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PRODID:-//Biomedical Mathematics Group - ECPv6.15.20//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:20200101T000000
END:STANDARD
END:VTIMEZONE
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20221109T160000
DTEND;TZID=Asia/Seoul:20221109T170000
DTSTAMP:20260409T201655
CREATED:20220825T012221Z
LAST-MODIFIED:20220902T003131Z
UID:6486-1668009600-1668013200@www.ibs.re.kr
SUMMARY:Modeling cell-to-cell heterogeneity from a signaling network
DESCRIPTION:Cells make individual fate decisions through linear and nonlinear regulation of gene network\, generating diverse dynamics from a single reaction pathway. In this colloquium\, I will present two topics of our recent work on signaling dynamics at cellular and patient levels. The first example is about the initial value of the model\, as a mechanism to generate different dynamics from a single pathway in cancer and the use of the dynamics for stratification of the patients [1-3]. Models of ErbB receptor signaling have been widely used in prediction of drug sensitivity for many types of cancers. We trained the ErbB model with the data obtained from cancer cell lines and predicted the common parameters of the model. By simulation of the ErbB model with those parameters and individual patient transcriptome data as initial values\, we were able to classify the prognosis of breast cancer patients and drug sensitivity based on their in silico signaling dynamics. This result raises the question whether gene expression levels\, rather than genetic mutations\, might be better suited to classify the disease. Another example is about the regulation of transcription factors\, the recipients of signal dynamics\, for target gene expression [4-6]. By focusing on the NFkB transcription factor\, we found that the opening and closing of chromatin at the DNA regions of the putative transcription factor binding sites and the cooperativity in their interaction significantly influenced the cell-to cell heterogeneity in gene expression levels. This study indicates that the noise in gene expression is rather strongly regulated by the DNA side\, even though the signals are similarly regulated in a cell population. Overall these mechanisms are important in our understanding the cell as a system for encoding and decoding signals for fate decisions and its application to human diseases. \n[References] \n[1] Nakakuki et al. Cell 2010\,\n[2] Imoto et al. iScience 2022\,\n[3] Imoto et al. STAR Protocols 2022\,\n[4] Shinohara et al. Science 2014\,\n[5] Michida et al. Cell Reports 2020\,\n[6] Wibisana et al. PLoS Genetics 2022
URL:https://www.ibs.re.kr/bimag/event/2022-11-09-colloquium/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/08/okada-250x250-1.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20221026T160000
DTEND;TZID=Asia/Seoul:20221026T170000
DTSTAMP:20260409T201655
CREATED:20220825T012029Z
LAST-MODIFIED:20220925T142427Z
UID:6482-1666800000-1666803600@www.ibs.re.kr
SUMMARY:Mathematical modelling of the sleep-wake cycle: light\, clocks and social rhythms
DESCRIPTION:Abstract: \nWe’re all familiar with sleep\, but how can we mathematically model it? And what determines how long and when we sleep? In this talk I’ll introduce the nonsmooth coupled oscillator systems that form the basis of current models of sleep-wake regulation and discuss their dynamical behaviour. I will describe how we are using models to unravel environmental\, societal and physiological factors that determine sleep timing and outline how we are using models to inform the quantitative design of light interventions for mental health disorders and address contentious societal questions such as whether to move school start time for adolescents.
URL:https://www.ibs.re.kr/bimag/event/2022-10-26-colloquium/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/08/anne-skeldon.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20221021T110000
DTEND;TZID=Asia/Seoul:20221021T120000
DTSTAMP:20260409T201655
CREATED:20220825T011824Z
LAST-MODIFIED:20220916T014258Z
UID:6478-1666350000-1666353600@www.ibs.re.kr
SUMMARY:Stationary distributions and positive recurrence of chemical reaction networks
DESCRIPTION:Abstract: \nCellular\, chemical\, and population processes are all often represented via networks that describe the interactions between the different population types (typically called the “species”). If the counts of the species are low\, then these systems are often modeled as continuous-time Markov chains on the d-dimensional integer lattice (with d being the number of species)\, with transition rates determined by stochastic mass-action kinetics. A natural (broad) mathematical question is: how do the qualitative properties of the dynamical system relate to the graph properties of the network? For example\, it is of particular interest to know which graph properties imply that the stochastically modeled reaction network is positive recurrent\, and therefore admits a stationary distribution. After a general introduction to the models of interest\, I will discuss this problem\, giving some of the known results. I will also discuss recent progress on the Chemical Recurrence Conjecture\, which has been open for decades\, which is the following: if each connected component of the network is strongly connected\, then the associated stochastic model is positive recurrent.
