• Ke, R., Sanche, S., Romero-Severson, E. and Hengartner, N.,
    Fast spread of COVID-19 in Europe and the US suggests the necessity of early, strong and comprehensive interventions. [link]
  • Sanche, S., Lin, Y., Xu, C., Romero-Severson, E., Hengartner, N., Ke, R.,
    The novel coronavirus, 2019-nCoV, is highly contagious and more infectious than initially estimated. [link]
  • Ke, R., Deng, K.,
    The dynamics of the HIV-1 latent reservoir – considering the heterogeneous subpopulations. [Link]
  • Farrell, A., Brooke, C.B., Koelle, K., Ke, R.,
    Coinfection of semi-infectious particles can contribute substantially to influenza infection dynamics. [Link]



  • Kupperman, M.D., Leitner, T., Ke, R.
    A deep learning approach to real-time HIV outbreak detection using genetic data.
    PLoS Computational Biology 18 (10), e1010598 [link]
  • Choudhary, M. C., Chew, K. W., Deo, R., Flynn, J. P., Regan, J., Crain, C. R., … , Ke, R., …, Li, J. Z. & ACTIV-2/A5401 Study Team.
    Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial.
    Nature Microbiology 7, 1906–1917 [link]
  • Ke, R., Martinez, P.P.,Smith, R.L., Gibson L.L., Mirza, A., Conte, M., Gallagher, N., … & Brooke, C.B.
    Daily sampling of early SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness.
    Nature Microbiology 7, 640–652. [link]
  • Chaturvedi, S., Pablo, M., Wolf, M., Rosas-Rivera, D., Calia, G., Kumar, A.J., Vardi, N., Du, K., Glazier, J., Ke, R., Chan, M., Perelson, A.S., Weinberger, L.S.
    Disrupting autorepression circuitry generates “open-loop lethality” to yield escape-resistant antiviral agents.
    Cell 185, 2086–2102. [link]
  • Sanche, S. Cassidy, T., Chu, P., Perelson, A.S., Ribeiro, R.M., Ke, R.
    A simple model of COVID-19 explains disease severity and the effect of treatments.
    Scientific Reports 12 (1), 1-14. [link]
  • Allender, M. C., Adkesson, M. J., Langan, J. N., Delk, K. W., Meehan, T., Aitken‐Palmer, C.,… , Ke, R., … & Wang, L.
    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, doi:10.1111/tbed.14662. [link]
  • Cuéllar, L., Torres, I., Romero-Severson, E., Mahesh, R., Ortega, N., Pungitore, S., Ke, R., Hengartner, N.
    Assessing the impact of human mobility to predict regional excess death in Ecuador.
    Scientific Reports 12 (1), 1-12. [link]
  • Ke, R., Martinez, P.P.,Smith, R.L., Gibson L.L., Achenback, C., … & Brooke, C.B.
    Longitudinal analysis of SARS-CoV-2 vaccine breakthrough infections reveal limited infectious virus shedding and restricted tissue distribution.
    Open Forum Infectious Diseases, ofac192. [link]
  • Cuéllar, L., Torres, I., Romero-Severson, E., Mahesh, R., Ortega, N., Pungitore, S., Hengartner, N., Ke, R.
    Excess deaths reveal the true spatial, temporal, and demographic impact of COVID-19 on mortality in Ecuador.
    International Journal of Epidemiology, 51 (1), 54-62. [link]


