that are well established in electrophysiology\, we demonstrate that IMD can reproduce experimental conductance measurements with a major reduction in sampling compared with a standard MSM approach. We further show how to find the optimal partition of all-atom protein simulations into weakly coupled subunits.
URL:https://www.ibs.re.kr/bimag/event/2021-05-20/
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:20210514T110000
DTEND;TZID=Asia/Seoul:20210514T120000
DTSTAMP:20260425T044852
CREATED:20210507T124508Z
LAST-MODIFIED:20210507T124508Z
UID:4555-1620990000-1620993600@www.ibs.re.kr
SUMMARY:Extending Transfer Entropy Improves Identification of Effective Connectivity in a Spiking Cortical Network Model
DESCRIPTION:We will discuss about “Extending Transfer Entropy Improves Identification of Effective Connectivity in a Spiking Cortical Network Model”\, Ito et. al.\, PloS ONE\, 2011 \nTransfer entropy (TE) is an information-theoretic measure which has received recent attention in neuroscience for its potential to identify effective connectivity between neurons. Calculating TE for large ensembles of spiking neurons is computationally intensive\, and has caused most investigators to probe neural interactions at only a single time delay and at a message length of only a single time bin. This is problematic\, as synaptic delays between cortical neurons\, for example\, range from one to tens of milliseconds. In addition\, neurons produce bursts of spikes spanning multiple time bins. To address these issues\, here we introduce a free software package that allows TE to be measured at multiple delays and message lengths. To assess performance\, we applied these extensions of TE to a spiking cortical network model (Izhikevich\, 2006) with known connectivity and a range of synaptic delays. For comparison\, we also investigated single-delay TE\, at a message length of one bin (D1TE)\, and cross-correlation (CC) methods. We found that D1TE could identify 36% of true connections when evaluated at a false positive rate of 1%. For extended versions of TE\, this dramatically improved to 73% of true connections. In addition\, the connections correctly identified by extended versions of TE accounted for 85% of the total synaptic weight in the network. Cross correlation methods generally performed more poorly than extended TE\, but were useful when data length was short. A computational performance analysis demonstrated that the algorithm for extended TE\, when used on currently available desktop computers\, could extract effective connectivity from 1 hr recordings containing 200 neurons in ∼5 min. We conclude that extending TE to multiple delays and message lengths improves its ability to assess effective connectivity between spiking neurons. These extensions to TE soon could become practical tools for experimentalists who record hundreds of spiking neurons.
URL:https://www.ibs.re.kr/bimag/event/2021-05-14/
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:20210507T123000
DTEND;TZID=Asia/Seoul:20210507T133000
DTSTAMP:20260425T044852
CREATED:20210503T075749Z
LAST-MODIFIED:20210503T075749Z
UID:4525-1620390600-1620394200@www.ibs.re.kr
SUMMARY:Introduction to Bayesian ML/DL\, with Application to Parameter Inference of Coupled Non-linear ODEs - Part 2
DESCRIPTION:In this talk\, the speaker will present introductory materials about Bayesian Machine Learning. \nAbstract\nThe problem of approximating the posterior distribution (or density estimation in general) is a crucial problem in Bayesian statistics\, in which intractable integrals often become the computational bottleneck. MCMC sampling is the most widely used family of algorithms for approximating posteriors. However\, if the underlying graphical model is too complex or the data is in very high dimensions\, then such sampling-based methodologies run into several problems. Variational inference (Jordan et al.\, 1999; Wainwright and Jordan\, 2008) is a family of machine learning methodologies that transforms the problem of approximating posterior densities to an optimization\, which lets us circumvent all such problems. In the first part\, I will introduce the general framework of variational inference and some underlying theory\, accompanied by an illustrative example of LDA (Blei et al.\, 2003). In the second part\, I will introduce some recent works on applying variational inference to parameter inference of coupled non-linear ODEs arising in various biological contexts.
URL:https://www.ibs.re.kr/bimag/event/introduction-to-bayesian-ml-dl-with-application-to-parameter-inference-of-coupled-non-linear-odes-part-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:20210430T160000
DTEND;TZID=Asia/Seoul:20210430T170000
DTSTAMP:20260425T044852
CREATED:20210319T021820Z
LAST-MODIFIED:20210412T013739Z
UID:4282-1619798400-1619802000@www.ibs.re.kr
SUMMARY:What is the role of oscillatory signals in intracellular systems?
