Papers

Please visit the link at Google Scholar for publications until 2020 [Click Here]

†: co-1st authors, *: co-corresponding authors

Submitted / Preprint

1. Junghyun Lee†, Yun Min Song†, Hwi-yeol Yun, Suein Choi*, Jae Kyoung Kim, Beyond Michaelis- Menten: A Modified Enzyme Kinetics Equation Improves Drug Metabolism Prediction in Bottom-Up PBPK Modeling
   Last update: June 30, 2025
2. Eui Min Jeong†, Chang Yoon Chung, Jae Kyoung Kim*, How cells tame noise while maintaining ultrasensitive transcriptional responses
   bioRxiv10.1101/2025.06.12.659288Last update: June 16, 2025
3. Le Na Lau†, Jun-Ho Cho, Seok Joo Chae, Ung-Gyu Kim, Jae Kyoung Kim*, In-Sung Luke Yeo*, Immune-Metabolic Regulation of Early Osseointegration: Insights from Untargeted RNA Sequencing
   Last update: May 29, 2025
4. Sunyoung Lee†, Seok Joo Chae†, In-Hwan Jang, Ji Hyun Kim, Jae Kyoung Kim*, and Tae-Don Kim*, Stress-induced self recognition by Natural Killer cells does not require HLA Class I, Submitted
   Last update: May 14, 2025
5. Dongju Lim †, Seokhwan Moon †, Yun Min Song, Jinyeong Kim, Kangsan Kim, Byung-Kwan Cho, Jinsu Kim*, Jae Kyoung Kim*, Toward Single-Cell Control: Noise-Robust Perfect Adaptation in Biomolecular Systems, Submitted
   Last update: May 14, 2025
6. Myna Lim†, Sewon Kim†, Saebom Jeon, Eui Min Jeong*, Jae Kyoung Kim*, Seockhoon Chung*, Machine learning approached a 14-item shortened version of the Positive and Negative Sleep Appraisal Measure (PANSAM-14)
   Last update: April 2, 2025
7. Hwang Gyuyoung †, Jo Hyeontae*,  Kim Jae Kyoung*, Data-Driven Inference of Coupling Functions in Oscillatory Systems via Physics-Informed Neural Networks
   Last update: April 2, 2025
8. Brenda Lyn Gavina†, Taeyong Lee , Olive Cawiding, Sunhwa Choi , Sungwook Choi, Soyoung Kim*, Jae Kyoung Kim*, Optimizing oral contraceptive timing: Morning intake reduces doses and enhances efficacy
   Last update: March 24, 2025
9. Sanghyeok Park†, Dae Wook Kim†, Hyun Kim, Joonho Byun, Sangjoon Chong, Sang Woo Song, Young-Hoon Kim, Young Hyun Cho, Seok Ho Hong, Chang-Ki Hong, Jeong Hoon Kim, Seungjoo Lee*, Jae Kyoung Kim*, Ji Min Lee, Effect of tumor resection time-of-day on overall survival of patients with glioblastoma multiforme and a circadian-regulated tumor microenvironment: an observational cohort study
   Last update: March 17, 2025
10. Seok Joo Chae†, Johanna Inhyang Kim†, Hyeontae Jo, Yun Min Song, Saebom Jeon, Sun-Young Moon, Ji-Hye Lee, Sohee Oh, Seockhoon Chung, Jae Kyoung Kim*, Jeong-Hyun Kim*, Identifying risk factors of PTSD among a nationwide cohort of firefighters using a machine learning algorithm
    Last update: March 17, 2025
11. Juhyeon Kim†, Dongju Lim†, Jee Hyun Kim, Jae Kyoung Kim*, Initial Condition Decision to Ensure Reliable Circadian Phase Estimation with Shorter-Term Wearable
    Last update: March 13, 2025
12. Gi-Chan Bae, Josselin Garnier, Seung-Yeal Ha, and Gyuyoung Hwang*, Semiclassical limit of the Schödinger-Lohe model in random media and collective dynamic
    Last update: March 10, 2025