  • Ke, R., Zitzmann, C., Ho, D.D., Ribeiro, R., Perelson, A.S.
    In vivo kinetics of SARS-CoV-2 infection and its relationship with a person’s infectiousness.
    Proceedings of the National Academy of Sciences 118(49), e2111477118 [link]
  • van Dorp, C.H., Goldberg, E., Hengartner, N., Ke, R., Romero-Severson, E.
    Estimating the strength of selection for new SARS-CoV-2 variants.
    Nature Communications 7239 (12) [link]
  • Cuéllar, L., Torres, I., Romero-Severson, E., Mahesh, R., Ortega, N., Pungitore, S., Ke, R., Hengartner, N.
    Excess deaths reveal unequal impact of COVID-19 in Ecuador.
    BMJ Global Health
    6(9), e006446. [link]
  • Perelson, A.S., Ke, R.
    Mechanistic modeling of SARS‐CoV‐2 and other infectious diseases and the effects of therapeutics.
    Clinical Pharmacology & Therapeutics 109 (4), 829-840 [link]
  • Kim, K.S., Ejima, K., Iwanami, S., Fujita, Y., Ohashi, H., Koizumi, Y., … & Iwami, S.
    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), e3001128 [link]
  • Smith, R.L., Gibson, L.L., Martinez, P.P., Ke, R., Mirza, A.,  … & Brooke, C.B.,
    Longitudinal assessment of diagnostic test performance over the course of acute SARS-CoV-2 infection.
    Journal of Infectious Diseases 224(6), 976-982. [link]
  • Lavigne, G.M., Russell, H., Sherry, B., Ke, R.
    Autocrine and paracrine interferon signalling as ‘ring vaccination’and ‘contact tracing’strategies to suppress virus infection in a host.
    Proceedings of the Royal Society B 288 (1945), 20203002
  • Ke, R., Romero-Severson, E., Sanche, S., Hengartner, N.
    Estimating the reproductive number R0 of SARS-CoV-2 in the United States and eight European countries and implications for vaccination.
    Journal of Theoretical Biology 517, 110621 [link]


  • Gonçalves, A., Bertrand, J., Ke, R., Comets, E., de Lamballerie, X., … & Guedj, J.
    Timing of antiviral treatment initiation is critical to reduce SARS‐CoV‐2 viral load.
    CPT: Pharmacometrics & Systems Pharmacology 9(9), 509-514 [link]
  • Sanche, S., Lin, Y., Xu, C., Romero-Severson, E., Hengartner, N., Ke, R.,
    High Contagiousness and Rapid Spread of Severe Acute Respiratory Syndrome Coronavirus 2.
    Emerging Infectious Diseases 26(7), 1470-1477. [link]
  • Mavigner, M., Liao, L.E., Brooks, A.D., Ke, R., Mattingly, C., Schoof, N., … & Chahroudi, A.
    CD8 Lymphocyte Depletion Enhances the Latency Reversal Activity of the SMAC Mimetic AZD5582 in ART-Suppressed Simian Immunodeficiency Virus-Infected Rhesus Macaques.
    Journal of Virology 95 (8), e01429-20. [link]
  • Schreiber, S., Ke, R., Loverdo, C., Park, M., Ahsan P., Lloyd-Smith, J. O.,
    Cross scale dynamics and the evolutionary emergence of infectious diseases.
    Virus Evolution 7 (1), veaa105 [link]
  • Sun, J., Vera, J.C., Drnevich, J., Lin, Y.T., Ke, R., Brooke, C.B.,
    Single cell heterogeneity in influenza A virus gene expression shapes the innate antiviral response to infection.
    PLoS Pathogens 16 (7), e1008671. [link]


  • Huang, Y., Dai, H., Ke, R.,
    Principles of effective and robust innate immune response to viral infections: a multiplex network analysis.
    Frontiers in Immunology 10, 1736.  [link]
  • Koelle, K., Farrell, A., Brooke, C.B., Ke, R.,
    Within-host infectious disease models accommodating cellular coinfection, with an application to influenza.
    Virus Evolution 5 (2), vez018. [link]


