Papers

    †: (co-)1st author, *: (co-)corresponding author. One can enter the website by clicking the underlined title of a paper.
  1. 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, 2022
  2. 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
  3. Yun Min Song†, Hyukpyo Hong† and Jae Kyoung Kim*, Universally valid reduction of multiscale stochastic biochemical systems with simple non-elementary propensities, PLoS Computational Biology, 2021
  4. Mark Jayson Cortez, Hyukpyo Hong, Boseung Choi†, Jae KyoungKim†, and Krešimir Josić†, Hierarchical Bayesian models for inference in biochemical reactions with delays, Bioinformatics, 2021
  5. 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
  6. 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.

Book chapters

  1. Hyukpyo Hong, Boseung Choi, and Jae Kyoung Kim, Beyond the Michaelis-Menten: Bayesian inference for enzyme kinetic analysis, Quentin Vanhaelen (Ed.), Computational Methods for Estimating the Kinetics Parameters of Biological Systems, vol 2385. Humana, New York, NY.

Invited talks

    Abbreviations
    SMB: Society for Mathematical Biology, KSMB: Korean SMB, SIAM: Society for Industrial and Applied Mathematics, KSIAM: Korean SIAM, KMS: Korean Mathematical Society

  • August 27, 2021: KSMB Annual Meeting, Special session, Online, Korea
  • June 16, 2021: SMB Annual Meeting, Minisymposium, Online
  • May 27, 2021: SIAM Conference on Dynamical Systems, Minisymposium, Online
  • May 13, 2021: Seminar on the Mathematics of Reaction Networks [link], Online, the recorded video is available in YouTube [link]
  • October 24, 2020: KMS Annual Meeting , Minisymposium, Online

Contirubed talks and Posters

  • September 28, 2021: Non-equilibrium collective phenomena workshop, Poster, Gyeongju, Korea
  • June 26, 2021: KSIAM Spring Conference, Contributed talk, Gangneung, Korea
  • November 13, 2020: KSIAM Annual Conference, Poster, Online
  • August 20, 2020: SMB Annual meeting, Contributed talk, Online
  • July 23, 2019: SMB Annual meeting, Poster, Montreal, Canada
  • July 8, 2019: Chemical Reaction Networks Workshop [link], Short talk, Torino, Italy
  • May 18, 2019: Spring meeting of Korean Society for Industrial and Applied Mathematics, Contributed talk, Seoul, Korea
  • May 11, 2019: A3 Workshop on Mathematical Biology, Contributed talk, Beijing, China

Journal club presentations

    the date of presentation: the presented article
  • March 25, 2022: Gupta and Khammash, Universal structural requirments for maximal robust perfect adaptation in biomolecular networks, bioRxiv, 2022
  • December 31, 2021: Kim and MacEachern, The Generalized Multiset Sampler, Journal of Computational and Graphical Statistics, 2015
  • October 22, 2021: Finkenstadt et al., Filtering and inference for stochastic oscillators with distributed delays, Bioinformatics, 2018
  • September 9, 2021: Glass et al., Nonlinear delay differential equations and their application to modeling biological network motifs, Nature Communications, 2021
  • July 30, 2021: Duso et al., Stochastic reaction networks in dynamic compartment populations, PNAS, 2020
  • June 11, 2021: Soloveichick et al., DNA as a universal substrate for chemical kinetics, PNAS, 2010
  • April 9, 2021: Chem et al., Highly accurate fluorogenic DNA sequencing with information theory-based error correction, Nature Biotechnology, 2017
  • February 4, 2021: Gupta and Khammash, Frequenc spectra and the color of cellular noise, bioRxiv, 2020
  • July 19, 2019: Shinar and Feinberg, Structural sources of robustness in biochemical reaction networks, Science, 2010
  • June 7, 2019: Marguet et al., Inheritance and variability of kinetic gene expression parameters in microbial cells: modeling and inference from lineage tree data, Bioinformatics, 2019
  • March 22, 2019: Horn, Necessay and sufficient conditions for complex balancing in chmical kinetics, Archive for Rational Mechanics and Analysis, 1972
  • February, 8, 2019: Anderson et al., Product-form stationary distributions for deficiency zero chemical reaction networks, Bulletin of Mathematical Biology, 2010
  • December 21, 2018: Ghusinga et al., Exact lower and upper bounds on stationary moments in stochastic biochemical systems, Physical Biology, 2017
  • November 8, 2018: Müller et al., A red/far-red light-responsive bi-stable toggle switch to control gene expression in mammalian cells, Nucleic Acids Research, 2013
  • November 2, 2018: Baaske et al., Dual-controlled optogenetic system for the rapid down-regulation of protein levels in mammalian cells, 2018, Scientific Reports, 2018
  • September 7, 2018: Kuznetsov and Rhea, Power considerations for the application of deterended fluctuation analysis in gait variability studies, PloS ONE, 2017
  • July 19, 2018: Hu et al., Reduction of scale invariance of activity fluctuations with aging and Alzheimer’s disease: Involvement of the circadian pacemaker, PNAS, 2009