{"id":3736,"date":"2021-02-08T15:58:34","date_gmt":"2021-02-08T06:58:34","guid":{"rendered":"https:\/\/bimag.dimag.kr\/?page_id=3736"},"modified":"2025-08-27T13:36:36","modified_gmt":"2025-08-27T04:36:36","slug":"collaborators","status":"publish","type":"page","link":"https:\/\/www.ibs.re.kr\/bimag\/collaborators\/","title":{"rendered":"Collaborators"},"content":{"rendered":"\n

Mathematics<\/strong><\/h2>\n\n\n\n
\"\"

Kre\u0161imir Josi\u0107<\/strong><\/h3>Department of Mathematics, U of Houston, USA<\/em><\/span>

Collaborative works<\/em>
Hierarchical Bayesian models of transcriptional and translational regulation processes with delays, Bioinformatics (2021)<\/em>
Long-range temporal coordination of gene expression in spatially extended synthetic microbial consortia, Nature Chem Biol <\/em>(2019)
Bayesian inference of distributed time delay in transcriptional and translational regulation, Bioinformatics <\/em>(2019)
The relationship between deterministic and stochastic quasi-steady-state approximation, BMC Syst Biol <\/em>(2015)
Emergent genetic oscillations in a synthetic microbial consortium, Science<\/em> (2015)
The Validity of Quasi-Steady-State Approximations in Discrete Stochastic Simulations, Biophy J <\/em>(2014)
Molecular mechanisms that regulate the coupled period of the mammalian circadian clock, Biophy J<\/em> (2014)
Curriculum-based Reinforcement Learning for Adaptive Hyperparameter Tuning in Hamiltonian Monte Carlo<\/p><\/div><\/div>\n\n\n\n

\"\"

John Tyson<\/strong><\/h3>Department of Biological Sciences, Virginia Tech, USA<\/em><\/span>

Collaborative works<\/em>
Time-keeping and decision-making in living cells: Part II, Interface Focus<\/em> (2022)
Time-keeping and decision-making in living cells: Part I, Interface Focus<\/em> (2022)
Misuse of the Michaelis-Menten rate law for protein-interaction networks and its remedy, PLoS Comput Bio<\/em>l (2020)
A systems-driven experimental approach reveals the complex regulatory distribution of p53 by circadian factors, PNAS<\/em> (2016)

<\/p><\/div><\/div>\n\n\n\n

\"\"


Sookkyung Lim<\/strong><\/h3>Mathematical Sciences, University of Cincinnati, USA<\/em><\/span>

Collaborative works<\/em>
Modeling reveals a key mechanism for light-dependent phase shifts of Neurospora<\/em> circadian rhythms, Biophy J <\/em>(2018)<\/p><\/div><\/div>\n\n\n\n

\"\"

Grzegorz Rempala<\/strong><\/h3>Division of Biostatistics and Mathematical Biosciences Institute, The Ohio State University, USA<\/em><\/span>

Collaborative works<\/em>
Reduction for stochastic reaction network with multi-scale conservation, SIAM Multiscale Model Simul<\/em> (2017)
Beyond Michaelis-Menten: Accurate and efficient estimation of enzyme kinetic parameters, Scientific Report <\/em>(2017)<\/p><\/div><\/div>\n\n\n\n

\"\"

Eduardo D. Sontag<\/strong><\/h3>Departments of Electrical and Computer Engineering and of Bioengineering, Northeastern University, USA<\/em><\/span>

Collaborative works<\/em>
Derivation of stationary distributions of biochemical reaction networks via structure transformation, Communications Biology<\/em> (2021)
Reduction of Multiscale Stochastic Biochemical Reaction Networks using Exact Moment Derivation, PLoS Comput Biol <\/em>(2017)<\/p><\/div><\/div>\n\n\n\n

\"\"

Victoria Booth<\/strong><\/h3>Department of Mathematics, U of Michigan<\/em>, USA<\/span>

Collaborative works<\/em>
Personalized sleep-wake patterns aligned with circadian rhythm relieve daytime sleepiness, iScience<\/em> (2021)<\/p><\/div><\/div>\n\n\n\n

\"\"

