Integrating genealogical and dynamical modelling to infer escape and reversion rates in HIV epitopes
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Gil McVean | Angela R. McLean | Duncan Palmer | John Frater | Rodney Phillips | G. McVean | A. McLean | R. Phillips | D. Palmer | J. Frater | R. Phillips
[1] Alan S. Perelson,et al. Fitness Costs and Diversity of the Cytotoxic T Lymphocyte (CTL) Response Determine the Rate of CTL Escape during Acute and Chronic Phases of HIV Infection , 2011, Journal of Virology.
[2] Alessandro Sette,et al. Selection, Transmission, and Reversion of an Antigen-Processing Cytotoxic T-Lymphocyte Escape Mutation in Human Immunodeficiency Virus Type 1 Infection , 2004, Journal of Virology.
[3] B. Rannala,et al. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method. , 1997, Molecular biology and evolution.
[4] Yoshiyuki Nagai,et al. Impaired Processing and Presentation of Cytotoxic-T-Lymphocyte (CTL) Epitopes Are Major Escape Mechanisms from CTL Immune Pressure in Human Immunodeficiency Virus Type 1 Infection , 2004, Journal of Virology.
[5] A. Telenti,et al. A prospective trial of structured treatment interruptions in human immunodeficiency virus infection. , 2003, Archives of internal medicine.
[6] Jiankang Zhang,et al. ON THE GENERALIZED BIRTH AND DEATH PROCESSES (II)––THE STAY TIME, LIMIT THEOREM AND ERGODIC PROPERTY , 1986 .
[7] T. Stadler. Sampling-through-time in birth-death trees. , 2010, Journal of theoretical biology.
[8] D. Heckerman,et al. Extensive Intrasubtype Recombination in South African Human Immunodeficiency Virus Type 1 Subtype C Infections , 2007, Journal of Virology.
[9] D. Kendall. On the Generalized "Birth-and-Death" Process , 1948 .
[10] E. Holmes,et al. Passive Sexual Transmission of Human Immunodeficiency Virus Type 1 Variants and Adaptation in New Hosts , 2006, Journal of Virology.
[11] P. Mahalanobis. On the generalized distance in statistics , 1936 .
[12] D. Heckerman,et al. Widespread Impact of HLA Restriction on Immune Control and Escape Pathways of HIV-1 , 2012, Journal of Virology.
[13] Angela R. McLean,et al. Modelling the Evolution and Spread of HIV Immune Escape Mutants , 2010, PLoS pathogens.
[14] Bette Korber,et al. Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA , 2004, Nature.
[15] 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.
[16] B. Walker,et al. HIV and HLA class I: an evolving relationship. , 2012, Immunity.
[17] D. Heckerman,et al. Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations , 2007, Science.
[18] Edward C. Holmes,et al. Clustered Mutations in HIV-1 Gag Are Consistently Required for Escape from Hla-B27–Restricted Cytotoxic T Lymphocyte Responses , 2001, The Journal of experimental medicine.
[19] Todd M. Allen,et al. HIV evolution: CTL escape mutation and reversion after transmission , 2004, Nature Medicine.
[20] M. Wand. Fast Computation of Multivariate Kernel Estimators , 1994 .
[21] F. Marincola,et al. HLA B*5701 is highly associated with restriction of virus replication in a subgroup of HIV-infected long term nonprogressors. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[22] M. Suchard,et al. Bayesian Phylogenetics with BEAUti and the BEAST 1.7 , 2012, Molecular biology and evolution.
[23] Sergei L. Kosakovsky Pond,et al. Phylodynamics of Infectious Disease Epidemics , 2009, Genetics.
[24] T. Stadler. On incomplete sampling under birth-death models and connections to the sampling-based coalescent. , 2009, Journal of theoretical biology.
[25] S. Tavaré,et al. Sampling theory for neutral alleles in a varying environment. , 1994, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.
[26] M. Altfeld,et al. Immune Selection for Altered Antigen Processing Leads to Cytotoxic T Lymphocyte Escape in Chronic HIV-1 Infection , 2004, The Journal of experimental medicine.
[27] P. Klenerman,et al. Cytotoxic T Lymphocyte Lysis Inhibited by Viable HIV Mutants , 1995, Science.
[28] T Jombart,et al. Reconstructing disease outbreaks from genetic data: a graph approach , 2010, Heredity.
[29] Alan S. Perelson,et al. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection , 2009, The Journal of experimental medicine.
[30] M. Slatkin,et al. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. , 1991, Genetics.
[31] HighWire Press. Philosophical Transactions of the Royal Society of London , 1781, The London Medical Journal.
[32] P. Klenerman,et al. The effects of natural altered peptide ligands on the whole blood cytotoxic T lymphocyte response to human immunodeficiency virus , 1995, European journal of immunology.
[33] D. Sullivan,et al. Human immunodeficiency virus type 1 long-term non-progressors: the viral, genetic and immunological basis for disease non-progression. , 2011, The Journal of general virology.
[34] Obi L. Griffith,et al. HIV Sequence Database , 2014 .
[35] C. Moore,et al. Evidence of HIV-1 Adaptation to HLA-Restricted Immune Responses at a Population Level , 2002, Science.
[36] C. Rinaldo,et al. High levels of anti-human immunodeficiency virus type 1 (HIV-1) memory cytotoxic T-lymphocyte activity and low viral load are associated with lack of disease in HIV-1-infected long-term nonprogressors , 1995, Journal of virology.
[37] Andrew Rambaut,et al. Evolutionary analysis of the dynamics of viral infectious disease , 2009, Nature Reviews Genetics.
[38] Xiping Wei,et al. Antiviral pressure exerted by HIV-l-specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus , 1997, Nature Medicine.
[39] Peter Parham,et al. The HLA FactsBook , 1999 .
[40] Sarah Rowland-Jones,et al. Cytotoxic T-cell activity antagonized by naturally occurring HIV-1 Gag variants , 1994, Nature.
[41] Brian T. Foley,et al. Retrieval and on-the-fly alignment of sequence fragments from the HIV database , 2001, Bioinform..
[42] Feng Gao,et al. Vertical T cell immunodominance and epitope entropy determine HIV-1 escape. , 2012, The Journal of clinical investigation.
[43] David Heckerman,et al. Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag , 2008, PLoS Comput. Biol..
[44] David A. Rasmussen,et al. Inference for Nonlinear Epidemiological Models Using Genealogies and Time Series , 2011, PLoS Comput. Biol..
[45] Katia Koelle,et al. Rates of coalescence for common epidemiological models at equilibrium , 2012, Journal of The Royal Society Interface.
[46] Elizabeth A. Thompson,et al. Human Evolutionary Trees , 1975 .
[47] S.. Sampling theory for neutral alleles in a varying environment , 2003 .
[48] P. Klenerman,et al. Positive selection of HIV-1 cytotoxic T lymphocyte escape variants during primary infection. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[49] B. Walker,et al. Effective T-Cell Responses Select Human Immunodeficiency Virus Mutants and Slow Disease Progression , 2007, Journal of Virology.
[50] J. Felsenstein. Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.
[51] R M May,et al. The reconstructed evolutionary process. , 1994, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.
[52] W. Gilks. Markov Chain Monte Carlo , 2005 .
[53] Tanja Gernhard,et al. The conditioned reconstructed process. , 2008, Journal of theoretical biology.