URL:https://www.ibs.re.kr/bimag/event/2022-10-21-colloquium/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/08/DAnderson2018-250x250-1.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20221021T103000
DTEND;TZID=Asia/Seoul:20221021T110000
DTSTAMP:20260409T201655
CREATED:20220916T014503Z
LAST-MODIFIED:20220916T014503Z
UID:6575-1666348200-1666350000@www.ibs.re.kr
SUMMARY:A Brief Introduction to Stochastic Reaction Networks
DESCRIPTION:Abstract: TBA
URL:https://www.ibs.re.kr/bimag/event/2022-10-21-colloquium-2/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/08/DAnderson2018-250x250-1.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20221007T110000
DTEND;TZID=Asia/Seoul:20221007T120000
DTSTAMP:20260409T201655
CREATED:20220825T011205Z
LAST-MODIFIED:20220901T005901Z
UID:6471-1665140400-1665144000@www.ibs.re.kr
SUMMARY:Time-keeping and Decision-making in the Cell Cycle
DESCRIPTION:Abstract: Cell growth\, DNA replication\, mitosis and division are the fundamental processes by which life is passed on from one generation of eukaryotic cells to the next. The eukaryotic cell cycle is intrinsically a periodic process but not so much a ‘clock’ as a ‘copy machine’\, making new daughter cells as warranted. Cells growing under ideal conditions divide with clock-like regularity; however\, if they are challenged with DNA-damaging agents or mitotic spindle disruptors\, they will not progress to the next stage of the cycle until the damage is repaired. These ‘decisions’ (to exit and re-enter the cell cycle) are essential to maintain the integrity of the genome from generation to generation. A crucial challenge for molecular cell biologists in the 1990s was to unravel the genetic and biochemical mechanisms of cell cycle control in eukaryotes. Central to this effort were biochemical studies of the clock-like regulation of ‘mitosis promoting factor’ during synchronous mitotic cycles of fertilized frog eggs and genetic studies of the switch-like regulation of ‘cyclin-dependent kinases’ in yeast cells. The complexity of these control systems demands a dynamical approach\, as described in the first lecture. Using mathematical models of the control systems\, I will uncover some of the secrets of cell cycle ‘clocks’ and ‘switches’.
URL:https://www.ibs.re.kr/bimag/event/2022-10-07-colloquium2/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/08/Tyson_profile-250x250-1.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20221007T103000
DTEND;TZID=Asia/Seoul:20221007T110000
DTSTAMP:20260409T201655
CREATED:20220825T011010Z
LAST-MODIFIED:20220901T010141Z
UID:6468-1665138600-1665140400@www.ibs.re.kr
SUMMARY:A Dynamic Paradigm for Molecular Cell Biology
DESCRIPTION:Abstract: The driving passion of molecular cell biologists is to understand the molecular mechanisms that control important aspects of cell physiology\, but this ambition is – paradoxically – limited by the very wealth of molecular details currently known about these mechanisms. Their complexity overwhelms our intuitive notions of how molecular regulatory networks might respond under normal and stressful conditions. To make progress we need a new paradigm for connecting molecular biology to cell physiology. I will outline an approach that uses precise mathematical methods to associate the qualitative features of dynamical systems\, as conveyed by ‘bifurcation diagrams’\, with ‘signal–response’ curves measured by cell biologists.
URL:https://www.ibs.re.kr/bimag/event/2022-10-01-colloquium1/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/08/Tyson_profile-250x250-1.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220902T110000
DTEND;TZID=Asia/Seoul:20220902T120000
DTSTAMP:20260409T201655
CREATED:20220825T010806Z
LAST-MODIFIED:20220829T000006Z
UID:6463-1662116400-1662120000@www.ibs.re.kr
SUMMARY:Cell signaling in 2D vs. 3D
DESCRIPTION:Abstract: \nThe activation of Ras depends upon the translocation of its guanine nucleotide exchange factor\, Sos\, to the plasma membrane. Moreover\, artificially inducing Sos to translocate to the plasma membrane is sufficient to bring about Ras activation and activation of Ras’s targets. There are many other examples of signaling proteins that must translocate to the membrane in order to relay a signal. \nOne attractive idea is that translocation promotes signaling by bringing a protein closer to its target. However\, proteins that are anchored to the membrane diffuse more slowly than cytosolic proteins do\, and it is not clear whether the concentration effect or the diffusion effect would be expected to dominate. Here we have used a reconstituted\, controllable system to measure the association rate for the same binding reaction in 3D vs. 2D to see whether association is promoted\, and\, if so\, how.
URL:https://www.ibs.re.kr/bimag/event/20220902_colloquium/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/08/Ferrell_profile-250x250-1.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220601T170000
DTEND;TZID=Asia/Seoul:20220601T180000
DTSTAMP:20260409T201655
CREATED:20220531T223000Z
LAST-MODIFIED:20220317T001720Z
UID:5601-1654102800-1654106400@www.ibs.re.kr
SUMMARY:From live cell imaging to moment-based variational inference
DESCRIPTION:This talk will be presented online. Zoom link: 997 8258 4700 (pw: 1234) \nAbstract: Quantitative characterization of biomolecular networks is important for the analysis and design of network functionality. Reliable models of such networks need to account for intrinsic and extrinsic noise present in the cellular environment. Stochastic kinetic models provide a principled framework for developing quantitatively predictive tools in this scenario. Calibration of such models requires an experimental setup capable of monitoring a large number of individual cells over time\, automatic extraction of fluorescence levels for each cell and a scalable inference approach. In the first part of the talk we will cover our microfluidic setup and a deep-learning based approach to cell segmentation and data extraction. The second part will introduce moment-based variational inference as a scalable framework for approximate inference of kinetic models based on single cell data.
