publications

2026

1. Integrating viral kinetics and population spread in a one health framework to explain variant-specific epidemic dynamics

   H. Lee, BN. Kim, and S. Lee

   One Health, 2026

   Abs DOI

   The COVID-19 pandemic underscored the importance of modeling frameworks that integrate biological mechanisms with heterogeneous social contact patterns to accurately characterize variant-specific transmission. Motivated by a One Health perspective that connects human infection biology, behavioral dynamics, and environmental transmission factors, we present a data-integrated and mechanistic approach designed to support proactive risk assessment and public-health preparedness. While classical compartmental models offer essential baseline insight, their simplifying assumptions limit the representation of time-varying infectiousness and realistic transmission heterogeneity. We introduce a multi-scale agent-based model that links empirically inferred SARS-CoV-2 viral kinetics to population-level spread through a mechanistic mapping from viral load to infection probability. Ct trajectories are estimated using hierarchical Bayesian inference and incorporated into a structured contact network, enabling coupling of within-host viral dynamics with social interaction patterns. This One Health-aligned modeling architecture supports rigorous data integration and biologically grounded estimation of variant-specific epidemic behavior. Our results demonstrate that differences in viral kinetics substantially reshape epidemic trajectories. Variants with rapid viral expansion and short infectious periods produce earlier and sharper peaks, whereas slower proliferation and prolonged clearance lead to delayed yet larger outbreaks. Incorporating time-varying infectiousness also generates heterogeneous secondary-case distributions and occasional high-impact transmission events without imposing ad-hoc superspreading parameters, highlighting biological drivers of overdispersion. By linking within-host viral dynamics to network-level transmission, this framework provides a scalable tool for variant surveillance, quantitative risk assessment, and timing-sensitive intervention planning. It can be extended to environmentally mediated pathogens, strengthening One Health-oriented data integration and epidemic estimation for future emerging threats.

2. COVID-19 transmission dynamics: age-specific patterns and super spreaders in South Korea

   Ganghyun Yoon, Hayoung Choi, Hyosun Lee, Arsen Abdulali, Gerardo Chowell, and Sunmi Lee

   BMC Public Health, 2026

   Abs DOI

   The global spread of COVID-19 has underscored the vital need for precise tracing of individuals involved in transmitting the virus through contact tracing. It is crucial to identify both those who spread the virus (infectors) and those who contract it (infectees) in order to gain a detailed understanding of the transmission dynamics.

3. Enhancing Influenza-Like Illness forecasting: An ensemble approach combining mathematical and deep learning models amidst the COVID-19 pandemic

   GH. Yoon, A. Bleichrodt, G. Chowell, and S. Lee

   Epidemics, 2026
4. State-level excess drug overdose mortality by race/ethnicity in the U.S., 2020–2023: A population-scaling analysis during the COVID-19 pandemic

   F. Alhassan, H. Karami, E. Cheng, S. Lee, ICH Fung, RM Bohler Jr., and G. Chowell

   Annals of Epidemiology, 2026
5. Enhancing time-varying reproduction number estimates for COVID-19 with behavior and surveillance data in South Korea, 2020–2022

   BN. Kim, S. Kim, H. Seo, G. Chowell, and S. Lee

   Archives of Public Health, 2026
6. Epidemic control under hidden transmission and network heterogeneity using individual-based modeling and reinforcement learning

   H. Lee, A. Abdulali, G. Chowell, and S. Lee

   Nonlinear Dynamics, 2026
7. Evaluating mobility restrictions through spatiotemporal effective reproduction number analysis in a multi-patch model with complex mobility data

   BN. Kim, M. Choi, H. Lee, and S. Lee

   Epidemics, 2026

2025

1. COVID-19 severity analysis for clinical decision support based on machine learning approach

   JE. Kim, T. Kim, G. Chowell, HS. Kim, and S. Lee

   Scientific Reports, 2025
2. A mobility-adjusted framework for regional R t estimation: enhancing spatial interpretation of transmission dynamics

   Y. Kim, J. Jo, BN. Kim, A. Abdulali, G. Chowell, and S. Lee

   BMC Infectious Diseases, 2025
3. Realistic mobility integration in agent-based model for targeted public health strategies

   Y. Kim, G. Jung, N. Geard, YB. Kim, and S. Lee

   Chaos, Solitons & Fractals, 2025
4. Multiscale Modeling of Hospital Length of Stay for Successive SARS-CoV-2 Variants: A Multi-State Forecasting Framework

   M. Choi, J. Kim, H. Kim, RJ. Tobin, and S. Lee

   Viruses, 2025
5. Impact of imported COVID-19 cases on South Korea’s response: variant transitions and regional patterns (2020–2023)