13. Olive R. Cawiding†, Heewon Bae†, Jee Hyun Kim, Eun Yeon Joo, Jae Kyoung Kim*, Simplified and accurate Approach to Sleep Disorder Prediction Using Body Composition Metrics: A Development and Validation Study, Submitted to Journal Of Medical Internet Research
    Last update: April 24, 2025
14. Dongju Lim†, Kyeong Tae Ko†, Hyojung Lee, Boseung Choi, Won Chang, Sunhwa Choi, Jae Kyoung Kim*, A History-Dependent Approach for Accurate Initial Condition Estimation in Epidemic Models
    Last update: December 22, 2024
15. Young Rong Bang†, Saebom Jeon†, Junseok Ahn, Oli Ahmed, Soyoung Yoo*; Seockhoon Chung*, Validation of the Korean version of the Anxiety and Preoccupation about Sleep Questionnaire and comparisons with other sleep-related cognition scales among the general population, submitted.
    Last update: December 17, 2024
16. Saebom Jeon†, Eui Min Jeong†, Young Rong Bang,  Junseok Ahn, Soyoung Yoo,  Jae Kyoung Kim*, Seockhoon Chung*, Validating the Korean version of the Sleep-Related Behaviours Questionnaire (SRBQ) among the general population, submitted.
    Last update: December 23, 2024
17. Eui Min Jeong†, Hwan Kim, Saebom Jeon*, Jae Kyoung Kim*, Seockhoon Chung*, The Dysfunctional Self-Focus Attributes Scale-7 (DSAS-7): A Machine Learning-Based Development of a Shortened Version of the DSAS.
    Last update: December 15, 2024
18. Mark Boyett†*, Pan Li, Yirong Xiang, Henggui Zhang, Jae Kyoung Kim and Alicia D’Souza*, Circadian determinants of heart rhythm and arrhythmias, submitted to PNA.
    Last update: November 20, 2024
19. Pan Li†, Sangbo Lee, Kwang-Yeon Choi, Jonathan E. Rubin*, and Jae Kyoung Kim*, Cardiogenic and Chronobiological Mechanisms in Seizure-Induced Sinus Arrhythmias
    Last update: July 18, 2024
20. Hyeontae Jo*, Kresimir Josic*, Jae Kyoung Kim*, Neural Network-Based Parameter Estimation for Non-Autonomous Differential Equations with Discontinuous Signals,
    Last update: July 15, 2024
21. Yun Min Song†, Saebom Jeon†, Ayeong Cho, Seockhoon Chung, Yeonsoon Ahn, Jae Kyoung Kim*, Sooyeon Suh*, Predictors of Sleep Quality Trajectories and Alertness in Shift Workers Undergoing Cognitive-Behavioral Therapy for insomnia.
    Last update: June 10, 2024
22. Gyeong-Im Shin†, Joon-Yung Cha†, Dongju Lim, Aliya Alimzhan, Gyeongik Ahn, Song Yi Jeong, Myung Geun Ji, Sang Yeol Lee, Min Gab Kim, Jeongsik Kim, Jae Kyoung Kim, Woe-Yeon Kim*, GIGANTEA gates TOR-mediated meristem activation to control plant diurnal root growth (Under Review in Science)
    Last update: December 25, 2023
23. 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
    Last update: September 10, 2023
24. Haobo Hua, Pu Han, Huan Han, Seunggyu Lee, Junseok Kim, Curvature-dependent area preserving immersed boundary method for binary immiscible fluids, submitted
    Last update: September 20, 2022
25. Jayrah Bena E. Rinon, Renier G. Mendoza, Aurelio A. de los Reyes V, Vicente Y. Belizario Jr., and Victoria May P. Mendoza, Management and control of schistosomiasis in Agusan del Sur, Philippines: A modeling study
    Last update: February 3, 2022