Daniel Forger<\/strong><\/h3>Department of Mathematics, U of Michigan<\/em>, USA<\/span>

Collaborative works<\/em>
<\/meta>Inferring causality in biological oscillators, Bioinformatics<\/em> (2021)
A Period2 Phosphoswitch Regulates and Compensates Circadian Period,\u00a0Molecular Cell<\/em> (2015)
Modeling and Validating Chronic Pharmacological Manipulation of Circadian Rhythms, CPT:PSP<\/em> (2013)
A Mechanism for Robust Circadian Timekeeping via stoichiometric balance, Mol Syst Biol <\/em> (2012)
On the Existence and Uniqueness of Biological Clock Models Matching Experimental Data,\u00a0SIAM J APPL MATH<\/em> (2012)<\/p><\/div><\/div>\n\n\n\n

\"\"

Jonathan Tyler<\/strong><\/h3>Department of Mathematics, U of Michigan<\/em>, USA<\/span>

Collaborative works<\/em>
Inferring causality in biological oscillators, Bioinformatics<\/em> (2021)<\/p><\/div><\/div>\n\n\n\n

\"\"

Jinsu Kim<\/strong><\/h3>Department of Mathematics, POSTECH, Republic of Korea<\/em><\/span>

Collaborative works<\/em>
Computational translation framework identifies biochemical reaction networks with special topologies and their long-term dynamics, SIAM J APPL MATH <\/em>(2023)
Derivation of stationary distributions of biochemical reaction networks via structure transformation <\/meta>Communications Biology<\/em> (2021) <\/p><\/div><\/div>\n\n\n\n

\"\"

Eder Zavala<\/strong><\/h3>Institute of Metabolism and Systems Research MRC Skills Development Fellow, University of Birmingham<\/em><\/span>

Collaborative works<\/em>
Wearable technology and systems modeling for personalized chronotherapy, Curr. Opin. Syst. Biol.<\/em> (2020)
<\/p><\/div><\/div>\n\n\n\n

\"\"

Yangjin Kim<\/strong><\/h3>Department of Mathematics, Konkuk University, Republic of Korea<\/em><\/span>

<\/em>Optimal regulation of tumor-associated neutrophils in cancer progression,\u00a0Royal Society Open Science<\/em> (2022)\u00a0<\/a><\/p><\/div><\/div>\n\n\n\n

\"\"

Eduardo R. Mendoza<\/strong><\/h3>Department of Mathematics and Statistics, De La Salle University, Republic of the Philippines<\/em><\/span>

<\/em>Management and control of schistosomiasis in Agusan del Sur, Philippines: A modeling study\u00a0(submitted)
Positive equilibria of power-law kinetics on networks with independent linkage classes\u00a0(submitted)
Weakly reversible CF-decompositions of chemical kinetic systems, accepted for\u00a0Journal of Mathematical Chemistry<\/em>\u00a0<\/a><\/a><\/a><\/p><\/div><\/div>\n\n\n\n

\"\"

Oleg A. Igoshin<\/strong><\/h3>Department of Bioengineering, Rice University, USA<\/em><\/span>

Beyond microtubules: The cellular environment at the
endoplasmic reticulum attracts proteins to the nucleus, enabling nuclear transport, iScience<\/em> (2024)<\/a><\/p><\/div><\/div>\n\n\n\n

\"\"

Won Chang<\/strong><\/strong><\/h3>Department of Statistics, Seoul National University<\/em><\/span>

Imputing Missing Sleep Data from Wearables with Neural Networks in Real-World Settings<\/a><\/p><\/div><\/div>\n\n\n\n

\"\"

Minseok Seo<\/strong><\/strong><\/h3>Department of Computer Convergence Software, Korea University, Sejong<\/em><\/span>

scLENS: data-driven signal detection for unbiased scRNA-seq data analysis, Nature Communications<\/em> (2024)
scICE:\u00a0Enhancing\u00a0Clustering\u00a0Reliability\u00a0and\u00a0Efficiency\u00a0of\u00a0scRNA-seq\u00a0Data\u00a0with\u00a0Multi-Cluster\u00a0Label\u00a0Consistency\u00a0Evaluation,\u00a0Nature\u00a0Communications<\/em>\u00a0(2025)<\/a><\/p><\/div><\/div>\n\n\n\n