URL:https://www.ibs.re.kr/bimag/event/2022-06-01/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/01/HK_250x250.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220525T170000
DTEND;TZID=Asia/Seoul:20220525T180000
DTSTAMP:20260409T201655
CREATED:20220524T230000Z
LAST-MODIFIED:20220224T003504Z
UID:5609-1653498000-1653501600@www.ibs.re.kr
SUMMARY:Multi-resolution methods for modelling intracellular processes
DESCRIPTION:This talk will be presented online. Zoom link: 997 8258 4700 (pw: 1234) \nAbstract: I will discuss the development\, analysis and applications of multi-resolution methods for spatio-temporal modelling of intracellular processes\, which use (detailed) Brownian dynamics or molecular dynamics simulations in localized regions of particular interest (in which accuracy and microscopic details are important) and a (less-detailed) coarser model in other regions in which accuracy may be traded for simulation efficiency. I will discuss the error analysis and convergence properties of the developed multi-resolution methods\, their software implementation and applications of these multiscale methodologies to modelling of intracellular calcium dynamics\, actin dynamics and DNA dynamics. I will also discuss the development of multiscale methods which couple molecular dynamics and coarser stochastic models in the same dynamic simulation.
URL:https://www.ibs.re.kr/bimag/event/2022-05-25-2/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/01/RE_250x250.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220525T163000
DTEND;TZID=Asia/Seoul:20220525T170000
DTSTAMP:20260409T201655
CREATED:20220524T223000Z
LAST-MODIFIED:20220224T003158Z
UID:5606-1653496200-1653498000@www.ibs.re.kr
SUMMARY:Stochastic modelling of reaction-diffusion processes
DESCRIPTION:This talk will be presented online. Zoom link: 997 8258 4700 (pw: 1234) \nAbstract: I will introduce mathematical and computational methods for spatio-temporal modelling in molecular and cell biology\, including all-atom and coarse-grained molecular dynamics (MD)\, Brownian dynamics (BD)\, stochastic reaction-diffusion models and macroscopic mean-field equations. Microscopic (BD\, MD) models are based on the simulation of trajectories of individual molecules and their localized interactions (for example\, reactions). Mesoscopic (lattice-based) stochastic reaction-diffusion approaches divide the computational domain into a finite number of compartments and simulate the time evolution of the numbers of molecules in each compartment\, while macroscopic models are often written in terms of mean-field reaction-diffusion partial differential equations for spatially varying concentrations.
URL:https://www.ibs.re.kr/bimag/event/2022-05-25-1/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/01/RE_250x250.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220512T110000
DTEND;TZID=Asia/Seoul:20220512T120000
DTSTAMP:20260409T201655
CREATED:20220511T170000Z
LAST-MODIFIED:20220224T002809Z
UID:5599-1652353200-1652356800@www.ibs.re.kr
SUMMARY:Plasticity and balance in neuronal networks
DESCRIPTION:This talk will be presented online. Zoom link: 997 8258 4700 (pw: 1234) \nAbstract: I will first describe how to extend the theory of balanced networks to account for synaptic plasticity. This theory can be used to show when a plastic network will maintain balance\, and when it will be driven into an unbalanced state. I will next discuss how this approach provides evidence for a novel form of rapid compensatory inhibitory plasticity. Experimental evidence for such plasticity comes from optogenetic activation of excitatory neurons in primate visual cortex (area V1) which induces a population-wide dynamic reduction in the strength of neuronal interactions over the timescale of minutes during the awake state\, but not during rest. I will shift gears in the final part of the talk\, and discuss how community detection algorithms can help uncover the large scale organization of neuronal networks from connectome data.
URL:https://www.ibs.re.kr/bimag/event/2022-05-12-2/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/03/KJ_250x250.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220512T103000
DTEND;TZID=Asia/Seoul:20220512T110000
DTSTAMP:20260409T201655
CREATED:20220511T163000Z
LAST-MODIFIED:20220224T002732Z
UID:5596-1652351400-1652353200@www.ibs.re.kr
SUMMARY:Introduction to balanced networks
DESCRIPTION:This talk will be presented online. Zoom link: 997 8258 4700 (pw: 1234) \nAbstract: The idea of balance between excitation and inhibition is central in the theory of biological neural networks.  I will give a brief introduction to the concept of such balance\, and an overview of the mathematical ideas that can be used to study it.
URL:https://www.ibs.re.kr/bimag/event/2022-05-12-1/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/03/KJ_250x250.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220428T110000
DTEND;TZID=Asia/Seoul:20220428T120000
DTSTAMP:20260409T201655
CREATED:20220427T170000Z
LAST-MODIFIED:20220224T002639Z
UID:5593-1651143600-1651147200@www.ibs.re.kr
SUMMARY:Scaling behaviors in physiological fluctuations: relevance to circadian regulation and insights into the development of Alzheimer’s disease
DESCRIPTION:This talk will be presented online. Zoom link: 997 8258 4700 (pw: 1234) \nAbstract: Outputs from health biological systems display complex fluctuations that are not random but display robust and often self-similar (fractal) temporal correlations at different time scales— scaling behaviors. The scaling behaviors in the fluctuations of biological outputs such as neural activities\, cardiac dynamics\, motor activity are believed to be originated from feedbacks within the complex biological networks\, reflecting the system adaptability to internal and external inputs. Supporting this concept\, our studies have demonstrated a mechanistic link between the scaling regulation of physiological fluctuations and the circadian control system— a result of evolutionary adaptation to daily environmental light-dark cycles on the earth. In this talk\, I will discuss certain evidence for this ‘scaling-circadian’ link and its related implications. Moreover\, I will review some recent studies\, in which we examined how the scaling patterns of human motor activity fluctuations change with aging and in Alzheimer’s disease. Our results showed that (1) alterations in scaling activity patterns occur before the clinical manifestation of Alzheimer’s disease (i.e.\, cognitive impairment) and predict cognitive decline and the risk for Alzheimer’s dementia; and (2) the progression of Alzheimer’s disease accelerates the aging effect on the scaling activity patterns. Our work provides strong evidence that altered scaling activity patterns may also be a risk factor for neurodegeneration\, playing a role in the development and progression of Alzheimer’s disease.