DESCRIPTION:Oscillatory signals are ubiquitously observed in many different intracellular systems such as immune systems and DNA repair processes. While we know how oscillatory signals are created\, we do not fully understand what a critical role they play to regulate signal pathway systems in cells. Recently by using a stochastic nucleosome system\, we found that a special signal (NFkB signal) in an immune cell can enhance the variability of the immune response to inflammatory stimulations when the signal is oscillatory. Hence in this talk\, we discuss the roles of oscillatory and non-oscillatory NFkB signals in an inflammatory system of immune cells as the main example for revealing the role of oscillatory signals. And then we will talk about how this finding can be generalized for other intra- or extra-cellular systems to study why cells use oscillations.
URL:https://www.ibs.re.kr/bimag/event/2021-04-30/
LOCATION:B305 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/03/Jinsu-Kim-9-e1617756454410.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210429T120000
DTEND;TZID=Asia/Seoul:20210429T130000
DTSTAMP:20260425T044852
CREATED:20210425T180554Z
LAST-MODIFIED:20210425T180554Z
UID:4499-1619697600-1619701200@www.ibs.re.kr
SUMMARY:Introduction to Bayesian ML/DL\, with Application to Parameter Inference of Coupled Non-linear ODEs - Part 1
DESCRIPTION:In this talk\, the speaker will present introductory materials about Bayesian Machine Learning. \nAbstract\nGaussian process(GP) is a stochastic process such that the joint distribution of an arbitrary finite subset of the random variables is a multivariate normal. It plays a fundamental role in Bayesian machine learning as it can be interpreted as a prior over functions (Rasmussen and Williams\, 2006)\, hence providing a nonparametric approach to various tasks. In the first part\, I will introduce the general framework of GP and some underlying theory\, accompanied by an illustrative example of GP regression\, also known as Kringing. In the second part\, I will introduce some recent works on applying GP to parameter inference of coupled non-linear ODEs arising in various biological contexts.
URL:https://www.ibs.re.kr/bimag/event/introduction-to-bayesian-ml-dl-with-application-to-parameter-inference-of-coupled-non-linear-odes-part-1/
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:20210422T120000
DTEND;TZID=Asia/Seoul:20210422T130000
DTSTAMP:20260425T044852
CREATED:20210417T101617Z
LAST-MODIFIED:20210419T021327Z
UID:4477-1619092800-1619096400@www.ibs.re.kr
SUMMARY:A Simple and Flexible Computational Framework for Inferring Sources of Heterogeneity from Single-Cell Dynamics
DESCRIPTION:We will discuss about “A Simple and Flexible Computational Framework for\nInferring Sources of Heterogeneity from Single-Cell\nDynamics”\, Dharmarajan et al.\, Cell Systems (2019) \nSingle-cell time-lapse data provide the means for disentangling sources of cell-to-cell and intra-cellular variability\, a key step for understanding heterogeneity in cell populations. However\, single-cell analysis with dynamic models is a challenging open problem: current inference methods address only single-gene expression or neglect parameter correlations. We report on a simple\, flexible\, and scalable method for estimating cell-specific and population-average parameters of non-linear mixed-effects models of cellular networks\, demonstrating its accuracy with a published model and dataset. We also propose sensitivity analysis for identifying which biological sub-processes quantitatively and dynamically contribute to cell-to-cell variability. Our application to endocytosis in yeast demonstrates that dynamic models of realistic size can be developed for the analysis of single-cell data and that shifting the focus from single reactions or parameters to nuanced and time-dependent contributions of sub-processes helps biological interpretation. Generality and simplicity of the approach will facilitate customized extensions for analyzing single-cell dynamics
URL:https://www.ibs.re.kr/bimag/event/2021-04-22/
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:20210421T170000
DTEND;TZID=Asia/Seoul:20210421T183000
DTSTAMP:20260425T044852
CREATED:20210324T050549Z
LAST-MODIFIED:20210421T074343Z
UID:4307-1619024400-1619029800@www.ibs.re.kr
SUMMARY:Advice to my younger self
DESCRIPTION:This talk will be presented online. Zoom link: 709 120 4849 (pw: 1234) \nFacebook live streaming: https://www.facebook.com/10226475900150025/videos/10226475902790091 \nAge brings the benefit of experience and looking back at my job as a professor\, there are a couple of things that fall into the category “I wish someone had told me that earlier”. In this seminar\, I would like to share some of the things I learned and which\, I hope\, will be useful for younger scientists. \nThe questions I will touch upon include \n\n\n\nWhat is productivity\, for a scientist?\nWhat are qualities of successful people?\nHow can one create motivation and success?\nHow to organize myself? (project management; getting things done)\nHow to communicate effectively?\nSeeking fulfillment\n\n\n\nThe seminar is targeted at PhD students\, postdocs\, and junior group leaders. \n \n 