\"\"

Jong-Eun Park<\/strong><\/strong><\/h3>Graduate\u00a0School\u00a0of\u00a0Medical\u00a0Science\u00a0and\u00a0Engineering,\u00a0KAIST<\/em><\/span>

scLENS: data-driven signal detection for unbiased scRNA-seq data analysis, Nature Communications<\/em> (2024)
scICE:\u00a0Enhancing\u00a0Clustering\u00a0Reliability\u00a0and\u00a0Efficiency\u00a0of\u00a0scRNA-seq\u00a0Data\u00a0with\u00a0Multi-Cluster\u00a0Label\u00a0Consistency\u00a0Evaluation,\u00a0Nature\u00a0Communications<\/em>\u00a0(2025)<\/a><\/p><\/div><\/div>\n\n\n\n

\"\"

Jong Kyoung Kim<\/strong><\/strong><\/h3>Department\u00a0of\u00a0Life\u00a0Sciences,\u00a0Pohang\u00a0University\u00a0of\u00a0Science\u00a0and\u00a0Technology\u00a0(POSTECH)<\/em><\/span>

scICE:\u00a0Enhancing\u00a0Clustering\u00a0Reliability\u00a0and\u00a0Efficiency\u00a0of\u00a0scRNA-seq\u00a0Data\u00a0with\u00a0Multi-Cluster\u00a0Label\u00a0Consistency\u00a0Evaluation,\u00a0Nature\u00a0Communications<\/em>\u00a0(2025)<\/a><\/p><\/div><\/div>\n\n\n\n

\"\"

Jeongbin\u00a0Park<\/strong><\/strong><\/h3>School\u00a0of\u00a0Biomedical\u00a0Convergence\u00a0Engineering,\u00a0Pusan\u00a0National\u00a0University<\/em><\/span>

stLENS\u00a0identifies\u00a0unbiased\u00a0complex\u00a0spatial\u00a0patterns\u00a0in\u00a0spatial\u00a0transcriptomics\u00a0data<\/a><\/p><\/div><\/div>\n\n\n\n

\"\"

William Ott<\/strong><\/strong><\/h3>Department\u00a0of\u00a0Mathematics,\u00a0University\u00a0of\u00a0Houston<\/em><\/span>

Noisy\u00a0delay\u00a0denoises\u00a0biochemical\u00a0oscillators, Phys. Rev. Lett. <\/em>(2024)<\/a><\/p><\/div><\/div>\n\n\n\n

Biology<\/strong><\/h2>\n\n\n\n
\"\"

Choogon Lee<\/strong><\/h3>Dept. of Biomedical Sciences & Neuroscience, Florida State U., USA<\/span>

Collaborative works<\/em>
Wake-sleep cycles are severely disrupted by diseases affecting cytoplasmic homeostasis, PNAS<\/em> (2020)
Stability of the circadian system requires a robust degradation of PERIOD, Current Biol<\/em> (2017)
A tunable artificial circadian clock in clock-defective mice, Nature Commun <\/em>(2015)<\/p><\/div><\/div>\n\n\n\n

\"\"

David Virshup<\/strong><\/h3>Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School<\/em>, Singapore<\/span>

Collaborative works<\/em>
Mutation of a PER2 phosphodegron perturbs the circadian phosphoswitch, PNAS <\/em>(2020)
CK1 protein kinases prime the PER2 circadian phosphoswitch, PNAS<\/em> (2018)
A Period2 Phosphoswitch Regulates and Temperature Compensates Circadian Period, Molecular Cell<\/em> (2015)<\/p><\/div><\/div>\n\n\n\n

\"\"

Carla Finkielstein<\/strong><\/h3>Department of Biological Sciences, Virginia Tech<\/em>, USA<\/span>

Collaborative works<\/em>
A systems biology approach identifies hidden regulatory connections between the circadian and cell-cycle checkpoints, Front Physiol<\/em> (2020)
Distinct control of PERIOD2 degradation and circadian rhythms by the oncoprotein MDM2, Science Signal <\/em>(2018)
A systems- driven experimental approach reveals the complex regulatory distribution of p53 by circadian factors, PNAS<\/em> (2016)<\/p><\/div><\/div>\n\n\n\n