Accepted

26. Hyeontae Jo†, Sung Woong Cho†, Hyung Ju Hwang*, Estimating the Distribution of Parameters in Differential Equations with Repeated Cross-Sectional Data, PLoS Computational Biology
    Last update: April 21, 2025

Published

2025

27. Aneta Koseska†, Jae Kyoung Kim*, Outside-in regulation of cellular clocks, Nature Physics
    doi10.1038/s41567-025-02882-0Last update: May 7, 2025
28. Junhyeok Byeon, Seung-Yeal Ha, Gyuyoung Hwang, Dongnam Ko*, and Jaeyoung Yoon, Consensus, error estimates and applications of first- and second-order consensus-based optimization algorithms, Mathematical Models and Methods in Applied Sciences
    doi10.1142/S0218202525400032Last update: March 5, 2025
29. Yun Min SongႵ, Su Jung ChoiႵ, Dongju Lim, Reinatt Hansel Wijaya, Hyeong Jun Jang, Hea Ree Park, Eun Yeon Joo*, Jae Kyoung Kim*, A Digital, Real-Time, History-Based Sleep-Management Tool to Enhance Alertness,  Sleep journal
    doi10.1093/sleep/zsaf160Last update: June 10, 2025
30. Olive R. Cawiding†, Hyeontae Jo†, Saebom Jeon, Faeyza Rishad Ardi, Jae Kyoung Kim*, Seockhoon Chung*, 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 Rythms
    doi10.1007/s41105-025-00594-9Last update: June 9, 2025
31. Yun Min Song†, Kangmin Lee, Jae Kyoung Kim*, Validity of the total QSSA in stochastic biochemical reaction networks, jKSIAM
    doi10.12941/jksiam.2025.29.001Last update: April 21, 2025
32. Hyun Kim†,  Issac Park, Jong-Eun Park, Jong Kyoung Kim, Minseok Seo, Jae Kyoung Kim*, scICE: Enhancing Clustering Reliability and Efficiency of Single-cell RNA Sequencing Data with Multi-Cluster Label Consistency Evaluation, Nature Communications.
    doi10.1038/s41467-024-47884-3Last update: July 10, 2025
33. Eui Min Jeong† and Jae Kyoung Kim*, Less is More: Machine Learning-Based Shortened Sleep Questionnaires for Efficient Clinical Practice, Sleep Medicine Research (SMR).
    doi10.17241/smr.2024.02523Last update: February 21, 2025
34. Hyeong Jun Jang†, Yun Min Song†, Jang Su Jeon, Hwi-yeol Yun, Sang Kyum Kim*, Jae Kyoung Kim*, Optimizing enzyme inhibition analysis: precise estimation with a single inhibitor concentration, Nature Communications
    doi10.1038/s41467-025-60468-zLast update: June 9, 2025
35. Seok Joo Chae†, Seolah Shin†, Kangmin Lee, Seunggyu Lee*, Jae Kyoung Kim*, From Homogeneity to Heterogeneity: Refining stochastic simulations of gene regulation, Computational and structural biotechnology journal.
    doi10.1016/j.csbj.2025.01.004Last update: April 21, 2025
36. Olive R. Cawiding†, Sieun Lee†, Hyeontae Jo, Sungmoon Kim, Sooyeon Suh, Eun Yeon Joo, Seockhoon Chung, Jae Kyoung Kim*,  SymScore: Machine Learning Accuracy Meets Transparency in a Symbolic Regression-Based Clinical Score Generator, Computers in Biology and Medicine
    doi10.1016/j.compbiomed.2024.109589Last update: February 21, 2025
37. Dongju Lim†, Su Jung Choi, Yun Min Song, Hea Ree Park, Eun Yeon Joo*, Jae Kyoung Kim*, Enhanced Circadian Phase Tracking: A 5 Hour DLMO Sampling Protocol Using Wearable Data, Journal of Biological Rhythms.
    doi10.1177/07487304251317577Last update: April 17, 2025
38. Olive R. Cawiding†, Saebom Jeon, Donnabel Tubera-Panes, Aurelio A. de los Reyes V, Jae Kyoung Kim*, Disentangling climate’s dual role in dengue dynamics: a multi-region causal analysis study, Science Advances
    doi10.1126/sciadv.adq1901Last update: February 21, 2025
39. Hyukpyo Hong†, Seokhwan Moon†, Yuji Hirono*, Jae Kyoung Kim*, Topological Criterion for Robust Perfect Adaptation of Reaction Fluxes in Biological Networks, i Science
    doi10.1016/j.isci.2025.112394 arXiv2302.01270Last update: April 15, 2025