URL:https://www.ibs.re.kr/bimag/event/2021-04-21/
LOCATION:ZOOM ID: 709 120 4849 (ibsbimag)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/03/olaf-wolkenhauer-e1617756681631.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210416T120000
DTEND;TZID=Asia/Seoul:20210416T130000
DTSTAMP:20260425T044852
CREATED:20210412T110458Z
LAST-MODIFIED:20210412T110458Z
UID:4423-1618574400-1618578000@www.ibs.re.kr
SUMMARY:Synthetic multistability in mammalian cells
DESCRIPTION:We will discuss about “Synthetic multistability in mammalian cells”\, Zhu et al.\, bioRxiv (2021) \nIn multicellular organisms\, gene regulatory circuits generate thousands of molecularly distinct\, mitotically heritable states\, through the property of multistability. Designing synthetic multistable circuits would provide insight into natural cell fate control circuit architectures and allow engineering of multicellular programs that require interactions among cells in distinct states. Here we introduce MultiFate\, a naturally-inspired\, synthetic circuit that supports long-term\, controllable\, and expandable multistability in mammalian cells. MultiFate uses engineered zinc finger transcription factors that transcriptionally self-activate as homodimers and mutually inhibit one another through heterodimerization. Using model-based design\, we engineered MultiFate circuits that generate up to seven states\, each stable for at least 18 days. MultiFate permits controlled state-switching and modulation of state stability through external inputs\, and can be easily expanded with additional transcription factors. Together\, these results provide a foundation for engineering multicellular behaviors in mammalian cells. \n  \n 
URL:https://www.ibs.re.kr/bimag/event/2021-04-16/
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:20210415T170000
DTEND;TZID=Asia/Seoul:20210415T173000
DTSTAMP:20260425T044852
CREATED:20210411T124935Z
LAST-MODIFIED:20210412T012752Z
UID:4429-1618506000-1618507800@www.ibs.re.kr
SUMMARY:Practical considerations for measuring the effective reproductive number
DESCRIPTION:Abstract: TBA
URL:https://www.ibs.re.kr/bimag/event/2021-04-15_2/
LOCATION:B305 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/04/SHC_profile2.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210415T163000
DTEND;TZID=Asia/Seoul:20210415T170000
DTSTAMP:20260425T044852
CREATED:20210411T124649Z
LAST-MODIFIED:20210412T013301Z
UID:4426-1618504200-1618506000@www.ibs.re.kr
SUMMARY:Mathematical modeling for infectious disease using epidemiological data
DESCRIPTION:Abstract: TBA
URL:https://www.ibs.re.kr/bimag/event/2021-04-15_1/
LOCATION:B305 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/04/HJL_profile5.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210415T110000
DTEND;TZID=Asia/Seoul:20210415T120000
DTSTAMP:20260425T044852
CREATED:20210314T044747Z
LAST-MODIFIED:20210412T021311Z
UID:4258-1618484400-1618488000@www.ibs.re.kr
SUMMARY:Dynamics-based data science in biology
DESCRIPTION:This talk will be presented online. Zoom link: 709 120 4849 (pw: 1234) \nAbstract: Life science has been a prosperous subject for a long time\, and is still developing with high speed now. One of its major aims is to study the mechanisms of various biological processes on the basis of biological big-data. Many statistics-based methods have been proposed to catch the essence by mining those data\, including the popular category classification\, variables regression\, group clustering\, statistical comparison\, dimensionality reduction\, and component analysis\, which\, however\, mainly elucidate static features or steady behavior of living organisms due to lack of temporal data. But\, a biological system is inherently dynamic\, and with increasingly accumulated time-series data\, dynamics-based approaches based on physical and biological laws are demanded to reveal dynamic features or complex behavior of biological systems. In this talk\, I will present a new concept “dynamics-based data science” and the approaches for studying dynamical bio-processes\, including dynamical network biomarkers (DNB)\, autoreservoir neural networks (ARNN) and partical cross-mapping. These methods are all data-driven or model-free approaches but based on the theoretical frameworks of nonlinear dynamics. We show the principles and advantages of dynamics-based data-driven approaches as explicable\, quantifiable\, and generalizable. In particular\, dynamics-based data science approaches exploit the essential features of dynamical systems in terms of data\, e.g. strong fluctuations near a bifurcation point\, low-dimensionality of a center manifold or an attractor\, and phase-space reconstruction from a single variable by delay embedding theorem\, and thus are able to provide different or additional information to the traditional approaches\, i.e. statistics-based data science approaches. The dynamical-based data science approaches will further play an important role in the systematical research of biology and medicine in future.