  • Gallagher, M.E., Brooke, C.B., Ke, R., Koelle, K.,
    Causes and consequences of spatial within-host viral spread.
    Viruses 2018; 10(11),627. [link]
  • Ke, R., Conway, J.M., Margolis, D.M., Perelson, A.S.,
    Determinants of the efficacy of HIV latency reversing agents and implications for drug and treatment design.
    JCI Insight 2018;3(20):e123052. [link]
  • Ke, R.*, Li, H.*, Wang, S., Ding W., Ribeiro, R.M., Giorgi, E.E., … & Perelson, A.S., (* equal contribution)
    Superinfection and cure of infected cells as mechanisms for hepatitis C virus adaptation and persistence.
    Proceedings of the National Academy of Sciences 2018; 115(30):E7139-E7148. [link]
  • Chang, C.C., Naranbhai, V., Stern, J., Roche, M., Dantanarayana, A., Ke, R., … & Lewin S.R.,
    Variation in cell associated unspliced HIV RNA on antiretroviral therapy is associated with the circadian regulator BMAL-1.
    AIDS 2018 doi: 10.1097/QAD.0000000000001937. [link]
  • Shan, L., Deng, K., Gao, H., Xing, S., Capoferri, A. A., Durand, C. M., … & Siliciano, R. F.,
    Transcriptional reprogramming during effector-to-memory transition renders CD4+ T cells permissive for latent HIV-1 infection.
    Immunity 2017; 47(4), 766-775. [link]
  • Ke, R., Cong, M., Li, D., Garcia-Lerma, G., Perelson, A. S.,
    On the death rate of abortively infected cells: estimation from simian/human immunodeficiency virus infection.
    Journal of Virology 2017. [link]
  • Benzine, T., Brandt, R., Lovell, W. C., Yamane, D., Neddermann, P.; de Francesco, R.; Lemon, S. M., Perelson, A. S.; Ke, R., McGivern, D. R.,
    NS5A inhibitors unmask differences in functional replicase complex half-life between different hepatitis C virus strains.
    PLoS Pathogens 2017; 13(6): e1006343.  [link]
  • Lau, G.K., Benhamou, Y., Chen, G., Li, J., Shao, Q., Ji, D., …, & Schinazi, R.F.,
    Efficacy and safety of 3-week response-guided triple direct-acting antiviral therapy for chronic hepatitis C infection: a phase 2, open-label, proof-of-concept study.
    The Lancet Gastroenterology & Hepatology 2016; 1(2): 97-104. [link]
  • Sherman, K.E., Ke, R., Rouster, S.D., Abdel-Hameed, E.A., Park, C., Palascak, J., Perelson, A.S.,
    Viral dynamic modeling of hepatitis C response to a telaprevir-based regimen in hemophiliacs.
    Haemophilia 2016; DOI: 10.1111/hae.12918. [link]

2015 and earlier

  • Ke, R., Elliott, J., Lewin, S. R., Perelson, A.S.,
    Modeling the effects of vorinostat in vivo reveals both transient and delayed HIV transcriptional activation and minimal killing of latently infected cells.
    PLoS Pathogens 2015; 11(10): e1005237.  [link]
  • Ke, R., Loverdo, C., Qi, H., Sun, R., Lloyd-Smith, J. O.,
    Rational design and adaptive management of combination therapies for hepatitis C virus infection.
    PLoS Computational Biology 2015; 11(6): e1004040. [link]
  • Qi, H., Olson, A., Wu, N., Ke, R., Loverdo, C., Chu, V., … & Sun, R.
    A quantitative high-resolution genetic profile rapidly identifies sequence determinants of hepatitis C viral fitness and drug sensitivity.
    PLoS Pathogens 2014; 10 (4): e1004064 [link]
  • Ke, R., Loverdo, C., Qi, H., Olson, A., Wu, N., Sun, R., Lloyd-Smith, J. O.,
    Modelling clinical data shows active tissue concentration of daclatasvir is ten-fold lower than its plasma concentration.
    Journal of Antimicrobial Chemotherapy 2014; 69 (3): 724-727. [link]
  • Ke, R., Lloyd-Smith, J.O.
    Coadaptive stability of interfering particles with HIV-1 when there is an evolutionary conflict. [Letter]
    Journal of Virology 2013; 87 (17), 9959-9959 [link]
  • Ke, R., Aaskov, J., Holmes, E.C., Lloyd-Smith, J.O.
    Phylodynamic analysis of the emergence and epidemiological impact of transmissible defective dengue viruses.
    PLoS Pathogens 2013; 9(2): e1003193 [link]

  • Ke, R., Haynes, K., Stark, J.
    Modelling the activation of the alkaline pH response transcription factor PacC in Aspergillus nidulans reveals the involvement of a negative feedback loop.
    Journal of Theoretical Biology 2013; 326:11-20 [link]
  • Ke, R., Ingram, P., Haynes, K.
    An integrative model of ion regulation in yeast.
    PLoS Computational Biology 2013; 9 (1), e1002879 [link]
  • Ke, R., Lloyd-Smith, J.O.
    Evolutionary analysis of human immunodeficiency virus type 1 therapies based on conditionally replicating vectors.
    PLoS Computational Biology 2012; 8 (10), e1002744 [link]

Conference Proceedings

  • Huang, Y., Dai, M., Zhang, Z., Ke, R.
    Network analysis of virus-innate immune interaction within a host.
    Information Sciences and Systems (CISS), 2018 52nd Annual Conference on, 1-6. DOI: 10.1109/CISS.2018.8362278