2024

40. Gyeonggyu Lee, Soobin Kwak, Yongho Choi, Seunggyu Lee, Seungyoon Kang, Junseok Kim, An operator splitting method for the Cahn–Hilliard equation on nonuniform grids, Computers & Mathematics with Applications, 2024
    doi10.1016/j.camwa.2024.05.021Last update: April 17, 2025
41. Seung-Yeal Ha†, Gyuyoung Hwang*, Dohyun Kim, On the semiclassical limit of the Schrödinger-Lohe model and concentration estimates, Journal of Mathematical Physics. 2024.
    doi10.1063/5.0194571Last update: April 21, 2025
42. Sunyoung Lee†, Seok Joo Chae†, In-Hwan Jang†, Se-Chan Oh, Seok-Min Kim, Soo Yun Lee, Ji Hyun Kim, Jesang Ko, Hang Joon Kim, Ik-Chan Song, Jae Kyoung Kim*, Tae-Don Kim*, B7H6 is the Predominant Activating Ligand Driving Natural Killer Cell-Mediated Killing in Patients with Liquid Tumours: Evidence from Clinical, In Silico, In Vitro, and In Vivo Studies, eBiomedicine, 2024
    doi10.1016/j.ebiom.2024.105459Last update: April 21, 2025
43. Dongju Lim†, Jaegwon Jeong†, Yun Min Song, Chul-Hyun Cho, Ji Won Yeom, Taek Lee, Jung-Been Lee, Heon-Jeong Lee*, Jae Kyoung Kim*, Accurately predicting mood episodes in mood disorder patients using wearable sleep and circadian rhythm features, NPJ Dig Med.
    doi10.1038/s41746-024-01333-zLast update: April 21, 2025
44. G.-C. Bae†*, S.-Y. Ha, G. Hwang and T. Ruggeri, On the comparison between phenomenological and kinetic theories of gas mixtures with applications to flocking, Physica D (2024)
    doi10.1016/j.physd.2024.134321Last update: April 21, 2025
45. Yun Min Song†, Jae Kyoung Kim*, What’s driving rhythmic gene expression: Sleep or the clock ?,  Cell Systems, 2024 .
    doi10.1016/j.cels.2024.06.006Last update: April 17, 2025
46. Dongnam Ko†, Hyeong-Ohk Bae, Seung-Yeal Ha, and Gyuyoung Hwang*, On the Interactions of Flocking Particles with the Stokes Flow in an Infinite Channel. Journal of Mathematical Fluid Mechanics, 2024
    doi10.1007/s00021-024-00876-1Last update: June 10, 2024
47. Rochelle H. Holm†, Grzegorz A. Rempala†, Boseung Choi†, J. Michael Brick, Alok R. Amraotkar, Rachel J.Keith, EricC.Rouchka, Julia H. Chariker, Kenneth E. Palmer, Ted Smith*, Aruni Bhatnagar*, Dynamic SARS-CoV-2 surveillance model combining seroprevalence and wastewater concentrations for postvaccine disease burden estimates, Communications Medicine, 2024
    doi10.1038/s43856-024-00494-yLast update: April 21, 2025
48. Hyukpyo Hong†, Eunjin Eom, Hyojung Lee, Sunhwa Choi, Boseung Choi, Jae Kyoung Kim*, Overcoming bias in estimating epidemiological parameters with realistic history-dependent disease spread dynamics, Nature Communications, 2024.
    doi10.1038/s41467-024-53095-7Last update: April 21, 2025
49. Jong Hyuk Byun†, Hye Seon Jeon*, Hwi-yeol Yun*, and Jae Kyoung Kim*, Validity Conditions of Approximations for a Target-Mediated Drug Disposition Model: A Novel First-Order Approximation and Its Comparison to Other Approximations, PLoS Comput. Biol.
    doi10.1371/journal.pcbi.1012066Last update: January 8, 2025
50. Seolah Shin†, Seok Joo Chae†, Seunggyu Lee*, and Jae Kyoung Kim*, Beyond homogeneity: Assessing the validity of the Michaelis–Menten rate law in spatially heterogeneous Environments, Plos Computational Biology, 2024.    
    doi10.1371/journal.pcbi.1012205Last update: June 10, 2024
51. Yuta Otobe†, Eui Min Jeong†, Shunsuke Ito†, Atsu Aiba, Yoshitaka Fukada*, Jae Kyoung Kim* and Hikari Yoshitane*, Phosphorylation of DNA-binding domains of CLOCK–BMAL1 complex for PER-dependent inhibition in circadian clock of mammalian cells, PNAS, 2024 .
    doi10.1073/pnas.2316858121Last update: June 10, 2024
52. 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, Sleep Medecine. 2024 .  
    doi10.1016/j.sleep.2024.04.027Last update: April 21, 2025
53. 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. Sleep Breath (2024)
    doi10.1007/s11325-024-03037-wLast update: April 30, 2024
54. Eui Min Jeong†, Jae Kyoung Kim*, Robust Ultrasensitive Transcriptional Switch in Noisy Cellular Environments, npj Systems Biology and Applications, 2024
    doi10.1038/s41540-024-00356-2Last update: April 29, 2024
55. Yun Min Song†, Jaegwon Jeong†, Aurelio V de los Reyes†, Dongju Lim, 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, eBioMedicine, 2024
    doi10.1016/j.ebiom.2024.105094Last update: April 5, 2024
56. Pan Li*, Jae Kyoung Kim*, Circadian regulation of sinoatrial nodal cell pacemaking function: dissecting the roles of autonomic control, body temperature, and local circadian rhythmicity, PLoS Comput Biol, 2024
    doi10.1371/journal.pcbi.1011907Last update: February 29, 2024
57. Seok Joo 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, iScience, 2024
    doi10.1016/j.isci.2024.109235Last update: March 18, 2024
58. 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, Nature Communications, 2024.
    doi10.1038/s41467-024-47884-3Last update: October 2, 2024
59. Yun Min Song†, Sean Campbell†, LieJune Shiau, Jae Kyoung Kim*, William Ott*, Noisy delay denoises biochemical oscillators, Physical Review Letters, 2024
    doi10.1103/PhysRevLett.132.078402Last update: February 16, 2024
60. 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, 2024  
    doi10.1093/sleep/zsad266Last update: February 3, 2024