URL:https://www.ibs.re.kr/bimag/event/2022-04-28/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/01/KH_250x250.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220414T110000
DTEND;TZID=Asia/Seoul:20220414T120000
DTSTAMP:20260409T201655
CREATED:20220413T170000Z
LAST-MODIFIED:20220224T002525Z
UID:5591-1649934000-1649937600@www.ibs.re.kr
SUMMARY:A systems biology approach using multi-scale modeling to understand the immune response to tuberculosis infection and treatment
DESCRIPTION:This talk will be presented online. Zoom link: 997 8258 4700 (pw: 1234) \nAbstract: Tuberculosis (TB) is one of the world’s deadliest infectious diseases. Caused by the pathogen Mycobacterium tuberculosis (Mtb)\, the standard regimen for treating TB consists of treatment with multiple antibiotics for at least six months. There are a number of complicating factors that contribute to the need for this long treatment duration and increase the risk of treatment failure. The structure of granulomas\, lesions forming in lungs in response to Mtb infection\, create heterogeneous antibiotic distributions that limit antibiotic exposure to Mtb.   We can use a systems biology approach pairing experimental data from non-human primates with computational modeling to represent and predict how factors impact antibiotic regimen efficacy and granuloma bacterial sterilization. We utilize an agent-based\, computational model that simulates granuloma formation\, function and treatment\, called GranSim.  A goal in improving antibiotic treatment for TB is to find regimens that can shorten the time it takes to sterilize granulomas while minimizing the amount of antibiotic required. We also created a whole host model\, called HOSTSIM\, to study Mtb dynamics within a human host.  Overall\, we use these models to help better understand TB treatment and strengthen our ability to predict regimens that can improve clinical treatment of TB.
URL:https://www.ibs.re.kr/bimag/event/2022-04-14-2/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/01/DK_250x250.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220414T103000
DTEND;TZID=Asia/Seoul:20220414T110000
DTSTAMP:20260409T201655
CREATED:20220413T163000Z
LAST-MODIFIED:20220130T045637Z
UID:5588-1649932200-1649934000@www.ibs.re.kr
SUMMARY:An overview of methods used for multi-scale modeling and analysis
DESCRIPTION:This talk will be presented online. Zoom link: 997 8258 4700 (pw: 1234) \nAbstract: TBA
URL:https://www.ibs.re.kr/bimag/event/2022-04-14-1/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/01/DK_250x250.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220407T110000
DTEND;TZID=Asia/Seoul:20220407T120000
DTSTAMP:20260409T201655
CREATED:20220406T170000Z
LAST-MODIFIED:20220224T002321Z
UID:5585-1649329200-1649332800@www.ibs.re.kr
SUMMARY:Universal biology in adaptation and evolution: dimensional reduction\, and fluctuation-response relationship
DESCRIPTION:This talk will be presented online. Zoom link: 997 8258 4700 (pw: 1234) \nAbstract: A macroscopic theory for cellular states with steady-growth is presented\, based on consistency between cellular growth and molecular replication\, together with robustness of phenotypes against perturbations. Adaptive changes in high-dimensional phenotypes are shown to be restricted within a low-dimensional slow manifold\, from which a macroscopic law for cellular states is derived\, as is confirmed by adaptation experiments of bacteria under stress. The theory is extended to phenotypic evolution\, leading to proportionality between phenotypic responses against genetic evolution and by environmental adaptation\, which explains the evolutionary fluctuation-response relationship previously uncovered.   \nReferences \n\n Kaneko K.\, Life: An Introduction to Complex Systems Biology\, Springer (2006)\n K. Kaneko\, C.Furusawa\, T. Yomo\, “Macroscopic phenomenology for cells in steady-growth state”\, Phys.Rev.X(2015) 011014\n C. Furusawa\, K. Kaneko “Global Relationships in Fluctuation and Response in Adaptive Evolution”\, J of Royal Society Interface 12(2015)\, 20150482.\n C. Furusawa\, K. Kaneko ” Formation of Dominant Mode by Evolution in Biological Systems” Phys. Rev. E 97(2018)042410\n K. Kaneko\, C. Furusawa “Macroscopic Theory for Evolving Biological Systems Akin to Thermodynamics”\, Annual Rev. Biophys. (2018) 47\, 273-290\n A. Sakata and K. Kaneko\, “Dimensional Reduction in Evolving Spin-Glass Model: Correlation of Phenotypic Responses to Environmental and Mutational Changes”\, Phys. Rev. Lett. (2020) 124\, 218101\n Q-Y. Tang and K. Kaneko\, “ Dynamics-evolution correspondence in protein structures”\,  Phys. Rev. Lett. (2021) 127\, 098103
URL:https://www.ibs.re.kr/bimag/event/2022-04-07/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/01/Kunihiko-Kaneko.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220331T110000
DTEND;TZID=Asia/Seoul:20220331T120000
DTSTAMP:20260409T201655
CREATED:20220330T170000Z
LAST-MODIFIED:20220317T000754Z
UID:5582-1648724400-1648728000@www.ibs.re.kr
SUMMARY:Design principles of physiological circuits
DESCRIPTION:This talk will be presented online. Zoom link: 997 8258 4700 (pw: 1234) \nAbstract: We will discuss hormone circuits and their dynamics using new models that take into account timescales of weeks due to growth of the hormone glands. This explains some mysteries in diabetes and autoimmune disease.