URL:https://www.ibs.re.kr/bimag/event/2021-04-15/
LOCATION:ZOOM ID: 709 120 4849 (ibsbimag)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/03/LC_profile2.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210409T120000
DTEND;TZID=Asia/Seoul:20210409T130000
DTSTAMP:20260425T044852
CREATED:20210323T105030Z
LAST-MODIFIED:20210407T041048Z
UID:4304-1617969600-1617973200@www.ibs.re.kr
SUMMARY:Highly accurate fluorogenic DNA sequencing with information theory–based error correction
DESCRIPTION:We will discuss about “Highly accurate fluorogenic DNA sequencing with information theory–based error correction”\, Chen et al.\, Nature Biotechnology (2017) \nEliminating errors in next-generation DNA sequencing has proved challenging. Here we present error-correction code (ECC) sequencing\, a method to greatly improve sequencing accuracy by combining fluorogenic sequencing-by-synthesis (SBS) with an information theory–based error-correction algorithm. ECC embeds redundancy in sequencing reads by creating three orthogonal degenerate sequences\, generated by alternate dual-base reactions. This is similar to encoding and decoding strategies that have proved effective in detecting and correcting errors in information communication and storage. We show that\, when combined with a fluorogenic SBS chemistry with raw accuracy of 98.1%\, ECC sequencing provides single-end\, error-free sequences up to 200 bp. ECC approaches should enable accurate identification of extremely rare genomic variations in various applications in biology and medicine. \n  \n 
URL:https://www.ibs.re.kr/bimag/event/2021-04-09/
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:20210401T120000
DTEND;TZID=Asia/Seoul:20210401T130000
DTSTAMP:20260425T044852
CREATED:20210331T003338Z
LAST-MODIFIED:20210406T075108Z
UID:4352-1617278400-1617282000@www.ibs.re.kr
SUMMARY:Yun Min Song\, A stochastic oscillator model simulates the entrainment of vertebrate cellular clocks by light
DESCRIPTION:We will discuss about “A stochastic oscillator model simulates the entrainment of vertebrate cellular clocks by light”\, Kumpost et al.\, bioRxiv (2021) \nThe circadian clock is a cellular mechanism that synchronizes various biological processes with respect to the time of the day. While much progress has been made characterizing the molecular mechanisms underlying this clock\, it is less clear how external light cues influence the dynamics of the core clock mechanism and thereby entrain it with the light-dark cycle. Zebrafish-derived cell cultures possess clocks that are directly light-entrainable\, thus providing an attractive laboratory model for circadian entrainment. Here\, we have developed a stochastic oscillator model of the zebrafish circadian clock\, which accounts for the core clock negative feedback loop\, light input\, and the proliferation of single-cell oscillator noise into population-level luminescence recordings. The model accurately predicts the entrainment dynamics observed in bioluminescent clock reporter assays upon exposure to a wide range of lighting conditions. Furthermore\, we have applied the model to obtain refitted parameter sets for cell cultures exposed to a variety of pharmacological treatments and predict changes in single-cell oscillator parameters. Our work paves the way for model-based\, large-scale screens for genetic or pharmacologically-induced modifications to the entrainment of circadian clock function.