2023

61. Mi-Sun Hur, Seunggyu Lee, Han-Sung Jung, Richard A. Schneider, Crossing fibers may underlie the dynamic pulling forces of muscles that attach to cartilage at the tip of the nose, Scientific Reports, 2023
    doi10.1038/s41598-023-45781-1Last update: December 16, 2024
62. Hee Young Kang†, Soo Yun Lee†, Hyun Min Kim†, Su Ui Lee, Hyunseung Lee, Mi Young Cho, Se-Chan Oh, Seok-Min Kim, Hye Sun Park, Eun Hee Han, Seong-Eun Kim, Hyori Kim, Suk Ran Yoon, Junsang Doh, Junho Chung, Kwan Soo Hong*, Inpyo Choi*, Tae-Don Kim*, A modifiable universal cotinine-chimeric antigen system of NK cells with multiple targets, Frontiers in Immunol, 2023
    doi10.3389/fimmu.2022.1089369Last update: December 11, 2023
63. Seok-Min Kim†, Se-Chan Oh, Sun-Young Lee, Ling-Zu Kong, Jong-Hee Lee, Tae-Don Kim*, FTO negatively regulates NK cell killing efficacy, EMBO Rep, 2023
    doi10.15252/embr.202255681Last update: December 11, 2023
64. Dahong Kim†, Seona Jo, Dongjin Lee, Seok-Min Kim, Ji Min Seok, Seon Ju Yeo, Jun Hee Lee, Jae Jong Lee, Kangwon Lee, Tae-Don Kim*, Su A Park*, NK cells encapsulated in micro/macropore-forming hydrogels via 3D bioprinting for tumor immunotherapy, Biomaterials Research, 2023
    doi10.1186/s40824-023-00403-9Last update: December 11, 2023
65. Ling-Zu Kong†,  Seok-Min Kim, Chunli Wang, Soo Yun Lee, Se-Chan Oh, Sunyoung Lee, Seona Jo, Tae-Don Kim*, Understanding nucleic acid sensing and its therapeutic applications, Experimental and Molecular Medicine, 2023
    doi10.1038/s12276-023-01118-6Last update: December 11, 2023
66. Hyeontae Jo†, Hyukpyo Hong†, Hyung Ju Hwang, Won Chang, Jae Kyoung Kim*, Density physics-informed neural network reveals sources of cell heterogeneity in signal transduction, Patterns, 2023
    doi10.1016/j.patter.2023.100899Last update: January 1, 2024
67. Yun Min Song†, Su Jung Choi†, 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
    doi10.1093/sleep/zsad179Last update: December 26, 2023
68. 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, J Med Internet Res, 2023
    doi10.2196/46520Last update: September 27, 2023
69. 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 Computational Biology, 2023
    doi10.1371/journal.pcbi.1011039Last update: December 17, 2023
70. 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
    doi10.1137/22M150469XLast update: December 17, 2023
71. 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
    doi10.1038/s41467-023-39983-4Last update: December 17, 2023
72. 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  
    doi10.1093/bioinformatics/btad670Last update: November 7, 2023
73. Se-Chan Oh, Seong-Eun Kim, In Hwan Jang, Seok-Min Kim, Soo Yun Lee, Sun-Young Lee, In-Sun Chu, Suk Ran Yoon, Haiyoung Jung, Inpyo Choi, Junsang Doh* and Tae-Don Kim*, Nogo receptor 1 is an NK cell inhibitory receptor that destabilizes immunological synapse by regulating actin dynamics, Nature Immunology, 2023  
