Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model
暂无分享,去创建一个
Tanja Stadler | Alexei J. Drummond | Denise Kühnert | Timothy G. Vaughan | A. Drummond | T. Vaughan | T. Stadler | D. Kühnert
[1] Evan Wood,et al. The case for expanding access to highly active antiretroviral therapy to curb the growth of the HIV epidemic , 2006, The Lancet.
[2] S. Bonhoeffer,et al. Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV) , 2012, Proceedings of the National Academy of Sciences.
[3] C. Andrieu,et al. The pseudo-marginal approach for efficient Monte Carlo computations , 2009, 0903.5480.
[4] David Welch,et al. Recursive algorithms for phylogenetic tree counting , 2013, Algorithms for Molecular Biology.
[5] M. Beaumont. Estimation of population growth or decline in genetically monitored populations. , 2003, Genetics.
[6] Daniel J. Wilson,et al. Coalescent inference for infectious disease: meta-analysis of hepatitis C , 2013, Philosophical Transactions of the Royal Society B: Biological Sciences.
[7] Jeffrey W. Eaton,et al. HIV Treatment as Prevention: Systematic Comparison of Mathematical Models of the Potential Impact of Antiretroviral Therapy on HIV Incidence in South Africa , 2012, PLoS medicine.
[8] Erik M. Volz,et al. Viral phylodynamics and the search for an ‘effective number of infections’ , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.
[9] The Swiss,et al. Cohort Profile: The Swiss HIV Cohort Study , 2010 .
[10] Beda Joos,et al. Estimating the basic reproductive number from viral sequence data. , 2012, Molecular biology and evolution.
[11] Alexei J. Drummond,et al. Phylogenetic and epidemic modeling of rapidly evolving infectious diseases , 2011, Infection, Genetics and Evolution.
[12] W. O. Kermack,et al. A contribution to the mathematical theory of epidemics , 1927 .
[13] David A. Rasmussen,et al. Inference for Nonlinear Epidemiological Models Using Genealogies and Time Series , 2011, PLoS Comput. Biol..
[14] D. Kendall. On the Generalized "Birth-and-Death" Process , 1948 .
[15] T. Gojobori,et al. A comparison of the molecular clock of hepatitis C virus in the United States and Japan predicts that hepatocellular carcinoma incidence in the United States will increase over the next two decades , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[16] R. Campos,et al. Phylodynamics of Hepatitis C Virus Subtype 2c in the Province of Córdoba, Argentina , 2011, PloS one.
[17] Erik M. Volz,et al. Complex Population Dynamics and the Coalescent Under Neutrality , 2012, Genetics.
[18] Huldrych F. Günthard,et al. Using an Epidemiological Model for Phylogenetic Inference Reveals Density Dependence in HIV Transmission , 2013, Molecular biology and evolution.
[19] O. Pybus,et al. Unifying the Epidemiological and Evolutionary Dynamics of Pathogens , 2004, Science.
[20] William Feller. Die Grundlagen der Volterraschen Theorie des Kampfes ums Dasein in wahrscheinlichkeitstheoretischer Behandlung , 1939 .
[21] O. Pybus,et al. The Epidemic Behavior of the Hepatitis C Virus , 2001, Science.
[22] W. K. Hastings,et al. Monte Carlo Sampling Methods Using Markov Chains and Their Applications , 1970 .
[23] Amalio Telenti,et al. Cohort profile: the Swiss HIV Cohort study. , 2010, International journal of epidemiology.
[24] Kholoud Porter,et al. The creation of a large UK‐based multicentre cohort of HIV‐infected individuals: The UK Collaborative HIV Cohort (UK CHIC) Study , 2004, HIV medicine.
[25] Stéphane Hué,et al. Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[26] P. Donnelly,et al. A new statistical method for haplotype reconstruction from population data. , 2001, American journal of human genetics.
[27] T. Stadler. Sampling-through-time in birth-death trees. , 2010, Journal of theoretical biology.
[28] Erik M. Volz,et al. Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection , 2012, PLoS Comput. Biol..
[29] W. O. Kermack,et al. Contributions to the mathematical theory of epidemics—II. The problem of endemicity , 1991, Bulletin of mathematical biology.
[30] Joachim Metallmann. Der Kampf um die Autonomie des Lebens , 1939 .