Park H, Raiki Y, Iwanami S, Kim K, Ejima K, Nakamura N, Aihara K, Miyazaki Y, Umeyama T, Miyazawa K, Morita T, Watashi K, Brooke CB, Ke R, Iwami S, Miyazaki T. (2026). Stratification of viral shedding patterns in saliva of COVID-19 patients. eLife, (13)
Jeong YD, Hart WS, Ishikane M, Kim KS, Byun JH, Jung IH, Harrison MT, Aihara K, Ohmagari N, Brooke CB, Ke R, Thompson RN, Iwami S. (2026). Identifying the optimal rapid antigen test for screening and determining the end of isolation: A modeling study. PLoS computational biology, 22(4)
Phan T, Mavigner M, Dashti A, Chahroudi A, Ribeiro RM, Ke R, Perelson AS. (2026). AZD5582 robustly reactivates latently infected cells and clears the majority of those reactivated from the SIV reservoir. bioRxiv : the preprint server for biology
Phan T, Brozak S, Pell B, Ciupe SM, Ke R, Ribeiro RM, Gitter A, Mena KD, Perelson AS, Kuang Y, Wu F. (2025). Post-recovery viral shedding shapes wastewater-based epidemiological inferences. Communications medicine, 5(1)
Kupperman MD, Ke R, Leitner T. (2025). Identifying impacts of contact tracing on HIV epidemiological inference from phylogenetic data. Virus evolution, 11(1)
Phan T, Conway JM, Pagane N, Kreig J, Sambaturu N, Iyaniwura S, Li JZ, Ribeiro RM, Ke R, Perelson AS. (2024). Understanding early HIV-1 rebound dynamics following antiretroviral therapy interruption: The importance of effector cell expansion. PLoS pathogens, 20(7)
Phan T, Zitzmann C, Chew KW, Smith DM, Daar ES, Wohl DA, Eron JJ, Currier JS, Hughes MD, Choudhary MC, Deo R, Li JZ, Ribeiro RM, Ke R, Perelson AS, . (2024). Modeling the emergence of viral resistance for SARS-CoV-2 during treatment with an anti-spike monoclonal antibody. PLoS pathogens, 20(4)
Zitzmann C, Ke R, Ribeiro RM, Perelson AS. (2024). How robust are estimates of key parameters in standard viral dynamic models?. PLoS computational biology, 20(4)
Feng Y, Goldberg EE, Kupperman M, Zhang X, Lin Y, Ke R. (2024). CovTransformer: A transformer model for SARS-CoV-2 lineage frequency forecasting. Virus evolution, 10(1)
Gay CL, Hanley PJ, Falcinelli SD, Kuruc JD, Pedersen SM, Kirchherr J, Raines SLM, Motta CM, Lazarski C, Chansky P, Tanna J, Shibli A, Datar A, McCann CD, Sili U, Ke R, Eron JJ, Archin N, Goonetilleke N, Bollard CM, Margolis DM. (2024). The Effects of Human Immunodeficiency Virus Type 1 (HIV-1) Antigen-Expanded Specific T-Cell Therapy and Vorinostat on Persistent HIV-1 Infection in People With HIV on Antiretroviral Therapy. The Journal of infectious diseases
Iyaniwura SA, Ribeiro RM, Zitzmann C, Phan T, Ke R, Perelson AS. (2024). The kinetics of SARS-CoV-2 infection based on a human challenge study. Proceedings of the National Academy of Sciences of the United States of America, 121(46)
Bonner X, Sondgeroth A, McCue A, Nicely N, Tripathy A, Spielvogel E, Moeser M, Ke R, Leiderman K, Joseph SB, Swanstrom R. (2024). Stoichiometry for entry and binding properties of the Env protein of R5 T cell-tropic HIV-1 and its evolutionary variant of macrophage-tropic HIV-1. mBio
Zath GK, Thomas MM, Loveday EK, Bikos DA, Sanche S, Ke R, Brooke CB, Chang CB. (2024). Influenza A viral burst size from thousands of infected single cells using droplet quantitative PCR (dqPCR). PLoS pathogens, 20(7)
Goldberg EE, Lin Q, Romero-Severson EO, Ke R. (2023). Swift and extensive Omicron outbreak in China after sudden exit from 'zero-COVID' policy. Nature communications, 14(1)
Farrell A, Phan T, Brooke CB, Koelle K, Ke R. (2023). Semi-infectious particles contribute substantially to influenza virus within-host dynamics when infection is dominated by spatial structure. Virus evolution, 9(1)