URL:https://www.ibs.re.kr/bimag/event/2022-03-31/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/01/UA_250x250.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220324T110000
DTEND;TZID=Asia/Seoul:20220324T120000
DTSTAMP:20260409T201655
CREATED:20220323T170000Z
LAST-MODIFIED:20220224T002127Z
UID:5579-1648119600-1648123200@www.ibs.re.kr
SUMMARY:Topological data analysis of spatial systems
DESCRIPTION:This talk will be presented online. Zoom link: 997 8258 4700 (pw: 1234) \nAbstract: From the venation patterns of leaves to spider webs\, roads in cities\, social networks\, and the spread of COVID-19 infections and vaccinations\, the structure of many systems is influenced significantly by space. In this talk\, I will discuss the application of topological data analysis (specifically\, persistent homology) to spatial systems. I will present a few examples\, such as voting in presidential elections\, city street networks\, spatiotemporal dynamics of COVID-19 infections and vaccinations\, and webs that were spun by spiders under the influence of various drugs.
URL:https://www.ibs.re.kr/bimag/event/2022-03-24-2/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/01/MP_250x250.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220324T103000
DTEND;TZID=Asia/Seoul:20220324T110000
DTSTAMP:20260409T201655
CREATED:20220323T163000Z
LAST-MODIFIED:20220324T045408Z
UID:5575-1648117800-1648119600@www.ibs.re.kr
SUMMARY:Introduction to topological data analysis
DESCRIPTION:This talk will be presented online. Zoom link: 997 8258 4700 (pw: 1234) \nAbstract: I will give an introduction to topological data analysis (TDA)\, in which one uses ideas from algebraic topology to study the “shape” of data. I will focus on persistent homology (PH)\, which is the most common approach in TDA.
URL:https://www.ibs.re.kr/bimag/event/2022-03-24-1/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/01/MP_250x250.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220303T110000
DTEND;TZID=Asia/Seoul:20220303T120000
DTSTAMP:20260409T201655
CREATED:20220302T170000Z
LAST-MODIFIED:20220224T001605Z
UID:5529-1646305200-1646308800@www.ibs.re.kr
SUMMARY:Spatiotemporal reconstruction of static single-cell genomics data
DESCRIPTION:This talk will be presented online. Zoom link: 997 8258 4700 (pw: 1234) \nAbstract: Cells make fate decisions in response to dynamic environments and multicellular structure emerges from interplays among cells in space and time. The recent single-cell genomics technology provides an unprecedented opportunity to profile cells. However\, those measurements are taken as snapshots for groups of individual cells with only static information. Can one infer interactions among cells from such datasets? Is it possible to recover spatial information from non-spatial datasets? How to obtain temporal relationships of cells from the static measurements? In this talk I will present our newly developed computational tools that reconstruct interactions and spatiotemporal relationships for cells using single-cell RNA-seq\, ATAC-seq\, and spatial transcriptomics datasets. Through applications of those methods to systems in development and regeneration\, we show the discovery power of such methods and identify areas for further development in spatiotemporal reconstruction.
URL:https://www.ibs.re.kr/bimag/event/2022-03-03/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2022/01/QN_250x250.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20211125T180000
DTEND;TZID=Asia/Seoul:20211125T190000
DTSTAMP:20260409T201655
CREATED:20211124T230000Z
LAST-MODIFIED:20211111T104319Z
UID:4808-1637863200-1637866800@www.ibs.re.kr
SUMMARY:Quantitative comparisons between models and data to provide new insights in cell and developmental biology
DESCRIPTION:This talk will be presented online. Zoom link: 709 120 4849 (pw: 1234) \nAbstract: \nSimple mathematical models have had remarkable successes in biology\, framing how we understand a host of mechanisms and processes. However\, with the advent of a host of new experimental technologies\, the last ten years has seen an explosion in the amount and types of quantitative data now being generated. This sets a new challenge for the field – to develop\, calibrate and analyse new models to interpret these data. In this talk I will use examples relating to intracellular transport and cell motility to showcase how quantitative comparisons between models and data can help tease apart subtle details of biological mechanisms. \nReferences: \n• T. P. Prescott\, K. Zhu\, M. Zhao and R. E. Baker (2021). Quantifying the impact of electric fields on single-cell motility. Biophys. J. In press. \n• J. U. Harrison\, R. M. Parton\, I. Davis and R. E. Baker (2019). Testing models of mRNA localization reveals robustness regulated by reducing transport between cells. Biophys. J. 117(11):2154-2165.
