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X-WR-CALNAME:Biomedical Mathematics Group
X-ORIGINAL-URL:https://www.ibs.re.kr/bimag
X-WR-CALDESC:Events for Biomedical Mathematics Group
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BEGIN:VTIMEZONE
TZID:Asia/Seoul
BEGIN:STANDARD
TZOFFSETFROM:+0900
TZOFFSETTO:+0900
TZNAME:KST
DTSTART:20200101T000000
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BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210305T130000
DTEND;TZID=Asia/Seoul:20210305T140000
DTSTAMP:20260510T134150
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:20210312T113000
DTEND;TZID=Asia/Seoul:20210312T130000
DTSTAMP:20260510T134150
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:20210319T113000
DTEND;TZID=Asia/Seoul:20210319T130000
DTSTAMP:20260510T134150
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:20210322T100000
DTEND;TZID=Asia/Seoul:20210322T110000
DTSTAMP:20260510T134150
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/
LOCATION:Daejeon
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:20210325T110000
DTEND;TZID=Asia/Seoul:20210325T120000
DTSTAMP:20260510T134150
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
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