    doi10.1038/s41590-022-01394-wLast update: December 17, 2023
74. 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
    doi10.1016/j.isci.2023.106554Last update: December 17, 2023
75. Seunggyu Lee, Yongho Choi, Jaemin Shin, Curvature-based interface restoration algorithm using phase-field equations, PLoS One, 2023  
    doi10.1371/journal.pone.0295527Last update: December 16, 2024
76. Seunggyu Lee, Sungha Yoon, Junseok Kim, A linear convex splitting scheme for the Cahn-Hilliard equation with a high-order polynomial free energy, International Journal for Numerical Methods in Engineering, 2023
    doi10.1002/nme.7288Last update: December 16, 2024
77. Seunggyu Lee, Unconditionally strong energy stable scheme for Cahn–Hilliard equation with second-order temporal accuracy, Mathematical Methods in the Applied Sciences, 2023
    doi10.1002/mma.8917Last update: December 16, 2024
78. 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
    doi10.1002/cpt.2824Last update: December 26, 2023
79. Loreniel E. Añonuevo, Zython Paul T. Lachica, Deza A. Amistas, Jayve Iay E. Lato, Hanna Lyka C. Bontilao, Jolly Mae G. Catalan, Rachel Joy F. Pasion, Annabelle P. Yumang, Alexis Erich S. Almocera, Jayrold P. Arcede, May Anne E. Mata, and Aurelio A. de los Reyes V, Transmission dynamics, baseline epidemiological parameter estimates of Coronavirus disease 2019 pre-vaccination: Davao City, Philippines, PLoS ONE, 2023
    doi10.1371/journal.pone.0283068Last update: December 17, 2023
80. Rey Audie S. Escosio, Olive R. Cawiding, Bryan S. Hernandez, Renier G. Mendoza, Victoria May P. Mendoza, Rhudaina Z. Mohammad, Carlene P.C. Pilar-Arceo, Pamela Kim N. Salonga, Fatima Lois E. Suarez, Polly W. Sy, Thomas Herald M. Vergara, and Aurelio A. de los Reyes V, A model-based strategy on COVID-19 vaccine roll-out in the Philippines, Journal of Theoretical Biology, 2023
    doi10.1016/j.jtbi.2023.111596Last update: December 26, 2023
81. Brenda Lyn A. Gavina, Aurelio A. de los Reyes V, Mette S. Olufsen, Suzanne Lenhart, and Johnny T. Ottesen, Toward an optimal contraception dosing strategy, PLoS Computational Biology, 2023
    doi10.1371/journal.pcbi.1010073Last update: December 26, 2023
82. Bryan S. Hernandez and Eduardo R. Mendoza, Weakly reversible CF-decompositions of chemical kinetic systems, Journal of Mathematical Chemistry, 2023
    doi10.1007/s10910-022-01332-zLast update: December 17, 2023
83. Dae Wook Kim†, Ja Min Byun†, Jeong-Ok Lee, Jae Kyoung Kim*, Youngil Koh*, Chemotherapy delivery time affects anti-lymphoma treatment outcome in a sex-dependent manner, JCI insight, 2023
    doi10.1172/jci.insight.164767Last update: December 17, 2023
84. Bryan S. Hernandez and Eduardo R. Mendoza, Positive equilibria of power-law kinetics on networks with independent linkage classes, Journal of Mathematical Chemistry, 2023
    doi10.1007/s10910-022-01432-wLast update: December 17, 2023