URL:https://www.ibs.re.kr/bimag/event/2021-11-25/
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/2021/07/RuthBaker_profile.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20211118T110000
DTEND;TZID=Asia/Seoul:20211118T120000
DTSTAMP:20260409T201655
CREATED:20211117T170000Z
LAST-MODIFIED:20211230T031249Z
UID:4820-1637233200-1637236800@www.ibs.re.kr
SUMMARY:Following the energy in cellular information processing
DESCRIPTION:This talk will be presented online. Zoom link: 709 120 4849 (pw: 1234) \nAbstract: John Hopfield first pointed out that there are barriers – we call them Hopfield barriers – to biological information-processing at thermodynamic equilibrium. I will explain how the widely-used Hill function with coefficient n is the universal Hopfield barrier to the sharpness of binding to n sites. Away from thermodynamic equilibrium\, I will describe the challenge of path dependent  complexity and introduce the entropy-production index as a measure of non-equilibrium complexity.
URL:https://www.ibs.re.kr/bimag/event/2021-11-18/
LOCATION:ZOOM ID: 709 120 4849 (ibsbimag)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/11/jeremy-scaled_250x250.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20211111T110000
DTEND;TZID=Asia/Seoul:20211111T120000
DTSTAMP:20260409T201655
CREATED:20211110T170000Z
LAST-MODIFIED:20210826T000813Z
UID:4816-1636628400-1636632000@www.ibs.re.kr
SUMMARY:Biofluiddynamics of reproduction
DESCRIPTION:This talk will be presented online. Zoom link: 709 120 4849 (pw: 1234) \nAbstract: From fertilization to birth\, successful mammalian reproduction relies on interactions of elastic structures with a fluid environment. Sperm flagella must move through cervical mucus to the uterus and into the oviduct\, where fertilization occurs. In fact\, some sperm may adhere to oviductal epithelia\, and must change their pattern of oscillation to escape. In addition\, coordinated beating of oviductal cilia also drive the flow. Sperm-egg penetration\, transport of the fertilized ovum from the oviduct to its implantation in the uterus and\, indeed\, birth itself are rich examples of elasto-hydrodynamic coupling. We will discuss successes and challenges in the mathematical and computational modeling of the biofluids of reproduction.
URL:https://www.ibs.re.kr/bimag/event/2021-11-11/
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/2021/07/fauci_profile_sqr-e1627697850446.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20211027T170000
DTEND;TZID=Asia/Seoul:20211027T180000
DTSTAMP:20260409T201655
CREATED:20211026T230000Z
LAST-MODIFIED:20210901T070035Z
UID:4812-1635354000-1635357600@www.ibs.re.kr
SUMMARY:Systems pharmacology towards personalized chronotherapy
DESCRIPTION:This talk will be presented online. Zoom link: 709 120 4849 (pw: 1234) \nAbstract: \nChronotherapeutics- that is administering drugs following the patient’s biological rhythms over the 24 h span- may largely impact on both drug toxicities and efficacy in various pathologies including cancer [1]. However\, recent findings highlight the critical need of personalizing circadian delivery according to the patient sex\, genetic background or chronotype. Chronotherapy personalization requires to reliably account for the temporal dynamics of molecular pathways of patient’s response to drug administration [2]. In a context where clinical molecular data is usually minimal in individual patients\, multi-scale- from preclinical to clinical- systems pharmacology stands as an adapted solution to describe gene and protein networks driving circadian rhythms of treatment efficacy and side effects and allow for the design of personalized chronotherapies.\nSuch a multiscale approach is being undertaken for personalizing the circadian administration of irinotecan\, one of the cornerstones of chemotherapies against digestive cancers. Irinotecan molecular chronopharmacology was studied at the cellular level in an in vitro/in silico investigation. Large transcription rhythms of period T= 28 h 06 min (SD 1 h 41 min) moderated drug bioactivation\, detoxification\, transport\, and target in synchronized Caco-2 colorectal cancer cell cultures. These molecular rhythms translated into statistically significant changes according to drug timing in irinotecan pharmacokinetics\, pharmacodynamics\, and drug-induced apoptosis. Clock silencing through siBMAL1 exposure ablated all the chronopharmacology mechanisms. Mathematical modeling highlighted circadian bioactivation and detoxification as the most critical determinants of irinotecan chronopharmacology [3]. The cellular model of irinotecan chronoPK-PD was further tested on SW480 and SW620 cell lines\, and connected to a new clock model to investigate the feasibility of irinotecan timing personalization solely based on clock gene expression monitoring (Hesse\, Martinelli et al.\, under review).\nTo step towards the clinics\, on one side\, mathematical models of irinotecan\, oxaliplatin and 5-fluorouracil pharmacokinetics were designed to precisely compute the exposure concentration of tissue over time after complex chronomodulated drug administration through programmable pumps [4]. On the other side\, we aimed to design a model learning methodology predicting from non-invasively measured circadian biomarkers (e.g. rest-activity\, body temperature\, cortisol\, food intake\, melatonin)\, the patient peripheral circadian clocks and associated optimal drug timing [5]. We investigated at the molecular scale the influence of systemic regulators on peripheral clocks in four classes of mice (2 strains\, 2 sexes). Best models involved a modulation of either Bmal1 or Per2 transcription most likely by temperature or nutrient exposure cycles. The strengths of systemic regulations were found to be significantly different according to mouse sex and genetic background.\nReferences\n1. Ballesta\, A.\, et al.\, Systems Chronotherapeutics. Pharmacol Rev\, 2017. 69(2): p. 161-199.\n2. Sancar\, A. and R.N. Van Gelder\, Clocks\, cancer\, and chronochemotherapy. Science\, 2021. 371(6524).\n3. Dulong\, S.\, et al.\, Identification of Circadian Determinants of Cancer Chronotherapy through In Vitro Chronopharmacology and Mathematical Modeling. Mol Cancer Ther\, 2015.\n4. Hill\, R.J.W.\, et al.\, Optimizing circadian drug infusion schedules towards personalized cancer chronotherapy. PLoS Comput Biol\, 2020. 16(1): p. e1007218.\n5. Martinelli\, J.\, et al.\, Model learning to identify systemic regulators of the peripheral circadian clock. 2021. \n 
