jaekyoungkim's homepage

Lab webpage

 

Senior researchers

 

1Hyeontae Jo (Senior Researcher, PhD. Postec, Korea)

Research topic: Big data analysis and neural-network with physics-informed neural network

 

 

 

 

1. Jo H, Hong H, Hwang H,J, Chang W, Kim JK, Density Physics-Informed Neural Network identifies sources of cell heterogeneity in signal transduction under antibiotic stress,Cell Patterns (2023)

2. Hyeontae Jo†, Hong Jun Jeon, Junseok Ahn, Saebom Jeon*, Jae Kyoung Kim*, Seockhoon Chung*, Dysfunctional Beliefs and Attitude about Sleep-6 (DBAS-6): Data-driven Shortened Version from A Machine Learning Approach (Submitted)

3. Hyeontae Jo†, Myna Lim†, Hong Jun Jeon, Junseok Ahn, Saebom Jeon, Jae Kyoung Kim*, Seockhoon Chung*, Data-driven Shortened Insomnia Severity Index: A Machine Learning Approach (Submitted)

 

 

1Pan Li (Senior Researcher, PhD. University of Leed, UK)

Research topic: Mathematical modeling for circadian rhythms in heart

 

 

 

 

1. Pan Li*, Jae Kyoung Kim*, Central and peripheral clocks synergistically enhance circadian robustness, flexibility and performance of cardiac pacemaking (In revision)

 

Postdoctoral fellows

1Hyun Kim (Postdoctoral Fellow, PhD. Korea U, Republic of Korea)

Research topic: Neuronal networks and DNA sequencing analysis.

 

 

 

 

 

1. Eui Min Jeong, Miri Kwon, Eunjoo Cho, Sang Hyuk Lee, Hyun Kim, Eun Young Kim, and Jae Kyoung Kim, Systematic modeling-driven experiments identify distinct molecular clockworks underlying hierarchically organized pacemaker neurons, PNAS (2022)

2. Hyun Kim†, Won Chang, Seok Joo Chae, Jong-Eun Park, Minseok Seo, Jae Kyoung Kim*, scLENS: Data-driven signal detection for unbiased scRNA-seq data analysis (In revision)

 

 

1Gavina, Brenda Lyn (Postdoctoral Fellow, Ph.D, U Philippines Diliman, Philippine)

Project: Mathematical modeling and control of the menstrual cycle

 

     

     

     

     

    1Euimin Jung (Postdoctoral Fellow, Ph.D, KAIST, Rep of Korea)

    Project: Mathematical modeling for pacemaker-neuron-dependent rhythm alteration by mutation/ Reduction of multi-timescale systems

    NIMS-SKKU MDA-TDA Summer School, 1st Prize (2016) Korean Society of Mathematical Biology Poster Award (2017) Korean society of Sleep Medicine Poster Award (2017) KSIAM Poster Award (2020) International Conference for Systems Biology 1st Poster Award (2022)

     

       

    1. Eui Min Jeong, Miri Kwon, Eunjoo Cho, Sang Hyuk Lee, Hyun Kim, Eun Young Kim, and Jae Kyoung Kim, Systematic modeling-driven experiments identify distinct molecular clockworks underlying hierarchically organized pacemaker neurons, PNAS (2022)
    2. Eui Min Jeong, Yun Min Song, Jae Kyougn Kim Combined multiple transcriptional repression mechanisms generate ultrasensitivity and oscillations, Interface Focus (2022)
    3. Eui Min Jeong†, Jae Kyoung Kim*, Robust Ultrasensitive Transcriptional Switch in Noisy Cellular Environments (Submitted)
    4. Otobe Y†, Jeong EM†, Ito S, Fukada Y* Kim JK* and Yoshitane H*, Phosphorylation of DNA-binding domains of CLOCK-BMAL1 complex is essential for mammalian circadian clockwork (In revision)

     

     

     

    Gradauate Students

    1Seokjoo Choe(Math Ph.D student)/TJ Park POSCO Science Fellowship (2018~2020)

