Papers

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

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

Submitted / Preprint

1. Loreniel E. Anonuevo, Zython Paul T. Lachica, Deza A. Amistas, Hanna Lyka C. Bontilao, 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 and baseline epidemiological parameter estimates of Coronavirus disease 2019 (COVID-19) pre-vaccination: Davao City, Philippines,
   Last update: June 23, 2022
2. 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
3. Computational translation framework identifies biochemical reaction networks with special topologies and their long-term dynamics, Hyukpyo Hong, Bryan S. Hernandez, Jinsu Kim, and Jae Kyoung Kim
   Last update: June 15, 2022
4. 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
   Last update: April 20, 2022
5. Hyo-jeong Ryu†, Won-ho Kang†, Taeheon Kim, Jae Kyoung Kim, Kwang-Hee Shin, Jung-woo Chae*, and Hwi-yeol Yun*, Evaluation of pharmacokinetic model compatibility with 20 real cases
   Last update: April 20, 2022
6. 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
7. 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
   Last update: January 14, 2022
8. Bryan S. Hernandez and Eduardo R. Mendoza, Positive equilibria of power-law kinetics on networks with independent linkage classes
   Last update: January 20, 2022

Accepted

9. Bryan S. Hernandez and Eduardo R. Mendoza, Weakly reversible CF-decompositions of chemical kinetic systems, accepted for Journal of Mathematical Chemistry
   Last update: March 1, 2022
10. 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, accepted for Immune Network
    Last update: May 4, 2022
11. 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, accepted for Nature Communications.
    Last update: May 1, 2022

Published

2022

12. 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
13. 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
14. 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
15. 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
16. 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
17. 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
18. 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
19. 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
20. 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

21. 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
22. Seunggyu Lee, Non-iterative compact operator splitting scheme for Allen–Cahn equation, Computational & Applied Mathematics, 2021
    Last update: January 3, 2022
23. 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
24. 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
25. 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
26. 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
27. 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
28. 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
29. 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
30. 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
31. 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