Rafael Lopes Post-doc

Biographical sketch

Rafael (Rafa) holds a PhD in theoretical physics, with a thesis on how temperature affects dengue dynamics in Brazil. He is an experienced infectious disease modeler, mainly in spatiotemporal models for arbovirus and respiratory infections. During his first postdoc at Yale University with Prof. Nathan Grubaugh, he developed models that integrate epidemiological and genomic data. At Yale, he also worked on climate change health impacts and attribution to arbovirus diseases. In November 2026, Rafa joined the Spatial Epidemiology Lab for his second post-doc, where he works on spatial models for infectious diseases, climate attribution to infectious diseases, and the impacts of climate and weather extremes on arboviruses.

External links: Google Scholar, ResearchGate, and BlueSky

Research interests

Rafa’s research interests lie at the intersection of infectious diseases modeling, nowcasting and forecasting methods, climate and weather science, and attribution of climate health impacts. More recently, during his first postdoc, he has also been interested in using phylogenetic data and phylogeography in climate change attribution to health impacts, particularly for arboviruses that have recently caused larger outbreaks.

Publications

Estimating the quality-adjusted life-year loss due to fatal and nonfatal COVID-19 outcomes across US qtates and counties, July 2020 to December 2022
F. Mikdashi, R. E. Murray-Watson, R. Lopes, A. Bilinski, and R. Yaesoubi. "MDM Policy & Practice", Vol. 11, Issue 2, Pages 23814683261461551, 2026.

Evolutionary history of Jamestown Canyon virus reveals complex multi-vector ecology
E. Bourgikos, S. Dellicour, P. Lemey, N. M. Feriancek, A. B. Bransfield, M. I. Breban, M. J. Misencik, T. A. Petruff, J. J. Shepard, T. G. Andreadis, J. F. Anderson, K. A. Ngo, J. G. Maffei, A. P. Dupuis, S. M. Rich, G. Xu, G. Sakolsky, K. J. Price, M. L. Metzger, M. A. Suchard, R. Lopes, F. Gámbaro, C. J. Carlson, G. Baele, A. T. Ciota, C. B. F. Vogels, V. Hill, P. M. Armstrong, and N. D. Grubaugh. "Current Biology", Vol. 36, Issue 9, Pages 2343-2356.e7, 2026.

Integrated analysis of the 2022 SARS-CoV-2 Omicron lineage replacement dynamics in Connecticut, US
N. F. Chen, K. Pham, C. Chaguza, R. Lopes, F. Klaassen, C. C. Kalinich, Yale SARS-CoV-2 Genomic Surveillance Initiative, N. Kerantzas, S. Pandya, and D. Ferguson. "Viruses", Vol. 17, Issue 7, Pages 1020, 2025.

National- and state-level SARS-CoV-2 immunity trends from January 2020 to December 2023: a mathematical modeling analysis
F. Klaassen, N. A. Swartwood, M. H. Chitwood, R. Lopes, M. Haraguchi, J. A. Salomon, T. Cohen, and N. A. Menzies. "The Journal of Infectious Diseases", Pages jiaf532, 2025.

Ambient temperature and dengue hospitalization in Brazil: A 10-year period case time series analysis
R. Lopes, X. Basagaña, L. S. Bastos, F. A. Bozza, and O. T. Ranzani. "Environmental Epidemiology", Vol. 9, Issue 1, Pages e360, 2025.

On the verge: outbreak risk after two years of record-breaking dengue epidemics in Brazil
R. Lopes, and L. S. Bastos. "The Lancet Regional Health – Americas", Vol. 45, 2025.

Combining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the US
R. Lopes, K. Pham, F. Klaassen, M. H. Chitwood, A. M. Hahn, S. Redmond, N. A. Swartwood, J. A. Salomon, N. A. Menzies, and T. Cohen. "Cell Reports", Vol. 43, Issue 7, 2024.

Ten quick tips for harnessing the power of ChatGPT in computational biology
T. Lubiana, R. Lopes, P. Medeiros, J. C. Silva, A. N. A. Goncalves, V. Maracaja-Coutinho, and H. I. Nakaya. "PLoS Computational Biology", Vol. 19, Issue 8, Pages e1011319, 2023.

Risk factors for long coronavirus disease 2019 (long COVID) among healthcare personnel, Brazil, 2020–2022
A. R. Marra, V. S. Sampaio, M. C. Ozahata, R. Lopes, A. F. Brito, M. Bragatte, J. Kalil, J. L. Miraglia, D. T. Malheiro, and G. Yang. "Infection Control and Hospital Epidemiology", Vol. 44, Issue 12, Pages 1972-1978, 2023.

Thinking out of the box: revisiting health surveillance based on medical records
V. S. Sampaio, R. Lopes, M. C. Ozahata, H. I. Nakaya, E. Sousa, J. D. Araújo, M. A. Bragatte, A. F. Brito, R. M. Z. Grespan, and M. L. D. Capuani. "Antimicrobial Stewardship & Healthcare Epidemiology", Vol. 3, Issue 1, Pages e185, 2023.