Identifying predictors of time-inhomogeneous viral evolutionary processes
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Guy Baele | Allen G. Rodrigo | Marc A. Suchard | Philippe Lemey | Filip Bielejec | M. Suchard | A. Rodrigo | P. Lemey | Filip Bielejec | G. Baele
[1] R. Fildes. Journal of the American Statistical Association : William S. Cleveland, Marylyn E. McGill and Robert McGill, The shape parameter for a two variable graph 83 (1988) 289-300 , 1989 .
[2] S. Williamson,et al. Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression. , 2003, Molecular biology and evolution.
[3] Arthur E. Bryson,et al. Applied Optimal Control , 1969 .
[4] Katia Koelle,et al. Reconciling Phylodynamics with Epidemiology: The Case of Dengue Virus in Southern Vietnam , 2013, Molecular biology and evolution.
[5] S. Muse,et al. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. , 1994, Molecular biology and evolution.
[6] Y. Takeuchi,et al. HIV evolution and progression of the infection to AIDS. , 2012, Journal of theoretical biology.
[7] Guy Baele,et al. Inferring Heterogeneous Evolutionary Processes Through Time: from Sequence Substitution to Phylogeography , 2013, Systematic biology.
[8] M. Suchard,et al. Impact of CCR5delta32 host genetic background and disease progression on HIV-1 intrahost evolutionary processes: efficient hypothesis testing through hierarchical phylogenetic models. , 2011, Molecular biology and evolution.
[9] Alexei J. Drummond,et al. Bayesian Phylogeography Finds Its Roots , 2009, PLoS Comput. Biol..
[10] George M. Siouris,et al. Applied Optimal Control: Optimization, Estimation, and Control , 1979, IEEE Transactions on Systems, Man, and Cybernetics.
[11] Y. Takeuchi,et al. Immune impairment thresholds in HIV infection. , 2009, Immunology letters.
[12] Sergei L. Kosakovsky Pond,et al. Purifying Selection Can Obscure the Ancient Age of Viral Lineages , 2011, Molecular biology and evolution.
[13] S. Muse,et al. Site-to-site variation of synonymous substitution rates. , 2005, Molecular biology and evolution.
[14] M. Suchard,et al. Bayesian Phylogenetics with BEAUti and the BEAST 1.7 , 2012, Molecular biology and evolution.
[15] Marc A. Suchard,et al. Many-core algorithms for statistical phylogenetics , 2009, Bioinform..
[16] S. Ho,et al. Relaxed Phylogenetics and Dating with Confidence , 2006, PLoS biology.
[17] Anne-Mieke Vandamme,et al. The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing , 2009 .
[18] A S Perelson,et al. Hepatitis C viral dynamics in vivo and the antiviral efficacy of interferon-alpha therapy. , 1998, Science.
[19] Hirohisa Kishino,et al. Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences. , 2004, Molecular biology and evolution.
[20] M. Suchard,et al. Bayesian random local clocks, or one rate to rule them all , 2010, BMC Biology.
[21] Stéphane Guindon,et al. Modelling the evolution of protein coding sequences sampled from Measurably Evolving Populations. , 2008, Genome informatics. International Conference on Genome Informatics.
[22] L. Wasserman,et al. Computing Bayes Factors by Combining Simulation and Asymptotic Approximations , 1997 .
[23] Michael Worobey,et al. A synchronized global sweep of the internal genes of modern avian influenza virus , 2014, Nature.
[24] Guy Baele,et al. The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates , 2014, PLoS Comput. Biol..
[25] Rebecca R. Gray,et al. The mode and tempo of hepatitis C virus evolution within and among hosts , 2011, BMC Evolutionary Biology.
[26] Sergei L. Kosakovsky Pond,et al. Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics , 2007, PLoS Comput. Biol..
[27] Alan S. Perelson,et al. This is an open-access article distributed under the terms of the Creative Commons Attribution Non Commercial License, which permits noncommercial use, distribution, and reproduction in other forums, provided the original authors and source are credited , 2022 .
[28] M. Suchard,et al. Hierarchical phylogenetic models for analyzing multipartite sequence data. , 2003, Systematic biology.
[29] Alan S. Perelson,et al. Hepatitis C Viral Dynamics in Vivo and the Antiviral Efficacy of Interferon-α Therapy , 1998 .
[30] John P. Huelsenbeck,et al. Variation in the Pattern of Nucleotide Substitution Across Sites , 1999, Journal of Molecular Evolution.
[31] Trevor Bedford,et al. Viral Phylodynamics , 2013, PLoS Comput. Biol..
[32] O. Pybus,et al. A New Evolutionary Model for Hepatitis C Virus Chronic Infection , 2012, PLoS pathogens.
[33] P. Lemey,et al. Rates of Viral Evolution Are Linked to Host Geography in Bat Rabies , 2012, PLoS Pathogens.
[34] Mandev S. Gill,et al. Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. , 2013, Molecular biology and evolution.
[35] T. Layden,et al. Hepatitis C viral dynamics. , 1999, Clinics in liver disease.
[36] Z. Yang,et al. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. , 1998, Molecular biology and evolution.
[37] Eric J. Arts,et al. Changes in Human Immunodeficiency Virus Type 1 Fitness and Genetic Diversity during Disease Progression , 2005, Journal of Virology.
[38] Joseph Heled,et al. The perils of plenty: what are we going to do with all these genes? , 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.
[39] J. Margolick,et al. Consistent Viral Evolutionary Changes Associated with the Progression of Human Immunodeficiency Virus Type 1 Infection , 1999, Journal of Virology.
[40] O. Pybus,et al. Bayesian coalescent inference of past population dynamics from molecular sequences. , 2005, Molecular biology and evolution.
[41] Vladimir N. Minin,et al. A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection , 2012, Bioinform..
[42] M. Volz Erik,et al. A gene genealogy illustrating internode intervals. , 2013 .
[43] Katia Koelle,et al. Rates of coalescence for common epidemiological models at equilibrium , 2012, Journal of The Royal Society Interface.
[44] C. Bustamante,et al. A statistical characterization of consistent patterns of human immunodeficiency virus evolution within infected patients. , 2005, Molecular biology and evolution.