    Project: Network inference using Convergent Cross mapping / NK cell cytotoxcity modeling using ligand expression/ Analysis of stochastic reaction-diffusion system

    Society of Mathematical Biology Poster Award (2020)

     

     

     

    1. Seok Joo Chae, Dae Wook Kim, Seunggyu Lee, and Jae Kyoung Kim, Spatially coordinated collective phosphorylation filters spatiotemporal noises for precise circadian timekeeping, iScience (2022)
    2. Sunyoung Lee+, Seok Joo Chae+, In-Hwan Jang, Se-Chan Oh, Seok-Min Kim, Soo Yun Lee, Jesang Ko, Hang J. Kim, Jae Kyoung Kim3,4*, Tae-Don Kim1,5*, A systematic approach based on multidimensional data: Activator-driven gating decides NK Killing (In review)
    3. Hyun Kim†, Won Chang, Seok Joo Chae, Jong-Eun Park, Minseok Seo, Jae Kyoung Kim*, scLENS: Data-driven signal detection for unbiased scRNA-seq data analysis (In review)
    4. Seokjoo Chae†, Dae Wook Kim, Oleg A. Igoshin, Seunggyu Lee and Jae Kyoung Kim*, Beyond microtubule: Cellular environment at the endoplasmic reticulum attracts proteins to the nucleus, essential for nuclear transport (In review)

     

     

    1Yun Min Song (Math Ph.D student)

    Project: Stochastic analysis of multi-timespcale stochastic systems/ Analysis of timeseries data from smartwatch/Analysis of non-Markovian dynamics

    Society of Mathematical Biology Poster Award (2020) Korean Society of Mathematical Biology Poster Award (2021)

     

     

     

    1. Yun Min Song, Hyukpyo Hong, and Jae Kyoung Kim, Universally valid reduction of multiscale stochastic biochemical systems using simple non-elementary propensities, PLOS Comp Biol (2021)
    2. Eui Min Jeong, Yun Min Song, Jae Kyougn Kim Combined multiple transcriptional repression mechanisms generate ultrasensitivity and oscillations, Interface Focus (2022)
    3. Ngoc-Anh Thi Vu†, Yun Min Song†, Quyen Thi Tran, Hwi-yeol Yun Sang Kyum Kim*, Jung-woo Chae*, and Jae Kyoung Kim*, Beyond the Michaelis-Menten: Accurate Prediction of Drug Interactions through Cytochrome P450 Induction, Clinical Pharmacology and Therapeutics (2023)
    4. Minki P. Lee†, Kien Hoang†, Sungkyu Park, Yun Min Song, Eun Yeon Joo, Won Chang*, Jee Hyun Kim*, Jae Kyoung Kim*, Imputing Missing Sleep Data from Wearables with Neural Networks in Real-World Settings, Sleep (2023)
    5. Yun Min SongႵ, Su Jung ChoiႵ, Se Ho Park, Soo Jin Lee, Eun Yeon Joo*, Jae Kyoung Kim*, A real-time, personalized sleep intervention using mathematical modelling and wearable devices, Sleep (2023)
    6. Yun Min Song†, Sean Campbell†, LieJune Shiau, Jae Kyoung Kim*, William Ott*, Noisy delay denoises biochemical oscillators, Physical Review Letters (2024)
    7. Yun Min Song†, Jaegwon Jeong†, Aurelio V de los Reyes†, Chul-Hyun Cho, Ji Won Yeom, Taek Lee, Jung-Been Lee, Heon-Jeong Lee*, and Jae Kyoung Kim*, Causal Dynamics of Sleep, Circadian Rhythm, and Mood in Major Depression and Bipolar Disorder Patients: Insights from Longitudinal Wearable Device Data (In revision)
    8. Dongju Lim†, Jaegwon Jeong†, Yun Min Song, Heon-Jeong Lee*, Jae Kyoung Kim*, Highly Accurate Prediction of Mood Episodes in Mood Disorder Patients Using Sleep and Circadian Rhythm Features from Wearables (Submitted)

