Towards Real Time Epidemiology: Data Assimilation, Modeling and Anomaly Detection of Health Surveillance Data Streams. - Luís M. A. Bettencourt; Ruy M. Ribeiro; Gerardo Chowell; Timothy Lant; Carlos Castillo-Chavez (BioSurveillance, 2007)

Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections. - Ken Tatebe; Ahmet Zeytun; Ruy M. Ribeiro; Robert Hoffmann; Kevin S. Harrod; Christian V. Forst (BMC Bioinform., 2010)

Current Estimates for HIV-1 Production Imply Rapid Viral Clearance in Lymphoid Tissues. - Rob J. De Boer; Ruy M. Ribeiro; Alan S. Perelson (PLoS Comput. Biol., 2010)

Effect of 1918 PB1-F2 Expression on Influenza A Virus Infection Kinetics. - Amber M. Smith; Frederick R. Adler; Julie L. McAuley; Ryan N. Gutenkunst; Ruy M. Ribeiro; Jonathan A. McCullers; Alan S. Perelson (PLoS Comput. Biol., 2011)

Parameter estimation and identifiability of a HIV-1 model. - Ana Portêlo; João Miranda Lemos; Susana Vinga; Ruy M. Ribeiro; J. P. Cruz; Emília Valadas (MED, 2013)

Antibody Responses during Hepatitis B Viral Infection. - Stanca M. Ciupe; Ruy M. Ribeiro; Alan S. Perelson (PLoS Comput. Biol., 2014)

Inferring Viral Dynamics in Chronically HCV Infected Patients from the Spatial Distribution of Infected Hepatocytes. - Frederik Graw; Ashwin Balagopal; Abraham J. Kandathil; Stuart C. Ray; David L. Thomas; Ruy M. Ribeiro; Alan S. Perelson (PLoS Comput. Biol., 2014)

Modeling the Effects of Morphine on Simian Immunodeficiency Virus Dynamics. - Naveen K. Vaidya; Ruy M. Ribeiro; Alan S. Perelson; Anil Kumar (PLoS Comput. Biol., 2016)

Zika virus dynamics: Effects of inoculum dose, the innate immune response and viral interference. - Katharine Best; Dan H. Barouch; Jérémie Guedj; Ruy M. Ribeiro; Alan S. Perelson (PLoS Comput. Biol., 2021)

Forecasting Large Realized Covariance Matrices: The Benefits of Factor Models and Shrinkage. - Rafael Alves; Diego S. de Brito; Marcelo C. Medeiros; Ruy M. Ribeiro (CoRR, 2023)

Modeling dynamics of acute HIV infection incorporating density-dependent cell death and multiplicity of infection. - Ellie Mainou; Ruy M. Ribeiro; Jessica M. Conway (PLoS Comput. Biol., 2024)

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)