URL:https://www.ibs.re.kr/bimag/event/2021-10-27/
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/2021/07/AnnabelleBallesta_profile_sqr-e1627697556509.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20211021T110000
DTEND;TZID=Asia/Seoul:20211021T120000
DTSTAMP:20260409T201655
CREATED:20211103T170000Z
LAST-MODIFIED:20210930T040222Z
UID:4787-1634814000-1634817600@www.ibs.re.kr
SUMMARY:Scaling in development
DESCRIPTION:This talk will be presented online. Zoom link: 709 120 4849 (pw: 1234)\n\nAbstract: \n Within a given species\, fluctuations in egg or embryo size is unavoidable. Despite this\, the gene expression pattern and hence the embryonic structure often scale in proportion with the body length. This scaling phenomenon is very common in development and regeneration and has long fascinated scientists. I will first discuss a generic theoretical framework to show how scaling gene expression pattern can emerge from non-scaling morphogen gradients. I will then demonstrate that the Drosophila gap gene system achieves scaling in a way that is entirely consistent with our theory. Remarkably\, a parameter-free model based on the theory quantitatively accounts for the gap gene expression pattern in nearly all morphogen mutants. Furthermore\, the regulation logic and the coding/decoding strategy of the gap gene system can be revealed. Our work provides a general theoretical framework on a large class of problems where scaling output is induced by non-scaling input\, as well as a unified understanding of scaling\, mutants’ behavior and regulation in the Drosophila gap gene and related systems.
URL:https://www.ibs.re.kr/bimag/event/2021-10-21/
LOCATION:ZOOM ID: 709 120 4849 (ibsbimag)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/07/resize.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20211007T110000
DTEND;TZID=Asia/Seoul:20211007T120000
DTSTAMP:20260409T201655
CREATED:20211006T170000Z
LAST-MODIFIED:20211230T031435Z
UID:4850-1633604400-1633608000@www.ibs.re.kr
SUMMARY:A temporal signaling code to specify immune responses
DESCRIPTION:This talk will be presented online. Zoom link: 709 120 4849 (pw: 1234) \nAbstract: \nImmune sentinel cells must initiate the appropriate immune response upon sensing the presence of diverse pathogens or immune stimuli. To generate stimulus-specific gene expression responses\, immune sentinel cells have evolved a temporal code in the dynamics of stimulus responsive transcription factors. I will present recent works 1) using an information theoretic approach to identify the codewords\, termed “signaling codons”\, 2) using a machine learning approach to characterize their reliability and points of confusion\, and 3) dynamical systems modeling to characterize the molecular circuits that allow for their encoding. I will present progress on how the temporal code may be decoded to specify immune responses.  Further\, I will discuss to what extent such a code may be harnessed to achieve greater pharmacological specificity when therapeutically targeting pleiotropic signaling hubs. \nNFκB Signaling: information theory\, signaling codons \nAdelaja\, A.\, Taylor\, B.\, Sheu\, K.M.\, Liu\, Y.\, Luecke\, S.\, Hoffmann\, A. 2021 Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responses. Immunity\, 54\, pp.916-930. e7. PMID: 33979588 \nTang\, Y.\, Adelaja\, A.\, Ye\, X\, Deeds\, E.\, Wollman\, R.\, Hoffmann\, A. 2021. Quantifying information accumulation encoded in the dynamics of biochemical signaling. Nature Communications 12\, pp.1-10 \nDecoding signaling codons to specify immune responses \nSen S.\, Cheng\, Z.\, Sheu\, K.\, Chen\, E.Y.H.\, Hoffmann\, A. 2020 Gene Regulatory Strategies that Decode the Duration of NFkB Dynamics Contribute to LPS- versus TNF-Specific Gene Expression. Cell Systems\, 10\, pp.1-14. PMID:31972132\, PMC7047529 \nCheng\, Q.J.\, Ohta\, S.\, Sheu\, K.M.\, Spreafico\, R.\, Adelaja\, A.\, Taylor\, B.\, Hoffmann\, A.  2021 NFκB dynamics determine the stimulus-specificity of epigenomic reprogramming in macrophages. Science\, 372\, pp.1349-1353; PMID: 34140389. \nPharmacologic manipulation of the code \nBehar\, M.\, Barken\, D.\, Werner\, S.L.\, Hoffmann\, A. 2013  The Dynamics of Signaling as a Pharmacological Target.  Cell\, 155\, pp.448-461. PMID: 24120141\, PMC3856316
URL:https://www.ibs.re.kr/bimag/event/2021-10-07/
LOCATION:ZOOM ID: 709 120 4849 (ibsbimag)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/10/AlexanderHoffmann_profile_250x250.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210916T110000
DTEND;TZID=Asia/Seoul:20210916T120000
DTSTAMP:20260409T201655
CREATED:20210915T170000Z
LAST-MODIFIED:20211230T030915Z
UID:4529-1631790000-1631793600@www.ibs.re.kr
SUMMARY:Stochastic processes as scientific instruments: efficient inference based on stochastic dynamical systems
DESCRIPTION:This talk will be presented online. Zoom link: 709 120 4849 (pw: 1234)\n\nAbstract: Questions about the mechanistic operation of biological systems are naturally formulated as stochastic processes\, but confronting such models with data can be challenging.  In this talk\, I describe the essence of the difficulty\, highlighting both the technical issues and the importance of the “plug-and-play property”.  I then illustrate some effective approaches to efficient inference based on such models.  I conclude by sketching promising new developments and describing some open problems.