2022

85. Seungjun Lee, Boseung Choi, Sung Jae Kim, Jinnam Kim, Dayun Kang, and Jiyoung Lee, Relationship between freshwater harmful algal blooms and neurodegenerative disease incidence rates in South Korea, Environ Health, 2022
    doi10.1186/s12940-022-00935-yLast update: December 18, 2023
86. Seunggyu Lee, Sungha Yoon, Chaeyoung Lee, Sangkwon Kim, Hyundong Kim, Junxiang Yang, Soobin Kwak, Youngjin Hwang, Junseok Kim*, Effective time step for the Allen-Cahn equation with a high-order polynomial free energy, International Journal for Numerical Methods in Engineering, 2022
    doi10.1002/nme.7053Last update: December 17, 2023
87. Ted Smith†, Rochelle H. Holm†, Rachel J. Keith, Alok R. Amraotkar, Chance R. Alvarado, Krzysztof Banecki, Boseung Choi, Ian C. Santisteban, Adrienne M. Bushau-Sprinkle, Kathleen T. Kitterman, Joshua Fuqua, Krystal T. Hamorsky, Kenneth E. Palmer, J. Michael Brick, Grzegorz A. Rempala, Aruni Bhatnagar*, Quantifying the relationship between sub-population wastewater samples and community-wide SARS-CoV-2 seroprevalence, Science of the Total Environment, 2022
    doi10.1016/j.scitotenv.2022.158567Last update: December 17, 2023
88. Seunggyu Lee, Sungha Yoon, and Junseok Kim*, Effective time step analysis of convex splitting for the Swift-Hohenberg equation, Journal of Computational and Applied Mathematics, 2022
    doi10.1016/j.cam.2022.114713Last update: December 17, 2023
89. John J. Tyson, Attila Csikasz-Nagy, Didier Gonze, Jae Kyoung Kim, Silvia Santos, and Jana Wolf, Time-keeping and decision-making in living cells: Part II, Interface Focus, 2022
    doi10.1098/rsfs.2022.0024Last update: December 17, 2023
90. John J. Tyson, Attila Csikasz-Nagy, Didier Gonze, Jae Kyoung Kim, Silvia Santos, and Jana Wolf, Time-keeping and decision-making in living cells: Part I, Interface Focus, 2022
    doi10.1098/rsfs.2022.0011Last update: December 17, 2023
91. Hyo-jeong Ryu†, Won-ho Kang†, Taeheon Kim, Jae Kyoung Kim, Kwang-Hee Shin, Jung-woo Chae*, and Hwi-yeol Yun*, A compatibility evaluation between the physiologically based pharmacokinetic (PBPK) model and the compartmental PK model using the lumping method with real cases , Frontiers in Pharmacology, section Translational Pharmacology, 2022
    doi10.3389/fphar.2022.964049Last update: December 17, 2023
92. Hyukpyo Hong†, Ji Yun Noh†, Hyojung Lee, Sunhwa Choi, Boseung Choi, Jae Kyoung Kim*, Eui-Cheol Shin*, Modeling incorporating the severity-reducing long-term immunity: higher viral transmission paradoxically reduces severe COVID-19 during endemic transition, Immune Network, 2022
    doi10.4110/in.2022.22.e23Last update: December 17, 2023
93. Hyun Kim, Cheolhong Min, Byeongha Jeong, and Kyoung J. Lee, Deciphering clock cell network morphology within the biological master clock, suprachiasmatic nucleus: From the perspective of circadian wave dynamics, PLoS Computational Biology, 2022
    doi10.1371/journal.pcbi.1010213Last update: December 18, 2023
94. 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
    doi10.1016/j.sleep.2022.06.005Last update: December 17, 2023
95. Aurelio A. de los Reyes V and Yangjin Kim, Optimal regulation of tumor-associated neutrophils in cancer progression, Royal Society Open Science, 2022
    doi10.1098/rsos.210705Last update: December 17, 2023
96. Eui Min Jeong, Yun Min Song, and Jae Kyoung Kim, Combined multiple transcriptional repression mechanisms generate ultrasensitivity and oscillations, Interface Focus, 2022
    doi10.1098/rsfs.2021.0084Last update: December 18, 2023
97. Miao Lin Paya, Dae Wook Kim, David E. Somers, Jae Kyoung Kim*, Mathias Foo*, Modeling of Plant Circadian Clock for CharacterizingHypocotyl Growth under Different Light QualityConditions, in silico Plants, 2022
    doi10.1093/insilicoplants/diac001Last update: December 17, 2023
98. Yasuko O. Abe, Hikari Yoshitane, Dae Wook Kim, Michinori Koebis, Atsu Aiba, Jae Kyoung Kim*, and Yoshitaka Fukada*, Rhythmic transcription of Bmal1 stabilizes the circadian timekeeping system in mammals, Nature Communications, 2022
    doi10.1038/s41467-022-32326-9Last update: December 17, 2023
99. 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
    doi10.1126/sciadv.abl4598Last update: December 17, 2023
100. 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, Proceedings of the National Academy of Science, 2022
     doi10.1073/pnas.2113403119Last update: December 17, 2023