   H. Seo, M. Choi, G. Chowell, H. Lee, BN. Kim, and S. Lee

   BMC Infectious Diseases, 2025
6. A novel approach to estimating R t through infection networks: understanding regional transmission dynamics of COVID-19

   BN. Kim, J. Jo, C. Oh, S. Moon, A. Abdulali, and S. Lee

   Frontiers in Public Health, 2025
7. The depth of tumor hierarchy and its impact on hypertumor susceptibility

   J. Choi, S. Kim, S. Lee, and J. Park

   Scientific Reports, 2025
8. Mathematical modeling of age-specific intervention strategies for latent tuberculosis infection

   H. Lee, W. Abbas, S. Lee, S. Kim, S. Lee, and JW. Kwon

   Computers in Biology and Medicine, 2025

2024

1. Comprehensive risk management of infectious diseases

   J. Hwang, H. Lee, S. Lee, B. Jang, Y. Do, and YC. Lai

   Chaos, Solitons & Fractals, 2024
2. Optimal region-specific social distancing strategies in a complex multi-patch model through reinforcement learning

   H. Lee, A. Abdulalib, H. Park, and S. Lee

   Mathematics and Computers in Simulation, 2024
3. Short-and long-term neuropsychiatric outcomes in long COVID in South Korea and Japan

   S. Kim, H. Lee, J. Lee, SW. Lee, R. Kwon, MS. Kim, A. Koyanagi, Smith, and 4 more authors

   Nature human behaviour, 2024
4. Uncovering COVID-19 transmission tree: identifying traced and untraced infections in an infection network

   H. Lee, H. Choi, H. Lee, S. Lee, and C. Kim

   Frontiers in Public Health, 2024
5. The effectiveness of intervention measures on MERS-CoV transmission by using the contact networks reconstructed from link prediction data

   E. Kim, Y. Kim, H. Jin, Y. Lee, H. Lee, and S. Lee

   Frontiers in Public Health, 2024
6. Variability in the serial interval of COVID-19 in South Korea: a comprehensive analysis of age and regional influences

   H. Lee, G. Lee, T. Kim, S. Kim, H. Kim, and S. Lee

   Frontiers in Public Health, 2024

2023

1. Adaptive Social Distancing Strategies for Controlling Infection Inequality in Emerging Infectious Diseases

   A. Azizi, C. Kazanci, and S. Lee

   Letters in Biomathematics, 2023
2. Improved time-varying reproduction numbers using the generation interval for COVID-19

   T. Kim, H. Lee, S. Kim, C. Kim, H. Son, and S. Lee

   Frontiers in Public Health, 2023
3. Age-specific risk factors for the prediction of obesity using a machine learning approach

   S. Lee J. Jeon and C. Oh

   Frontiers in Public Health, 2023
4. Heterogeneity is a key factor describing the initial outbreak of COVID-19

   A. Abdulalib S. Kim and S. Lee

   Applied Mathematical Modelling, 2023

2022

1. Epidemiology and transmission dynamics of infectious diseases and control measures

   S. Ryu, J. Chun, S. Lee, D. Yoo, Y. kim, S. T. Ali, and B. Chun

   Viruses, 2022
2. Association between the relaxation of public health and social measures and transmission of the SARS-CoV-2 Omicron variant in South Korea

   S. Ryu, C. Han, D. Kim, T. K, Tsang, B. J Cowling, and S. Lee

   JAMA network open, 2022
3. Booster vaccination strategies for “living with COVID-19”

   J. Kim, S. Lee, and H. Kim

   Frontiers in public health, 2022
4. Optimal control of a discrete-time plant–herbivore/pest model with bistability in fluctuating environments

   S. Lee, C. Han, M. Kim, and Y. Kang

   Mathematical Biosciences and Engineering, 2022
5. Evolution of responses to COVID-19 and epidemiological characteristics in South Korea

   J. Jeon, C. Han, T. Kim, and S. Lee

   International journal of environmental research and public health, 2022
6. # ShoutYourAbortion on Instagram: exploring the visual representation of hashtag movement and the public’s responses

   Y. Kim and S. Lee

   SAGE Open, 2022
7. Estimation of serial interval and reproduction number to quantify the transmissibility of SARS-CoV-2 omicron variant in South Korea

   D. Kim, ST. Ali, S. Kim, J. Jo, JS. Lim, S. Lee, and S. Ryu

   Viruses, 2022

2021

1. Discovering spatiotemporal patterns of COVID-19 pandemic in South Korea

   S. Kim, M. Kim, S. Lee, and Y. Lee

   Scientific Reports, 2021
2. Analysis of superspreading potential from transmission clusters of COVID-19 in South Korea