Phan T, Brozak S, Pell B, Oghuan J, Gitter A, Hu T, Ribeiro RM, Ke R, Mena KD, Perelson AS, Kuang Y, Wu F. (2023). Making waves: Integrating wastewater surveillance with dynamic modeling to track and predict viral outbreaks. Water research, (243)
Phan T, Brozak S, Pell B, Ciupe SM, Ke R, Ribeiro RM, Gitter A, Mena KD, Perelson AS, Kuang Y, Wu F. (2023). Prolonged viral shedding from noninfectious individuals confounds wastewater-based epidemiology. medRxiv : the preprint server for health sciences
Kupperman MD, Ke R, Leitner T. (2023). Predicting Impacts of Contact Tracing on Epidemiological Inference from Phylogenetic Data. bioRxiv : the preprint server for biology
Dashti A, Sukkestad S, Horner AM, Neja M, Siddiqi Z, Waller C, Goldy J, Monroe D, Lin A, Schoof N, Singh V, Mavigner M, Lifson JD, Deleage C, Tuyishime M, Falcinelli SD, King HAD, Ke R, Mason RD, Archin NM, Dunham RM, Safrit JT, Jean S, Perelson AS, Margolis DM, Ferrari G, Roederer M, Silvestri G, Chahroudi A. (2023). AZD5582 plus SIV-specific antibodies reduce lymph node viral reservoirs in antiretroviral therapy-suppressed macaques. Nature medicine
Ke R, Martinez PP, Smith RL, Gibson LL, Achenbach CJ, McFall S, Qi C, Jacob J, Dembele E, Bundy C, Simons LM, Ozer EA, Hultquist JF, Lorenzo-Redondo R, Opdycke AK, Hawkins C, Murphy RL, Mirza A, Conte M, Gallagher N, Luo CH, Jarrett J, Conte A, Zhou R, Farjo M, Rendon G, Fields CJ, Wang L, Fredrickson R, Baughman ME, Chiu KK, Choi H, Scardina KR, Owens AN, Broach J, Barton B, Lazar P, Robinson ML, Mostafa HH, Manabe YC, Pekosz A, McManus DD, Brooke CB. (2022). Longitudinal Analysis of SARS-CoV-2 Vaccine Breakthrough Infections Reveals Limited Infectious Virus Shedding and Restricted Tissue Distribution. Open forum infectious diseases, 9(7)
Ke R, Martinez PP, Smith RL, Gibson LL, Mirza A, Conte M, Gallagher N, Luo CH, Jarrett J, Zhou R, Conte A, Liu T, Farjo M, Walden KKO, Rendon G, Fields CJ, Wang L, Fredrickson R, Edmonson DC, Baughman ME, Chiu KK, Choi H, Scardina KR, Bradley S, Gloss SL, Reinhart C, Yedetore J, Quicksall J, Owens AN, Broach J, Barton B, Lazar P, Heetderks WJ, Robinson ML, Mostafa HH, Manabe YC, Pekosz A, McManus DD, Brooke CB. (2022). Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness. Nature microbiology, 7(5)
Choudhary MC, Chew KW, Deo R, Flynn JP, Regan J, Crain CR, Moser C, Hughes MD, Ritz J, Ribeiro RM, Ke R, Dragavon JA, Javan AC, Nirula A, Klekotka P, Greninger AL, Fletcher CV, Daar ES, Wohl DA, Eron JJ, Currier JS, Parikh UM, Sieg SF, Perelson AS, Coombs RW, Smith DM, Li JZ, . (2022). Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial. Nature microbiology, 7(11)
Sanche S, Cassidy T, Chu P, Perelson AS, Ribeiro RM, Ke R. (2022). A simple model of COVID-19 explains disease severity and the effect of treatments. Scientific reports, 12(1)
Allender MC, Adkesson MJ, Langan JN, Delk KW, Meehan T, Aitken-Palmer C, McEntire MM, Killian ML, Torchetti M, Morales SA, Austin C, Fredrickson R, Olmstead C, Ke R, Smith R, Hostnik ET, Terio K, Wang L. (2022). Multi-species outbreak of SARS-CoV-2 Delta variant in a zoological institution, with the detection in two new families of carnivores. Transboundary and emerging diseases, 69(5)
Chaturvedi S, Pablo M, Wolf M, Rosas-Rivera D, Calia G, Kumar AJ, Vardi N, Du K, Glazier J, Ke R, Chan MF, Perelson AS, Weinberger LS. (2022). Disrupting autorepression circuitry generates "open-loop lethality" to yield escape-resistant antiviral agents. Cell, 185(12)
Kupperman MD, Leitner T, Ke R. (2022). A deep learning approach to real-time HIV outbreak detection using genetic data. PLoS computational biology, 18(10)