2021

101. Jaewoo Park, Won Chang, Boseung Choi, An Interaction Neyman-Scott Point Process Model for Coronavirus Disease-19, Spatial Statistics, 2021
     doi10.1016/j.spasta.2021.100561Last update: December 17, 2023
102. Seunggyu Lee, Non-iterative compact operator splitting scheme for Allen–Cahn equation, Computational & Applied Mathematics, 2021
     doi10.1007/s40314-021-01648-7Last update: December 17, 2023
103. Mi-Sun Hur, Seunggyu Lee, Tong Mook Kang, and Chang-Seok Oh, The three muscle layers in the pyloric sphincter and their possible function during antropyloroduodenal motility, Scientific Reports, 2021
     doi10.1038/s41598-021-99463-xLast update: December 17, 2023
104. Jae Kyoung Kim. Tick, Tock, Circadian Clocks. In Pavel Kraikivski (Ed.) Case Studies in Systems Biology (pp. 48-64). Springer International Publishing, 2021
     doi10.1007/978-3-030-67742-8Last update: December 17, 2023
105. Hyukpyo Hong, Boseung Choi, Jae Kyoung Kim, 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 US, 2021
     doi10.1007/978-1-0716-1767-0_3Last update: December 17, 2023
106. 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
     doi10.1093/bioinformatics/btab618Last update: December 17, 2023
107. Youri G. Bolsius, Matias D. Zurbriggen, Jae Kyoung Kim, Martien J.Kas, Peter Meerlo, Sara J.Aton, and Robbert Havekes, The role of clock genes in sleep, stress and memory, Biochemical Pharmacology, 2021
     doi10.1016/j.bcp.2021.114493Last update: December 17, 2023
108. Yun Min Song†, Hyukpyo Hong†, and Jae Kyoung Kim,  Universally valid reduction of multiscale stochastic biochemical systems using simple non-elementary propensities, PLoS Computational Biology, 2021
     doi10.1371/journal.pcbi.1008952Last update: December 17, 2023
109. 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, Communications Biology, 2021
     doi10.1038/s42003-021-02117-xLast update: December 17, 2023
110. Jonathan Tyler, Daniel Forger, and Jae Kyoung Kim, Inferring causality in biological oscillators, Bioinformatics, 2021
     doi10.1093/bioinformatics/btab623Last update: December 17, 2023
111. 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
     doi10.1016/j.isci.2021.103129Last update: December 17, 2023