URL:https://www.ibs.re.kr/bimag/event/2021-04-02/
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:20210325T110000
DTEND;TZID=Asia/Seoul:20210325T120000
DTSTAMP:20260425T044852
CREATED:20210301T013812Z
LAST-MODIFIED:20210406T075105Z
UID:4167-1616670000-1616673600@www.ibs.re.kr
SUMMARY:Daniel Forger\, The mathematics of the wearables with applications to circadian rhythms and sleep
DESCRIPTION:This talk will be presented online. Zoom link: 709 120 4849 (pw: 1234) \nAbstract: Millions of individuals track their steps\, heart rate\, and other physiological signals through wearables. This data scale is unprecedented; I will describe several of our apps and ongoing studies\, each of which collects wearable and mobile data from thousands of users\, even in > 100 countries. This data is so noisy that it often seems unusable and in desperate need of new mathematical techniques to extract key signals used in the (ode) mathematical modeling typically done in mathematical biology. I will describe several techniques we have developed to analyze this data and simulate models\, including gap orthogonalized least squares\, a new ansatz for coupled oscillators\, which is similar to the popular ansatz by Ott and Antonsen\, but which gives better fits to biological data and a new level-set Kalman Filter that can be used to simulate population densities. My focus applications will be determining the phase of circadian rhythms\, the scoring of sleep and the detection of COVID with wearables.
URL:https://www.ibs.re.kr/bimag/event/2021-03-25/
LOCATION:ZOOM ID: 709 120 4849 (ibsbimag)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium,Seminar
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/03/dannyg.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210322T100000
DTEND;TZID=Asia/Seoul:20210322T110000
DTSTAMP:20260425T044852
CREATED:20210315T062250Z
LAST-MODIFIED:20210406T075215Z
UID:4261-1616407200-1616410800@www.ibs.re.kr
SUMMARY:Dae Wook Kim\, Revealing causes of disrupted wake-sleep cycles using mathematical model (BRIC Webinar)
DESCRIPTION:Registration is required to attend this talk (link: https://www.ibric.org/seminar/#)\, and it will be presented in Korean. \nAbstract: 생체 시계 (Circadian clock)를 구성하는 핵심 단백질인 PERIOD (PER)의 양은 12시간 동안 증가했다가 12시간 동안 감소하며 24시간 주기로 변화한다. 이 24시간 주기의 PER 리듬이 우리 몸의 시계 역할을 하여 수면 시간 등 다양한 행동 및 생리 작용의 시간을 결정한다. PER의 24시간 주기 리듬 생성 원리는 2017년 노벨생리의학상을 수상한 마이클 영\, 제프리 홀 그리고 마이클 로스배시 교수에 의해서 밝혀졌다. 12시간 동안 세포질에서 축적된 PER 단백질은 세포 핵 안으로 들어가 스스로 PER 유전자의 전사 (Transcription)를 방해함으로써 12시간 동안 PER 단백질의 양을 감소 시킨다. 하지만 12시간 동안 다른 시간에 생산된 수 천개의 PER 분자들이 어떻게 매일 같은 시간에 핵 안으로 들어가는지는 생체시계 분야의 큰 난제였다. \n본 연구에서는 PER 단백질의 세포 내 움직임을 묘사하는 시공간적 확률론적 모형을 개발하여 분석함으로써 이 난제를 해결하였다. 구체적으로\, PER 단백질이 핵에 들어가는데 필요한 인산화가 핵 주변에서 PER 단백질의 농도가 충분히 높을 때에만 발생함을 밝혔다. 이러한 PER 인산화의 동기화 덕분에 수천 개의 PER 단백질이 매일 일정한 시간에 함께 핵 안으로 들어갈 수 있었고 안정적인 24시간 주기의 일주기 리듬 (Circadian rhythms)과 수면 사이클을 유지할 수 있었던 것이다. \n이러한 핵 주변에서 PER인산화 동기화가 발생하기 위해서는 핵 주변으로 PER이 충분히 응축되어야 한다. 하지만\, 세포 내 환경이 과도하게 혼잡해져 PER 분자의 움직임이 크게 방해를 받으면 PER이 충분히 응축되지 않고 PER 인산화 동기화가 발생하지 않게 된다. 그 결과\, PER이 핵 안으로 들어가는 시간이 불규칙해져 일주기 리듬과 수면 사이클이 불안정해진다. \n이러한 수리 모델 예측은 미국 플로리다 주립대학 이주곤 교수 팀과의 협업을 통해 실험으로 검증하였다. 이는 세포질 혼잡 (Cytoplasmic trafficking)을 유발하는 것으로 알려진 비만\, 치매\, 노화가 어떻게 수면 질환을 유발하는지에 대한 메커니즘과 더불어 새로운 수면 장애 치료법을 제시한다. \n 
URL:https://www.ibs.re.kr/bimag/event/2021-03-22/
CATEGORIES:Biomedical Mathematics Seminar,Seminar
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/03/DaeWookKim_profile.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210319T113000
DTEND;TZID=Asia/Seoul:20210319T130000
DTSTAMP:20260425T044852
CREATED:20210312T062049Z
LAST-MODIFIED:20210406T075219Z
UID:4254-1616153400-1616158800@www.ibs.re.kr
SUMMARY:Seokjoo Chae\, Unified rational protein engineering with sequence-based deep representation learning