\"\"

Christian I. Hong<\/strong><\/h3>Pharmacology and Systems Physiology, U of Cincinnati, USA<\/em><\/span>

Collaborative works<\/em>
Modeling reveals a key mechanism for light-dependent phase shifts of Neurospora<\/em> circadian rhythms, Biophys. J. <\/em>(2018)<\/p><\/div><\/div>\n\n\n\n

\"\"

Matthew Bennett<\/strong><\/h3>Department of Biosciences, Rice University, USA<\/em><\/span>

Collaborative works<\/em>
Long-range temporal coordination of gene expression in spatially extended synthetic microbial consortia, Nature Chem Biol <\/em>(2019)
The relationship between deterministic and stochastic quasi-steady-state approximation, BMC Syst Biol<\/em> (2015)
Emergent genetic oscillations in a synthetic microbial consortium, Science <\/em>(2015)
The validity of quasi-steady-state approximations in discrete stochastic simulations, Biophys. J. <\/em>(2014)
Molecular mechanisms that regulate the coupled period of the mammalian circadian clock, Biophys. J. <\/em>(2014)<\/p><\/div><\/div>\n\n\n\n

\"\"

Dae-Jin Yun<\/strong><\/h3>Department of Biomedical Science & Engineering, Konkuk University<\/em>, Republic of Korea<\/em><\/span>

Collaborative works<\/em>
Rheostatic control of ABA signaling through HOS15-mediated OST1 degradation, Molecular Plant<\/em> (2019)<\/p><\/div><\/div>\n\n\n\n

\"\"

Woe Yeon Kim<\/strong><\/h3>Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University<\/em>, Republic of Korea<\/em><\/span>

Collaborative works<\/em>
Rheostatic control of ABA signaling through HOS15-mediated OST1 degradation, Molecular Plant<\/em> (2019)<\/p><\/div><\/div>\n\n\n\n

\"\"

Eun Young Kim<\/strong><\/h3>Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Republic of Korea<\/em><\/span>

Collaborative works<\/em>
Systematic modeling-driven experiments identify distinct molecular clockworks underlying hierarchically organized pacemaker neurons,\u00a0PNAS<\/em> (2022)\u00a0<\/a><\/p><\/div><\/div>\n\n\n\n

\"\"

Sara Aton<\/strong><\/h3>Department of Molecular, Cellular, and Developmental Biology, U of Michigan<\/em><\/span>

Collaborative works<\/em>
Possible “non-clock” functions of circadian clock genes – Potential roles in sleep, stress, and memory, <\/meta>Biochemical Pharmacology<\/em> (2021)<\/p><\/div><\/div>\n\n\n\n

\"\"

Matias D. Zurbriggen<\/strong><\/h3>Institute of Synthetic Biology and CEPLAS, Heinrich Heine University D\u00fcsseldorf, Germany<\/em><\/span>

Collaborative works<\/em>
Possible “non-clock” functions of circadian clock genes – Potential roles in sleep, stress, and memory, Biochemical Pharmacology (2021)<\/p><\/div><\/div>\n\n\n\n

\"\"

Robbert Havekes<\/strong><\/h3>Department of Biology, University of Pennsylvania, USA
Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, The Netherlands<\/em><\/span>

Collaborative works<\/em>
Possible “non-clock” functions of circadian clock genes – Potential roles in sleep, stress, and memory, Biochemical Pharmacology (2021)<\/p><\/div><\/div>\n\n\n\n

\"\"

Yoshitaka Fukada<\/strong><\/h3>Department of Biophysics and Biochemistry (UG), Department of Biological Sciences (GR), Graduate School of Science, University of Tokyo, Japan<\/em><\/span>

<\/meta><\/em>Rhythmic transcription of Bmal1 stabilizes the circadian timekeeping system in mammals (submitted)
Mutation of a PER2 phosphodegron perturbs the circadian phosphoswitch, PNAS <\/em><\/em>(2020)<\/p><\/div><\/div>\n\n\n\n

\"\"

Sooyeon Suh<\/strong><\/h3>Department of Psychology, Sungshin Women’s University, Republic of Korea<\/em><\/span>