    1 Dong joo Lim (Math Ph.D student)

    Project: Analysis of timeseries data from smartwatch via machine learning

     

     

     

    1. Dongju Lim†, Jaegwon Jeong†, Yun Min Song, Heon-Jeong Lee*, Jae Kyoung Kim*, Highly Accurate Prediction of Mood Episodes in Mood Disorder Patients Using Sleep and Circadian Rhythm Features from Wearables (Submitted)

     

    1 Olive Cawiding (Math Ph.D student)

    Project: Analysis of causal relationship between climates and Dengue

     

     

     

     

    Undergradauate Students

     

    1Reinatt Hansel Wijaya (CS Undergrad student)

    Project: Development of website and app for sleep-disorders

     

     

     

    1. Seokmin Ha†, Su Jung Choi†, Sujin Lee, Reinatt Hansel Wijaya, Jee Hyun Kim, Eun Yeon Joo*, Jae Kyoung Kim*, A machine learning-based simple questionnaire for predicting the risk of sleep disorders , JMIR (2023)

     

     

    1Abbas Abbasli (Physics Undergrad student)

    Project: Development of a new equation predicting drug-drug interaction

     

     

     

    1Hyeongjoon Jang (Transdisciplinary studies Undergrad student)

    Project: Development of a new equation predicting drug-drug interaction

     

     

     

    Former members

     

    1Hyukpyo Hong (Math Ph.D student)/ Global Ph.D Fellowship (2019-2023)

    Project: Analysis of human activity patterns using a fractal analysis for diagnois/ Inference of time delay distributio from timeseries data/ Stochatic analysis of chemical reaction network

    KSIAM Poster Award (2021)

    Currently, Van Vleck Assistant Professor, U of Wisconsin, Madison (2023. 9~)

     

     

    1. Hyukpyo Hong, Jinsu Kim, M Ali Al-Radhawi, Eduardo Sontag, and Jae Kyoung Kim, Derivation of stationary distributions of biochemical reaction networks via structure transformation, Communicaiton Biology (2021)
    2. Yun Min Song, Hyukpyo Hong, and Jae Kyoung Kim, Universally valid reduction of multiscale stochastic biochemical systems using simple non-elementary propensities,PLOS Comp Biol(2021)
    3. Jaehyoung Hong, Su Jung Choi, Se Ho Park, Hyukpyo Hong, Victoria Booth, Eun Yeon Joo, and Jae Kyoung Kim, Personalized sleep-wake patterns aligned with circadian rhythm relieve daytime sleepiness, iScience (2021)
    4. Hyukpyo Hong, Boseung Choi, Jae Kyoung Kim (2021), Beyond the Michaelis–Menten: Bayesian Inference for Enzyme Kinetic Analysis. In Quentin Vanhaelen (Ed.) Computational Methods for Estimating the Kinetic Parameters of Biological Systems, Springer U
    5. Mark Jayson Cortez, Hyukpyo Hong, Boseung Choi*, Jae Kyoung Kim*, and Krešimir Josic*, Hierarchical Bayesian models of transcriptional and translational regulation processes with delays, Bioinformatics (2021)
    6. Dae Wook Kim†, Hyukpyo Hong†, and Jae Kyoung Kim, Systematic inference identifies a major source of heterogeneity in cell signaling dynamics: the rate-limiting step number, Science Advances (2022)
    7. Hyukpyo Hong†, Ji Yun Noh†, Hyojung Lee, Sunhwa Choi, Boseung Choi, Jae Kyoung Kim*, Eui-Cheol Shin*, Increasing viral transmission paradoxically reduces progression rates to severe COVID-19 during endemic transition, Immune Network (2022)
    8. Hyukpyo Hong, Bryan S. Hernandez, Jinsu Kim, Jae Kyoung Kim*, Computational translation framework identifies biochemical reaction networks with special topologies and their long-term dynamics, SIAM Journal on Applied Mathematics (2023)
    9. Hyukpyo Hong, Mark Jayson Cortez, Yu-Yu Cheng, Hang Joon Kim, Boseung Choi, Kresimir Josic, and Jae Kyoung Kim, Inferring delays in partially observed gene regulatory networks, Bioinformatics (2023)
    10. Hyeontae Jo, Hyukpyo Hong, and Jae Kyoung Kim*, Density Physics-Informed Neural Network reveals sources of cell heterogeneity in signal transduction, Cell Patterns (2023)
    11. Yuji Hirono†*, Seokhwan Moon†, Hyukpyo Hong, Jae Kyoung Kim*, Topological Criterion for Robust Perfect Adaptation of Reaction Fluxes in Biological Networks (Submitted)