   H. Lee, C. Han, J. Jung, and S. Lee

   International Journal of Environmental Research and Public Health, 2021
3. Risk assessment of importation and local transmission of COVID-19 in South Korea: statistical modeling approach

   H. Lee, Y. Kim, E. Kim, and S. Lee

   JMIR public health and surveillance, 2021
4. Personality of public health organizations’ Instagram accounts and according differences in photos at content and pixel levels

   Y. Kim and S. Lee

   International journal of environmental research and public health, 2021
5. Age-specific mathematical model for tuberculosis transmission dynamics in South Korea

   S. Lee, HY. Park, H. Ryu, and JW. Kwon

   Mathematics, 2021
6. Effectiveness of intervention strategies on MERS-CoV transmission dynamics in South Korea, 2015: Simulations on the network based on the real-world contact data

   Y. Kim, H. Ryu, and S. Lee

   International journal of environmental research and public health, 2021
7. The Seasonal Reproduction Number of p. vivax Malaria Dynamics in Korea

   Fernando A. M., Barber A. Vivas, and S. Lee

   Statistics, 2021
8. Assessing the effectiveness of isolation and contact-tracing interventions for early transmission dynamics of COVID-19 in South Korea

   H. Ryu, A. Abulali, and S. Lee

   Ieee Access, 2021

2020

1. Mathematical model of COVID-19 transmission dynamics in South Korea: the impacts of travel restrictions, social distancing, and early detection

   BN. Kim, E. Kim, S. Lee, and C. Oh

   Processes, 2020
2. Exploration of superspreading events in 2015 MERS-CoV outbreak in Korea by branching process models

   S. Choe, H. Kim, and S. Lee

   International journal of environmental research and public health, 2020
3. Resource allocation in two-patch epidemic model with state-dependent dispersal behaviors using optimal control

   S. Lee, O. Baek, and L. Melara

   Processes, 2020
4. Joint demosaicing and denoising based on interchannel nonlocal mean weighted moving least squares method

   Y. Kim, H. Ryu, S. Lee, and Y. Lee

   Sensors, 2020
5. A two-patch mathematical model for temperature-dependent dengue transmission dynamics

   Jung Eun Kim, Yongin Choi, James Slghee Kim, Sunmi Lee, and Chang Hyeong Lee

   Processes, 2020
6. Modeling influenza transmission dynamics with media coverage data of the 2009 H1N1 outbreak in Korea

   Y. Kim, A. Barber, and S. Lee

   Plos one, 2020
7. Exploration of the characteristics of emotion distribution in Korean TV series: common pattern and statistical complexity

   Y. Kim and S. Lee

   IEEE Access, 2020

2019

1. Integro-Differential Age-Structured System for Influenza Transmission Dynamics

   A. V. Barber and S. Lee

   Mathematics and Statistics, 2019
2. The role of vertical transmission in the control of dengue fever

   D. Murillo, A. Murillo, and S. Lee

   International journal of environmental research and public health, 2019

2018

1. Agent-based modeling for super-spreading events: A case study of MERS-CoV transmission dynamics in the Republic of Korea

   Y. Kim, H. Ryu, and S. Lee

   International journal of environmental research and public health, 2018
2. The role of immune response in optimal HIV treatment interventions

   H. D. Toro-Zapata, A. Caicedo-Casso, and S. Lee

   Processes, 2018
3. Potential effects of climate change on dengue transmission dynamics in Korea

   J. Kim, H. Lee, S. Lee, and C. Lee

   PLoS One, 2018
4. Dynamics of trapped solitary waves for the forced KdV equation

   S. Lee

   Symmetry, 2018
5. Assessing the effects of daily commuting in two-patch dengue dynamics: A case study of Cali, Colombia

   E. Barrios, S. Lee, and O. Vasilieva

   Journal of Theoretical Biology, 2018
6. Cost-Benefit analysis of malaria chemoprophylaxis and early diagnosis for Korean soldiers in malaria risk regions

   H. Kim, G. Kang, S. Lee, C. Yoon, and M. Kim

   Journal of Korean Medical Science, 2018

2017

1. Assessment of optimal strategies in a two-patch dengue transmission model with seasonality

   Jung Eun Kim, Hyojung Lee, Chang Hyeong Lee, and Sunmi Lee

   PloS one, 2017
2. Exploring optimal control strategies in seasonally varying flu-like epidemics

   S. Lee and G. Chowell

   Journal of theoretical biology, 2017

2016

1. Extended phase-matching properties of periodically poled potassium niobate crystals for mid-infrared polarization-entangled photon-pair generation

   K. Lee, S. Lee, and H. Shin

   Applied Optics, 2016
2. Explicit solutions of the fifth-order KdV type nonlinear evolution equation using the system technique

   H. Kim and S. Lee

   Results in physics, 2016
3. Fully localized solitary waves for the forced Kadomtsev–Petviashvili equation