<\/meta><\/em>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 Med. (2022)<\/p><\/div><\/div>\n\n\n\n

\"\"

Mathias Foo<\/strong><\/h3>School of Engineering, University of Warwick, Coventry University, United Kingdom<\/em><\/span>

<\/em>\u00a0Modeling of Plant Circadian Clock for CharacterizingHypocotyl Growth under Different Light QualityConditions,\u00a0in silico Plants<\/em> (2022)<\/p><\/div><\/div>\n\n\n\n

Medicine<\/strong><\/h2>\n\n\n\n
\"\"

Eun Yeon Joo<\/strong><\/h3>Department of Neurology, Neuroscience Center, Samsung Medical Center, Republic of Korea<\/em><\/span>

Collaborative works<\/em>
Personalized sleep-wake patterns aligned with circadian rhythm relieve daytime sleepiness, iScience<\/em> (2021)
A real-time, personalized sleep intervention using mathematical modelling and wearable devices,\u00a0Sleep<\/em> (2023)<\/p><\/div><\/div>\n\n\n\n

\"\"

Su Jung Choi<\/strong><\/h3>Graduate School of Clinical Nursing Science, Sungkyunkwan University, Republic of Korea<\/em><\/span>

Collaborative works<\/em>
Personalized sleep-wake patterns aligned with circadian rhythm relieve daytime sleepiness<\/meta>, iScience<\/em> (2021)
A real-time, personalized sleep intervention using mathematical modelling and wearable devices,\u00a0Sleep<\/em> (2023)<\/p><\/div><\/div>\n\n\n\n

\"\"

Jeong Whun Kim<\/strong><\/h3>Department of Otorhinolaryngology, Seoul National University Bundang Hospital<\/em>, Republic of Korea<\/span>

Collaborative works<\/em>
Combined unsupervised-supervised machine learning for phenotyping complex diseases with its application to obstructive sleep apnea, Scientific Reports <\/em>(2021)<\/p><\/div><\/div>\n\n\n\n

\"\"

Young Il Koh<\/strong><\/h3>Department of Internal Medicine, Seoul National University Hospital<\/em>, Republic of Korea<\/span>

Collaborative works<\/em>
Chemotherapy delivery time affects anti-lymphoma treatment outcome in a sex-dependent manner (submitted)<\/p><\/div><\/div>\n\n\n\n

\"\"

Jee Hyun Kim<\/strong><\/h3>Department of Neurology<\/em>, Ewha Womans University Medical Center<\/em>, Republic of Korea<\/span>

Collaborative works<\/em>
Imputing Missing Sleep Data from Wearables with Neural Networks in Real-World Settings, Sleep<\/em> (2023)<\/p><\/div><\/div>\n\n\n\n

\"\"

Seockhoon Chung<\/strong><\/h3>Department of Psychiatry, Asan Medical Center, University of Ulsan College of Medicine, Republic of Korea<\/em><\/span>

Collaborative works<\/em>
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 Med. (2022)
Data-driven Shortened Insomnia Severity Index: A Machine Learning Approach, Sleep Breath<\/em> (2024)
Cancer-related Dysfunctional Beliefs and Attitude about Sleep-6 (C-DBAS-6): a practical and accurate shortened version using XGBoost and SymScore, Sleep and Biological Rhythms<\/em> (2025)
Machine learning approached a 14-item shortened version of the Positive and Negative Sleep Appraisal Measure (PANSAM-14)
<\/p><\/div><\/div>\n\n\n\n

\"\"

Heon-Jeong Lee<\/strong><\/h3>Department of Psychiatry, Korea University College of Medicine, Republic of Korea
Chronobiology Institute, Korea University, Republic of Korea<\/span>

Collaborative works<\/em>
Highly Accurate Prediction of Mood Episodes in Mood Disorder Patients Using Sleep and Circadian Rhythm Features from Wearables (Under Review in Nature Mental Health)
Causal Dynamics of Sleep, Circadian Rhythm, and Mood in Major Depression and Bipolar Disorder Patients: Insights from Longitudinal Wearable Device Data, (Under Review in eBioMedicine)<\/p><\/div><\/div>\n\n\n\n

\"\"

Suein Choi<\/strong><\/h3>College of Medicine, The Catholic University of Korea<\/span>