    1Daewook Kim (Ph.D. student 2016-2021)

    Math Ph.D. Thesis: Theoretical Frameworks and Mathematical Models to Study Biological Systems with Time Delay/ Global Ph.D Fellowship (2018-2021)/ 2021 KSIAM Young Researcher Paper Award

    Currently, Van Loo Assistant Professor at the Department of Mathematics, University of Michigan, Ann Arbor

     

     

     

    1. Kim DW, Chang C, Chen X, Doran A, Gaudreault F, Wager T, DeMarco GJ, Kim JK, Systems approach reveals photosensitivity and PER2 level as determinants of clock‐modulator efficacy, Molecular Systems Biology (2019)
    2. Kim DW, Zavala E, Kim JK, Wearable technology and systems modeling for personalized chronotherapy, Curr Opin Syst Biol (2020)
    3. Zou X, DW Kim, Gotoh T, Liu J, Kim JK, Finkielstein CV, A systems biology approach identifies hidden regulatory connections between the circadian and cell-cycle checkpoints, Front. Physiol. (2020)
    4. Beesley S†, Kim DW†, DAlessandro M, Jin Y, Lee K, Joo H, Young Y, Tomko R, Kim JK, Lee C, Wake-sleep cycles are severely disrupted by diseases affecting cytoplasmic homeostasis, PNAS (2020)
    5. Pay ML†, Kim DW†, Somers DE, Kim JK, Foocor M, Modeling of Plant Circadian Clock for Characterizing Hypocotyl Growth under Different Light Quality Conditions, in silico Plants (2022) 
    6. Dae Wook Kim†, Hyukpyo Hong†, and Jae Kyoung Kim, Systematic inference identifies a major source of heterogeneity in cell signaling dynamics: the rate-limiting step number, Science Advances (2022)
    7. Abe YO, Yoshitane H, Kim DW, Koebis M, Aiba A, Kim JK, Fukada Y, Rhythmic transcription of Bmal1 stabilizes the circadian timekeeping system in mammals, Nature Communications (2022)
    8. Kim DW, Byun JM, Lee JK, Kim JK, Koh Y, Chemotherapy delivery time affects anti- lymphoma treatment outcome in a sex-dependent manner, JCI Insight (2022)
    9. Seok Joo Chae, Dae Wook Kim, Seunggyu Lee, and Jae Kyoung Kim, Spatially coordinated collective phosphorylation filters spatiotemporal noises for precise circadian timekeeping, iScience (2023)
    10. Seokjoo Chae†, Dae Wook Kim, Oleg A. Igoshin, Seunggyu Lee and Jae Kyoung Kim*, Beyond microtubule: Cellular environment at the endoplasmic reticulum attracts proteins to the nucleus, essential for nuclear transport (Submitted)
    11. Song Yi Jeong†, Dae Wook Kim†, Seokmin Ha†, Gyeongik Ahn, Gyeong-Im Shin, Cam Chau Nguyen, Joon-Yung Cha, Jae Kyoung Kim*, Woe-Yeon Kim*, Unraveling strong circadian rhythms: synergy in protein degradation and synthesis (Submitted)

     

    1Bryan S. Hernandez (Postdoctoral Fellow 2021-2022, PhD. University of the Philippines Diliman. Philippines)

    Research topic: Chemical reaction networks

    Currently, Assistant Professor, University of the Philippines Diliman.