   S. Whang and S. Lee

   Computers & Mathematics with Applications, 2016
4. Stochastic methods for epidemic models: An application to the 2009 H1N1 influenza outbreak in Korea

   H. Lee H, S. Lee, and C. Lee

   Applied Mathematics and Computation, 2016
5. The characteristics of Middle Eastern respiratory syndrome coronavirus transmission dynamics in South Korea

   Y. Kim, S. Lee, C. Chu, S. Choe, S. Hong, and Y. Shin

   Osong public health and research perspectives, 2016

2015

1. Modeling optimal treatment strategies in a heterogeneous mixing model

   S. Choe and S. Lee

   Theoretical Biology and Medical Modelling, 2015
2. Transmission characteristics of MERS and SARS in the healthcare setting: a comparative study

   G. Chowell, F. Abdirizak, S. Lee, J. Lee, E. Jung, H. Nishiura, and C. Viboud

   BMC medicine, 2015
3. The role of residence times in two-patch dengue transmission dynamics and optimal strategies

   S. Lee and C. Castillo-Chavez

   Journal of theoretical biology, 2015
4. Assessment of intensive vaccination and antiviral treatment in 2009 influenza pandemic in Korea

   C. Chu and S. Lee

   Osong public health and research perspectives, 2015
5. Trapped supercritical waves for the forced KdV equation with two bumps

   S. Lee and S. Whang

   Applied Mathematical Modelling, 2015

2014

1. Assessment of the Intensive Countermeasures in the 2009 Pandemic Influenza in Korea

   J. Choi, Y. Kim, S. Choe, and S. Lee

   Osong public health and research perspectives, 2014
2. Role of active and inactive cytotoxic immune response in human immunodeficiency virus dynamics.

   H.D. Toro-Zapata, A. Caicedo-Casso, B. Derdei, and S. Lee

   Osong Public Health and Research Perspectives, 2014
3. What does a mathematical model tell about the impact of reinfection in Korean tuberculosis infection?

   S. Kim, S. Choe, J. Kim, S. Nam, Y. Shin, and S. Lee

   Osong public health and research perspectives, 2014
4. A locally conservative Eulerian–Lagrangian finite difference method for the forced KdV equation

   S. Yi and S. Lee

   Applied Mathematics and Computation, 2014
5. Optimal control for a discrete time influenza model

   P. Gonzalez-Parra, M. Ceberio, S. Lee, and C. Castillo-Chavez

   In Advances in Computational Biology: Proceedings of the 2nd Colombian Congress on Computational Biology and Bioinformatics (CCBCOL), 2014

2013

1. Epidemiology Modeling

   C. Castillo-Chavez and S. Lee

   In Encyclopedia of Applied and Computational Mathematics, 2013

2012

1. Modeling optimal age-specific vaccination strategies against pandemic influenza

   S. Lee, M. Golinski, and G. Chowell

   Bulletin of mathematical biology, 2012

2011

1. A note on the use of influenza vaccination strategies when supply is limited

   S. Lee, R. Morales-Rosado, and C. Castillo-Chavez

   Math. Biosci. Eng, 2011
2. A note on the use of optimal control on a discrete time model of influenza dynamics

   P. Gonzalez-Parra, S. Lee, C. Castillo-Chavez, and L. Velazquez

   Math. Biosc. & Eng, 2011

2010

1. Optimal control intervention strategies in low-and high-risk problem drinking populations

   S. Lee, E. Jung, and C. Castillo-Chavez

   Socio-Economic Planning Sciences, 2010
2. Optimal control of influenza pandemics: the role of antiviral treatmen and isolation

   S. Lee, G. Chowell, and C. Castillo-Chavez

   J. Theor. Biol, 2010

2009

1. Simulations of valveless pumping in an open elastic tube

   W. Lee, E. Jung, and S. Lee

   SIAM Journal on Scientific Computing, 2009

2008

1. A two-chamber model of valveless pumping using the immersed boundary method

   S. Lee and E. Jung

   Applied mathematics and computation, 2008
2. Computational models of valveless pumping using the immersed boundary method

   E. Jung, S. Lim, W. Lee, and S. Lee

   Computer methods in applied mechanics and engineering, 2008
3. Absorbing boundary conditions for the stationary forced KdV equation

   S. Whang and S. Lee

   Applied mathematics and computation, 2008

2006

1. Exact artificial boundary conditions for continuum and discrete elasticity

   S. Lee, R. E. Caflisch, and YJ. Lee

   SIAM Journal on Applied Mathematics, 2006

2005

1. Artificial boundary conditions for linear elasticity and atomistic strain models(Ph. D thesis, UCLA)

   S. Lee

   2005