Publications

 Articles

  • 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., Li, F., Li, B., Liu, J., Hou, J., Sun, J., Wang, C., Chen, J., Wu, V., Wong, A., Wong, C.L.P., Tsang, S.T.Y., Wang, Y., Bassit, L., Tao, S., Jiang, Y., Hsiao, H-M., Ke, R., Perelson, A.S., 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; DOI: http://dx.doi.org/10.1016/S2468-1253(16)30015-2.
  • 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]
  • 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., et al.
    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]

Submitted

  • Wu, N. C., Le, S., Ke, R., Hu, F., Lloyd-Smith, J. O., Sun, R.
    High-resolution monitoring of host-parasite antagonistic coevolution reveals distinct patterns of genetic dynamics.
  • Loverdo, C., Ke, R., Qi, H., Olson, A., Wu, N.C., Sun, R., Lloyd-Smith, J. O.,
    Measuring mutation rates along with fitness in high-throughput mutational screening.
  • Schreiber, S., Ke, R., Loverdo, C., Park, M., Ahsan P., Lloyd-Smith, J. O.,
    Cross scale dynamics and the evolutionary emergence of infectious diseases. [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.