     

     

     

    1. Hyukpyo Hong, Bryan S. Hernandez, Jinsu Kim, Jae Kyoung Kim*, Computational translation framework identifies biochemical reaction networks with special topologies and their long-term dynamics, SIAM Journal on Applied Mathematics (2023)

    2. Bryan S Hernandez, Patrick Vincent N. Lubenia, Matthew Johnston, Jae Kyoung Kim, A framework for deriving analytic long-term behavior of biochemical reaction networks, PLOS Comp Biol (2022)

     

     

    1Aurelio A. de los Reyes V (Senior Researcher 2022-2023, PhD. Karl-Franzens Universitaet Graz, Austria)

    Research topic: Sleep-wake cycle, cardiovascular-respiratory system, and COVID-19.

    Currently, Professor, University of the Philippines Diliman.

     

     

     

     

    1Canden Celik (Postdoctoral Fellow 2022-2023, PhD. Comenius University. Slovekia)

    Research topic: Stochastic Chemical Reaction Network

     

     

     

     

    1Seho Park (Math Undergrad student, 2020~2023)

    Project: Analyzing sleep pattern of shift workers via PCR model/ Inference of causation from timeseries data

    2022 URP Best Award (최우수상)

    Currently, e a graduate student at Dept. Math, U Wisconsin Madison (2023. 9-)

     

     

    1. Jaehyoung Hong, Su Jung Choi, Se Ho Park, Hyukpyo Hong, Victoria Booth, Eun Yeon Joo, and Jae Kyoung Kim, Personalized sleep-wake patterns aligned with circadian rhythm relieve daytime sleepiness, iScience (2021)
    2. Se Ho Park, Seokmin Ha, Jae Kyoung Kim, A general model-based causal inference overcomes the curse of synchrony and indirect effect, Nature Communications (2023)
    3. Yun Min SongႵ, Su Jung ChoiႵ, Se Ho Park, Soo Jin Lee, Eun Yeon Joo*, Jae Kyoung Kim*, A real-time, personalized sleep intervention using mathematical modelling and wearable devices, SLEEP, 2023

     

    1Seokmin Ha (Math Undergrad student, 2021~2023)

    Project: Inference of causation from timeseries data/ Mathematical modeling of plant circadian clock

    2021 URP Best Award (최우수상)

    Currently, e a graduate student at Dept. Math, MIT (2023. 9-)

     

     

    1. Joohee Lee†, Seokmin Ha†, Oli Ahmed, Inn-Kyu Cho, Dongin Lee, Kyumin Kim, Solbi Kang, Sangha Lee, Sooyeon Suh*, Seockhoon Chung*, Jae Kyoung Kim, Validation of a Korean version of the Metacognitions Questionnaire-Insomnia (MCQ-I) and development of shortened versions of the rating scale: a random forest approach, Sleep Medicine (2022)
    2. Seokmin Ha†, Su Jung Choi†, Sujin Lee, Reinatt Hansel Wijaya, Jee Hyun Kim, Eun Yeon Joo*, Jae Kyoung Kim*, A machine learning-based simple questionnaire for predicting the risk of sleep disorders , JMIR (2023)
    3. Se Ho Park, Seokmin Ha, Jae Kyoung Kim, A general model-based causal inference overcomes the curse of synchrony and indirect effect, Nature Communications (2023)
    4. Song Yi Jeong†, Dae Wook Kim†, Seokmin Ha†, Gyeongik Ahn, Gyeong-Im Shin, Cam Chau Nguyen, Joon-Yung Cha, Jae Kyoung Kim*, Woe-Yeon Kim*, Unraveling strong circadian rhythms: synergy in protein degradation and synthesis (Submitted)

     

     