Cuéllar L, Torres I, Romero-Severson E, Mahesh R, Ortega N, Pungitore S, Ke R, Hengartner N. (2022). Assessing the impact of human mobility to predict regional excess death in Ecuador. Scientific reports, 12(1)
van Dorp C, Goldberg E, Ke R, Hengartner N, Romero-Severson E. (2022). Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron. Virus evolution, 8(2)
Smith RL, Gibson LL, Martinez PP, Ke R, Mirza A, Conte M, Gallagher N, Conte A, Wang L, Fredrickson R, Edmonson DC, Baughman ME, Chiu KK, Choi H, Jensen TW, Scardina KR, Bradley S, Gloss SL, Reinhart C, Yedetore J, Owens AN, Broach J, Barton B, Lazar P, Henness D, Young T, Dunnett A, Robinson ML, Mostafa HH, Pekosz A, Manabe YC, Heetderks WJ, McManus DD, Brooke CB. (2021). Longitudinal assessment of diagnostic test performance over the course of acute SARS-CoV-2 infection. The Journal of infectious diseases
Cuéllar L, Torres I, Romero-Severson E, Mahesh R, Ortega N, Pungitore S, Hengartner N, Ke R. (2021). Excess deaths reveal the true spatial, temporal, and demographic impact of COVID-19 on mortality in Ecuador. medRxiv : the preprint server for health sciences
Kim KS, Ejima K, Iwanami S, Fujita Y, Ohashi H, Koizumi Y, Asai Y, Nakaoka S, Watashi K, Aihara K, Thompson RN, Ke R, Perelson AS, Iwami S. (2021). A quantitative model used to compare within-host SARS-CoV-2, MERS-CoV, and SARS-CoV dynamics provides insights into the pathogenesis and treatment of SARS-CoV-2. PLoS biology, 19(3)
Michael Lavigne G, Russell H, Sherry B, Ke R. (2021). Autocrine and paracrine interferon signalling as 'ring vaccination' and 'contact tracing' strategies to suppress virus infection in a host. Proceedings. Biological sciences, 288(1945)
Ke R, Romero-Severson E, Sanche S, Hengartner N. (2021). Estimating the reproductive number R(0) of SARS-CoV-2 in the United States and eight European countries and implications for vaccination. Journal of theoretical biology, (517)
Cuéllar L, Torres I, Romero-Severson E, Mahesh R, Ortega N, Pungitore S, Hengartner N, Ke R. (2022). Excess deaths reveal the true spatial, temporal and demographic impact of COVID-19 on mortality in Ecuador. International journal of epidemiology, 51(1)
Dorp CHV, Goldberg EE, Hengartner N, Ke R, Romero-Severson EO. (2021). Estimating the strength of selection for new SARS-CoV-2 variants. Nature communications, 12(1)
Mavigner M, Liao LE, Brooks AD, Ke R, Mattingly C, Schoof N, McBrien J, Carnathan D, Liang S, Vanderford TH, Paiardini M, Kulpa D, Lifson JD, Dunham RM, Easley KA, Margolis DM, Perelson AS, Silvestri G, Chahroudi A. (2021). CD8 lymphocyte depletion enhances the latency reversal activity of the SMAC mimetic AZD5582 in ART-suppressed SIV-infected rhesus macaques. Journal of virology, 95(8)
Perelson AS, Ke R. (2021). Mechanistic Modeling of SARS-CoV-2 and Other Infectious Diseases and the Effects of Therapeutics. Clinical pharmacology and therapeutics, 109(4)
Ke R, Zitzmann C, Ho DD, Ribeiro RM, Perelson AS. (2021). In vivo kinetics of SARS-CoV-2 infection and its relationship with a person's infectiousness. Proceedings of the National Academy of Sciences of the United States of America, 118(49)
Cuéllar L, Torres I, Romero-Severson E, Mahesh R, Ortega N, Pungitore S, Ke R, Hengartner N. (2021). Excess deaths reveal unequal impact of COVID-19 in Ecuador. BMJ global health, 6(9)
Schreiber SJ, Ke R, Loverdo C, Park M, Ahsan P, Lloyd-Smith JO. (2020). Cross-scale dynamics and the evolutionary emergence of infectious diseases. Virus evolution, 7(1)
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