Papers

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

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

Submitted / Preprint

1. 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
2. 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
   Last update: September 8, 2023
3. Eui Min Jeong†, Jae Kyoung Kim*, Robust Ultrasensitive Transcriptional Switch in Noisy Cellular Environments
   bioRxiv10.1101/2023.08.15.553401v1Last update: September 3, 2023
4. 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
   Last update: August 28, 2023
5. Pan Li*, Jae Kyoung Kim*, Central and peripheral clocks synergistically enhance circadian robustness, flexibility and performance of cardiac pacemaking
   bioRxiv10.1101/2023.08.07.552251Last update: August 9, 2023
6. Hyeontae Jo, Hyukpyo Hong, and Jae Kyoung Kim*, Density Physics-Informed Neural Network reveals sources of cell heterogeneity in signal transduction
   Last update: August 3, 2023
7. 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
   Last update: July 31, 2023
8. 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
   Last update: July 31, 2023
9. Yun Min Song†, Sean Campbell†, LieJune Shiau, Jae Kyoung Kim*, William Ott*, Noisy delay denoises biochemical oscillators (in revision)
   bioRxiv10.1101/2023.05.17.541178Last update: August 28, 2023
10. 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  
    Last update: May 11, 2023
11. Yuji Hirono, Hyukpyo Hong, Jae Kyoung Kim, Robust Perfect Adaptation of Reaction Fluxes Ensured by Network Topology
    arXiv2302.01270Last update: March 13, 2023
12. Hyeontae Jo†, Hyukpyo Hong†, Hyung Ju Hwang, Won Chang, Jae Kyoung Kim*, Density Physics-Informed Neural Network identifies sources of cell heterogeneity in signal transduction under antibiotic stress
    Last update: March 13, 2023
13. 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, bioRxiv  
    bioRxiv10.1101/2022.11.27.518074v1Last update: December 6, 2022
14. Seunggyu Lee, Yongho Choi, Jaemin Shin, Curvature-based interface restoration algorithm using phase-field equations, submitted  
    Last update: September 20, 2022
15. 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
16. Seunggyu Lee, Sungha Yoon, Junseok Kim, A linear convex splitting scheme for the Cahn-Hilliard equation with a high-order polynomial free energy, submitted
    Last update: September 20, 2022
17. Seunggyu Lee, Unconditionally strong energy stable scheme for Cahn–Hilliard equation with second-order temporal accuracy, submitted
    Last update: September 20, 2022
18. 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
    Last update: June 23, 2022
19. 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

Published

2023

20. Yun Min Song^Ⴕ, Su Jung Choi^Ⴕ, 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: July 31, 2023
21. 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
22. 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
    Last update: April 17, 2023
23. 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
    Last update: May 31, 2023
24. 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: July 31, 2023
25. 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  
    Last update: January 31, 2023
26. Seok Joo Chae, Dae Wook Kim, Seunggyu Lee, and Jae Kyoung Kim, Spatially coordinated collective phosphorylation filters spatiotemporal noises for precise circadian timekeeping, iScience
    Last update: April 17, 2023
27. 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
    Last update: January 31, 2023
28. 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: July 5, 2023
29. 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: July 5, 2023
30. Bryan S. Hernandez and Eduardo R. Mendoza, Weakly reversible CF-decompositions of chemical kinetic systems, accepted for Journal of Mathematical Chemistry, 2023
    Last update: March 13, 2023
31. 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
    Last update: January 31, 2023
32. Bryan S. Hernandez and Eduardo R. Mendoza, Positive equilibria of power-law kinetics on networks with independent linkage classes, Journal of Mathematical Chemistry, 2023
    Last update: March 13, 2023

2022

33. 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
    Last update: November 30, 2022
34. 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
    Last update: September 20, 2022
35. 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
    Last update: September 20, 2022
36. 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
    Last update: September 20, 2022
37. 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
    Last update: June 12, 2022
38. 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
    Last update: June 12, 2022
39. 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
    Last update: August 16, 2022
40. 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
    Last update: July 4, 2022
41. 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
    Last update: June 8, 2022
42. 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
    Last update: June 20, 2022
43. Aurelio A. de los Reyes V and Yangjin Kim, Optimal regulation of tumor-associated neutrophils in cancer progression, Royal Society Open Science, 2022
    Last update: February 4, 2022
44. Eui Min Jeong, Yun Min Song, and Jae Kyoung Kim, Combined multiple transcriptional repression mechanisms generate ultrasensitivity and oscillations, Interface Focus, 2022
    Last update: April 20, 2022
45. 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
    Last update: February 4, 2022
46. 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.
    Last update: August 23, 2022
47. 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
    Last update: March 20, 2022
48. 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
    Last update: February 23, 2022

2021

49. Jaewoo Park, Won Chang, Boseung Choi, An Interaction Neyman-Scott Point Process Model for Coronavirus Disease-19, Spatial Statistics, 2021
    Last update: December 24, 2021
50. Seunggyu Lee, Non-iterative compact operator splitting scheme for Allen–Cahn equation, Computational & Applied Mathematics, 2021
    Last update: January 3, 2022
51. 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
    Last update: January 3, 2022
52. Jae Kyoung Kim (2021). Tick, Tock, Circadian Clocks. In Pavel Kraikivski (Ed.) Case Studies in Systems Biology (pp. 48-64). Springer International Publishing. doi: 10.1007/978-3-030-67742-8
    Last update: October 9, 2021
53. 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 US, doi: 10.1007/978-1-0716-1767-0_3
    Last update: December 13, 2021
54. 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
    bioRxiv10.1101/2021.08.16.456485v1Last update: September 11, 2021
55. 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
    Last update: September 11, 2021
56. 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
    bioRxiv10.1101/2021.04.08.438974v1Last update: October 20, 2021
57. 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
    bioRxiv10.1101/2021.03.23.436681v1Last update: September 11, 2021
58. Jonathan Tyler, Daniel Forger, and Jae Kyoung Kim, Inferring causality in biological oscillators, Bioinformatics, 2021
    bioRxiv10.1101/2021.03.18.435997v1Last update: September 11, 2021
59. 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
    bioRxiv10.1101/2021.03.15.435366v1Last update: September 15, 2021