URL:https://www.ibs.re.kr/bimag/event/2021-09-16/
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/2021/09/imagev2.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210908T170000
DTEND;TZID=Asia/Seoul:20210908T180000
DTSTAMP:20260409T201655
CREATED:20210907T230000Z
LAST-MODIFIED:20210907T103108Z
UID:4648-1631120400-1631124000@www.ibs.re.kr
SUMMARY:[CANCELED] Approaches to understanding tumour-immune interactions
DESCRIPTION:CANCELED due to unexpected circumstances\nThis talk will be presented online. Zoom link: 709 120 4849 (pw: 1234) \nAbstract: While the presence of immune cells within solid tumours was initially viewed positively\, as the host fighting to rid itself of a foreign body\, we now know that the tumour can manipulate immune cells so that they promote\, rather than inhibit\, tumour growth. Immunotherapy aims to correct for this by boosting and/or restoring the normal function of the immune system. Immunotherapy has delivered some extremely promising results. However\, the complexity of the tumour-immune interactions means that it can be difficult to understand why one patient responds well to immunotherapy while another does not. In this talk\, we will show how mathematical\, statistical and topological methods can contribute to resolving this issue and present recent results which illustrate the complementary insight that different approaches can deliver.
URL:https://www.ibs.re.kr/bimag/event/2021-09-08/
LOCATION:ZOOM ID: 709 120 4849 (ibsbimag)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/06/Helen-Byrne_Photo_crop2.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210902T100000
DTEND;TZID=Asia/Seoul:20210902T110000
DTSTAMP:20260409T201655
CREATED:20210901T160000Z
LAST-MODIFIED:20211230T030825Z
UID:4540-1630576800-1630580400@www.ibs.re.kr
SUMMARY:Exploiting evolution to design better cancer therapies
DESCRIPTION:This talk will be presented online. Zoom link: 709 120 4849 (pw: 1234)\n\nAbstract: Our current approach to cancer treatment has been largely driven by finding molecular targets\, those patients fortunate enough to have a targetable mutation will receive a fixed treatment schedule designed to deliver the maximum tolerated dose (MTD). These therapies generally achieve impressive short-term responses\, that unfortunately give way to treatment resistance and tumor relapse. The importance of evolution during both tumor progression\, metastasis and treatment response is becoming more widely accepted. However\, MTD treatment strategies continue to dominate the precision oncology landscape and ignore the fact that treatments drive the evolution of resistance. Here we present an integrated theoretical/experimental/clinical approach to develop treatment strategies that specifically embrace cancer evolution. We will consider the importance of using treatment response as a critical driver of subsequent treatment decisions\, rather than fixed strategies that ignore it. We will also consider using mathematical models to drive treatment decisions based on limited clinical data. Through the integrated application of mathematical and experimental models as well as clinical data we will illustrate that\, evolutionary therapy can drive either tumor control or extinction using a combination of drug treatments and drug holidays. Our results strongly indicate that the future of precision medicine shouldn’t be in the development of new drugs but rather in the smarter evolutionary\, and model informed\, application of preexisting ones.
URL:https://www.ibs.re.kr/bimag/event/2021-09-02/
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/2021/09/AndersonAlexander2.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210728T170000
DTEND;TZID=Asia/Seoul:20210728T180000
DTSTAMP:20260409T201655
CREATED:20210407T040301Z
LAST-MODIFIED:20210717T235315Z
UID:4383-1627491600-1627495200@www.ibs.re.kr
SUMMARY:Theory and design of molecular integral feedback controllers
DESCRIPTION:This talk will be presented online. Zoom link: 709 120 4849 (pw: 1234)\nAbstract: \nHomeostasis is a recurring theme in biology that ensures that regulated variables robustly adapt to environmental perturbations. This robust perfect adaptation feature is achieved in natural circuits by using integral control\, a negative feedback strategy that performs mathematical integration to achieve structurally robust regulation. Despite its benefits\, the synthetic realization of integral feedback in living cells has remained elusive owing to the complexity of the required biological computations. In this talk I will show that there is a single fundamental biomolecular controller topology that realizes integral feedback and achieves robust perfect adaptation in arbitrary intracellular networks with noisy dynamics. This adaptation property is guaranteed both for the population-average and for the time-average of single cells. On the basis of this concept\, I will describe a genetically engineered synthetic integral feedback controller in living cells and demonstrate its tunability and adaptation properties. A growth-rate control application in Escherichia coli shows the intrinsic capacity of our integral controller to deliver robustness and highlights its potential use as a versatile controller for regulation of biological variables in uncertain networks. These results provide conceptual and practical tools in the area of cybergenetics\, for engineering synthetic controllers that steer the dynamics of living systems.
URL:https://www.ibs.re.kr/bimag/event/2021-07-28/
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/MustafaKhammash_profile-e1617768310550.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
END:VCALENDAR