    1 Minki Lee (Visiting Undergraduate Student 2022)

    Research topic: Analysis of time-series data from wearable devices

    Currently, an undergraduate student at the Department of Mathematics, University of Michigan, Ann Arbor

     

     

     

     

    1. Minki P. Lee†, Kien Hoang†, Sungkyu Park, Yun Min Song, Eun Yeon Joo, Won Chang*, Jee Hyun Kim*, Jae Kyoung Kim*, Imputing Missing Sleep Data from Wearables with Neural Networks in Real-World Settings, Sleep (2023)

     

     

    1Kien Hoang (Undergraduate Student 2022)

    Research topic: Analysis of time-series data from wearable devices

    Currently, a graduate student in Artificial Intelligence & Advanced Visual Computing at École Polytechnique

     

     

     

     

    1. Minki P. Lee†, Kien Hoang†, Sungkyu Park, Yun Min Song, Eun Yeon Joo, Won Chang*, Jee Hyun Kim*, Jae Kyoung Kim*, Imputing Missing Sleep Data from Wearables with Neural Networks in Real-World Settings, Sleep (2023)

     

     

     

     

    1Tyczynska Malgorzata Anna (Master student, 2016-2017)

    Math MS student Thesis: Detecting Causality in Oscillating Systems

    Currently, Ph.D. student in Moffit Cancetr Center (FL, USA).

     

     

    A video introducing research life in our lab

         

    Avaiable Positions

    Postdocs

    IBS Biomedical Mathematics Group Postdoc

    We have several postdoc posotions for IBS Biomedical Matheamtics Group (https://www.ibs.re.kr/bimag/), which consists of intracellular, intercelluar and systematic dynamics teams. Please visist the website for the details.

    Samsung STF Postdoc

    We have a postdoctoral fellow position for a Samsung STF-funded project: Inference of dynamic networks from timeseries big data in biological systems. We aim develop methods infering the structure of network and time delay distribution in network interactions from timeseries data.

    Data analysis experience (e.g. Bayesian inference) is recommended, but not required. For inquiries, please contact Prof. Jae Kyoung Kim via email at jaekkim@kaist.ac.kr. Applications, including a full CV, a cover letter explaining suitability for the position, and the names and addresses of two referees should be sent to Prof. Kim.

    BK21 Postdoc positions are available in Dept. of Math, KAIST, every semseter (June or Dec)

    http://mathsci.kaist.ac.kr/home/

    Graduarte Students

    Our lab does not hire graduate students directly according to the math department policy. The admission process of the math department is as follows.

    Step 1. Getting an admission from Dept of Math, KAIST (written exam + interview)

    Step 2. Taking a semster course work.

    Step 3. Deciding a reserach advisor after a semester.

    For those who have interest in Math Biol Lab, please come to our Journal club seminar, where we study a paper together per week. https://www.ibs.re.kr/bimag/events/category/seminar/journal-club/ For those who have interest in, please let me know.

    Undergradatue Students

    Each year, one or two undergraduate students have worked in Math Bio lab. Taking at least one of following courses is recommended before asking the independent study or URP study:

    Method of Applied Mathematics, Introduction for Mathematical Biology, ODE & Nonlinear Dynamics or any of my class.

    You can find the application form in https://www.ibs.re.kr/bimag/job-application/internship/

    Previous URP students in KAIST Math Biol Lab:

    2022 Seho Park, Development of inference method for dynamic networks (2022 S URP Best Award/최우수상)

    2021 Seokmin Ha, Analysis of Plant Circadian Clock Considering Post Translational Regulation (2021 W URP Best Award/최우수상)

    2021 Eun Han Goo, Development of a mathematical model for predicting accurate hepatic clearance of drug

    2019 Minyoo Kim, The Total Quasi-Steady-State Approximation for a Competitive System (2019 KSIAM Poster award)

    2017 Oleg Magnes, Revealing new components of circadian clock using machine learning

    2016 Seokjoo Choe, The effect of non-specific binding of transcription factor on circadian rhythms