DESCRIPTION:In this presentation\, we are going to discuss the paper\, “Unified rational protein engineering with sequence-based deep representation learning” \nAbstract\nRational protein engineering requires a holistic understanding of protein function. Here\, we apply deep learning to unlabeled amino-acid sequences to distill the fundamental features of a protein into a statistical representation that is semantically rich and structurally\, evolutionarily and biophysically grounded. We show that the simplest models built on top of this unified representation (UniRep) are broadly applicable and generalize to unseen regions of sequence space. Our data-driven approach predicts the stability of natural and de novo designed proteins\, and the quantitative function of molecularly diverse mutants\, competitively with the state-of-the-art methods. UniRep further enables two orders of magnitude efficiency improvement in a protein engineering task. UniRep is a versatile summary of fundamental protein features that can be applied across protein engineering informatics.
URL:https://www.ibs.re.kr/bimag/event/2021-03-19/
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:20210312T113000
DTEND;TZID=Asia/Seoul:20210312T130000
DTSTAMP:20260425T044852
CREATED:20210305T084406Z
LAST-MODIFIED:20210406T075224Z
UID:4227-1615548600-1615554000@www.ibs.re.kr
SUMMARY:Dae Wook Kim\, Maximum Entropy Framework for Predictive Inference of Cell Population Heterogeneity and Responses in Signaling Networks
DESCRIPTION:We will discuss about “Maximum Entropy Framework for Predictive Inference of Cell Population Heterogeneity and Responses in Signaling Networks”\, Dixit et al.\, Cell Systems (2020) \nPredictive models of signaling networks are essential for understanding cell population heterogeneity and designing rational interventions in disease. However\, using computational models to predict heterogeneity of signaling dynamics is often challenging because of the extensive variability of biochemical parameters across cell populations. Here\, we describe a maximum entropy-based framework for inference of heterogeneity in dynamics of signaling networks (MERIDIAN). MERIDIAN estimates the joint probability distribution over signaling network parameters that is consistent with experimentally measured cell-to-cell variability of biochemical species. We apply the developed approach to investigate the response heterogeneity in the EGFR/Akt signaling network. Our analysis demonstrates that a significant fraction of cells exhibits high phosphorylated Akt (pAkt) levels hours after EGF stimulation. Our findings also suggest that cells with high EGFR levels predominantly contribute to the subpopulation of cells with high pAkt activity. We also discuss how MERIDIAN can be extended to accommodate various experimental measurements. \n  \n 
URL:https://www.ibs.re.kr/bimag/event/2021-03-12/
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:20210305T130000
DTEND;TZID=Asia/Seoul:20210305T140000
DTSTAMP:20260425T044852
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:20260425T044852
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:20260425T044852
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:20260425T044852
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:20260425T044852
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:20260425T044852
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:20260425T044852
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:20260425T044852
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:20260425T044852
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:20260425T044852
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
END:VCALENDAR