Collaborative works<\/em>
Beyond Michaelis- Menten: A Modified Enzyme Kinetics Equation Improves Drug Metabolism Prediction in Bottom-Up PBPK Modeling
<\/p><\/div><\/div>\n\n\n\n

\"\"

Jeong-Hyun Kim<\/strong><\/h3>Seoul National University Hospital<\/span>

Collaborative works<\/em>
Identifying risk factors of PTSD among a nationwide cohort of firefighters using a machine learning algorithm
<\/p><\/div><\/div>\n\n\n\n

\"\"

In\u00eas M.A. Ribeiro<\/strong><\/h3>Institute of Medical Psychology, LMU Munich<\/span>

Collaborative works<\/em>
Friend or foe: how insects see their peers
<\/p><\/div><\/div>\n\n\n\n

\"\"

Bei Bei<\/strong><\/h3>Turner Institute for Brain and Mental Health, Monash University, Australia<\/span>

Collaborative works<\/em>
Application of mathematical model of sleep to Australian teenager cohort
<\/p><\/div><\/div>\n\n\n\n

\"\"

Ki-Young Jeong<\/strong><\/h3>Department of Neurology, Seoul National University Hospital<\/span>

Collaborative works<\/em>
Delayed Circadian Rhythm in Restless Legs Syndrome and its Association with Symptom Severity: An Actigraphy-Based Study
<\/p><\/div><\/div>\n\n\n\n

Pharmacology<\/strong><\/h2>\n\n\n\n
\"\"

Cheng Chang<\/strong><\/h3>Clinical Pharmacology, Pfizer Global Product Development, Pfizer Inc, USA<\/em><\/span>

Collaborative works<\/em>
Systems approach reveals photosensitivity and PER2 level as determinants of clock modulator efficacy, Mol Syst Biol <\/em>(2019)
Modeling and Validating Chronic Pharmacological Manipulation of Circadian Rhythms, CPT:PSP<\/em> (2013)<\/p><\/div><\/div>\n\n\n\n

\"\"

Francois Gaudreault<\/strong><\/h3>Clinical Pharmacology and Pharmacometrics, Biogen Inc, USA
<\/span>

Collaborative works<\/em>
Systems approach reveals photosensitivity and PER2 level as determinants of clock modulator efficacy, Mol Syst Biol <\/em>(2019)
<\/p><\/div><\/div>\n\n\n\n

\"\"

Hwi\u2010yeol Yun<\/strong><\/h3>College of Pharmacy, Chungnam National University, Republic of Korea<\/span>

Collaborative works<\/em>
Beyond the Michaelis-Menten: Prediction of in vivo clearance for drugs with low KM, Clin Transl Sci<\/em> (2020)
Beyond the Michaelis-Menten: Accurate Prediction of Drug Interactions\u00a0 through Cytochrome P450 Induction,\u00a0CPT<\/em> (2023)
Optimizing enzyme inhibition analysis: precise estimation with a single inhibitor concentration, Nature Communications<\/em> (2025)<\/a><\/p><\/div><\/div>\n\n\n\n

\"\"

Sang Kyum Kim<\/strong><\/h3>College of Pharmacy, Chungnam National University, Republic of Korea<\/em><\/span>

Collaborative works<\/em>
Beyond the Michaelis-Menten: Prediction of in vivo clearance for drugs with low KM, Clin Transl Sci<\/em> (2020)
Beyond the Michaelis-Menten: Accurate Prediction of Drug Interactions\u00a0 through Cytochrome P450 Induction,\u00a0CPT<\/em> (2023)
Optimizing enzyme inhibition analysis: precise estimation with a single inhibitor concentration, Nature Communications<\/em> (2025)<\/p><\/div><\/div>\n\n\n\n

\"\"

Jungwoo Chae<\/strong><\/strong><\/h3>College of Pharmacy, Chungnam National University, Republic of Korea<\/em><\/span>

Collaborative works<\/em>
Beyond the Michaelis-Menten: Accurate Prediction of Drug Interactions\u00a0 through Cytochrome P450 Induction,\u00a0CPT<\/em> (2023)<\/p><\/div><\/div>\n\n\n\n

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