Evolutionary Analysis of Human Immunodeficiency Virus Type 1 Therapies Based on Conditionally Replicating Vectors. - Ruian Ke; James O. Lloyd-Smith (PLoS Comput. Biol., 2012)

An Integrative Model of Ion Regulation in Yeast. - Ruian Ke; Piers J. Ingram; Ken Haynes (PLoS Comput. Biol., 2013)

Rational Design and Adaptive Management of Combination Therapies for Hepatitis C Virus Infection. - Ruian Ke; Claude Loverdo; Hangfei Qi; Ren Sun; James O. Lloyd-Smith (PLoS Comput. Biol., 2015)

Network analysis of virus-innate immune interaction within a host. - Yufan Huang; Michelle Dai; Zhihao Zhang; Ruian Ke (CISS, 2018)

Ensemble UNet++ for Locating the Exponential Growth Virus Samples. - Yahe Yu; Ruian Ke; Hien Tran (IntelliSys (3), 2021)

A deep learning approach to real-time HIV outbreak detection using genetic data. - Michael D. Kupperman; Thomas Leitner; Ruian Ke (PLoS Comput. Biol., 2022)

How robust are estimates of key parameters in standard viral dynamic models? - Carolin Zitzmann; Ruian Ke; Ruy M. Ribeiro; Alan S. Perelson (PLoS Comput. Biol., 2024)

Roadmap for using large language models (LLMs) to accelerate cross-disciplinary research with an example from computational biology. - Ruian Ke; Ruy M. Ribeiro (CoRR, 2025)