Ruby Kim

Research

Research Interests

I am an applied mathematician interested in leveraging mathematical modeling, dynamical systems theory, and data science to study biological systems. Some major directions in my research include dynamics-based data science and the analysis of complex biological phenomena. My work applies dynamical systems theory to analyze time-evolving data, revealing mechanisms, patterns, and behaviors that are not directly observable. In addition, I am interested in characterizing and investigating the nonlinear dynamics in complex systems. Through my research program, I aim to harness both the predictive strength of mechanistic models and the richness of large-scale datasets to uncover novel insights about real-world systems.

Publications

*: Corresponding author, ‡: Co-first author
  1. Tianyong Yao and Ruby Kim* (2025). Mathematical modeling of dopamine rhythms and timing of dopamine reuptake inhibitors. PLOS Computational Biology. Article.
  2. Ruby Kim*, Yu Fang, Minki Lee, Dae Wook Kim, Zhengxu Tang, Srijan Sen, and Daniel B Forger* (2025). Seasonal timing and interindividual differences in shiftwork adaptation. npj Digital Medicine. Article.
  3. Minki P Lee, Dae Wook Kim, Yu Fang, Ruby Kim, Amy SB Bohnert, Srijan Sen, and Daniel B Forger (2024). The real-world association between digital markers of circadian disruption and mental health risks. NPJ Digital Medicine. Article.
  4. Janet Best, Ruby Kim, Michael Reed, and H Frederik Nijhout (2024). A mathematical model of melatonin synthesis and interactions with the circadian clock. Mathematical Biosciences. Article.
  5. Lihong Zhao‡, Ruby Kim‡, Lucy S Oremland, Mukti Chowkwale, Lisette G de Pillis, and Heather Z Brooks (2024). A Survey of Mathematical Modeling of Hormonal Contraception and the Menstrual Cycle. Mathematical Modeling for Women's Health: Collaborative Workshop for Women in Mathematical Biology. Article.
  6. Ruby Kim, H Frederik Nijhout, and Michael C Reed (2023). Mathematical insights into the role of dopamine signaling in circadian entrainment. Mathematical Biosciences. Article.
  7. Ruby Kim* and Thomas P Witelski (2022). Uncovering the dynamics of a circadian-dopamine model influenced by the light--dark cycle. Mathematical Biosciences. Article.
  8. Ruby Kim and Michael C Reed (2021). A mathematical model of circadian rhythms and dopamine. Theoretical Biology and Medical Modelling. Article.
  9. Ruby Kim, H Frederik Nijhout, and Michael C Reed (2021). One-carbon metabolism during the menstrual cycle and pregnancy. PLOS Computational Biology. Article.
  10. Ruby Kim, Timothy Woods II, and Ami Radunskaya (2018). Mathematical modeling of tumor immune interactions: A closer look at the role of a PD-L1 inhibitor in cancer immunotherapy. Spora: A Journal of Biomathematics. Article.

Awards & Honors