Online Bayesian Phylodynamic Inference in BEAST with Application to Epidemic Reconstruction
暂无分享,去创建一个
Philippe Lemey | Guy Baele | Marc A. Suchard | Andrew Rambaut | Mandev S. Gill | M. Suchard | P. Lemey | A. Rambaut | G. Baele | M. Gill
[1] Alexandros Stamatakis,et al. PUmPER: phylogenies updated perpetually , 2014, Bioinform..
[2] Simon Whelan,et al. New approaches to phylogenetic tree search and their application to large numbers of protein alignments. , 2007, Systematic biology.
[3] Bradley P. Carlin,et al. Markov Chain Monte Carlo in Practice: A Roundtable Discussion , 1998 .
[4] Trevor Bedford,et al. Virus genomes reveal factors that spread and sustained the Ebola epidemic , 2017, Nature.
[5] Vu C. Dinh,et al. Effective Online Bayesian Phylogenetics via Sequential Monte Carlo with Guided Proposals , 2017, bioRxiv.
[6] Timothy J. Robinson,et al. Sequential Monte Carlo Methods in Practice , 2003 .
[7] Marc A Suchard,et al. Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates. , 2016, Systematic biology.
[8] S. Ho,et al. Relaxed Phylogenetics and Dating with Confidence , 2006, PLoS biology.
[9] N. R. Faria,et al. Establishment and cryptic transmission of Zika virus in Brazil and the Americas , 2017, Nature.
[10] S.. Sampling theory for neutral alleles in a varying environment , 2003 .
[11] S. Jeffery. Evolution of Protein Molecules , 1979 .
[12] O. J. Dunn. Multiple Comparisons among Means , 1961 .
[13] Guy Baele,et al. The epidemic dynamics of hepatitis C virus subtypes 4a and 4d in Saudi Arabia , 2017, Scientific Reports.
[14] Richard A Neher,et al. TreeTime: Maximum-likelihood phylodynamic analysis , 2017, bioRxiv.
[15] Arnaud Doucet,et al. Bayesian Phylogenetic Inference Using a Combinatorial Sequential Monte Carlo Method , 2015 .
[16] M. Plummer,et al. CODA: convergence diagnosis and output analysis for MCMC , 2006 .
[17] M. Suchard,et al. Gradients do grow on trees: a linear-time ${\cal O}\hspace{-0.2em}\left( N \right)$-dimensional gradient for statistical phylogenetics , 2019, 1905.12146.
[18] Forrest W. Crawford,et al. Unifying the spatial epidemiology and molecular evolution of emerging epidemics , 2012, Proceedings of the National Academy of Sciences.
[19] Guy Baele,et al. Recent advances in computational phylodynamics. , 2018, Current opinion in virology.
[20] Babak Shahbaba,et al. An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics , 2014, Bioinform..
[21] H. Kishino,et al. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA , 2005, Journal of Molecular Evolution.
[22] Guy Baele,et al. Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak , 2018, Nature Communications.
[23] Rachel S. G. Sealfon,et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak , 2014, Science.
[24] Xiang Ji,et al. Gradients do grow on trees: a linear-time 𝒪 (N)-dimensional gradient for statistical phylogenetics. , 2020, Molecular biology and evolution.
[25] Gareth O. Roberts,et al. Convergence assessment techniques for Markov chain Monte Carlo , 1998, Stat. Comput..
[26] Benoit Morel,et al. EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences , 2018, bioRxiv.
[27] Anthony J. Geneva,et al. RWTY (R We There Yet): An R Package for Examining Convergence of Bayesian Phylogenetic Analyses. , 2017, Molecular biology and evolution.
[28] Marco A. R. Ferreira,et al. Bayesian analysis of elapsed times in continuous‐time Markov chains , 2008 .
[29] J. Huelsenbeck,et al. Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics. , 2008, Systematic biology.
[30] Guy Baele,et al. Emerging Concepts of Data Integration in Pathogen Phylodynamics , 2016, Systematic biology.
[31] Cécile Viboud,et al. Global migration of influenza A viruses in swine , 2015, Nature Communications.
[32] M. Suchard,et al. The early spread and epidemic ignition of HIV-1 in human populations , 2014, Science.
[33] Paul Kellam,et al. Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases , 2016, Virus evolution.
[34] Alexei J. Drummond,et al. Bayesian Phylogeography Finds Its Roots , 2009, PLoS Comput. Biol..
[35] Alexandros Stamatakis,et al. Methods for automatic reference trees and multilevel phylogenetic placement , 2018, bioRxiv.
[36] Z. Yang,et al. Among-site rate variation and its impact on phylogenetic analyses. , 1996, Trends in ecology & evolution.
[37] Radford M. Neal. MCMC Using Hamiltonian Dynamics , 2011, 1206.1901.
[38] J. Felsenstein,et al. A Hidden Markov Model approach to variation among sites in rate of evolution. , 1996, Molecular biology and evolution.
[39] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[40] Olivier Gascuel,et al. Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle , 2002, WABI.
[41] Karthik Gangavarapu,et al. Genome sequencing reveals Zika virus diversity and spread in the Americas , 2017, bioRxiv.
[42] Trevor Bedford,et al. Nextstrain: real-time tracking of pathogen evolution , 2017, bioRxiv.
[43] T. Jukes. CHAPTER 24 – Evolution of Protein Molecules , 1969 .
[44] Nicolas Lartillot,et al. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating , 2009, Bioinform..
[45] M. Suchard,et al. Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2 , 2014, PLoS pathogens.
[46] Trevor Bedford,et al. Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone , 2015, Cell.
[47] Liangliang Wang,et al. An Annealed Sequential Monte Carlo Method for Bayesian Phylogenetics. , 2018, Systematic biology.
[48] J. Felsenstein,et al. PHYLIP: phylogenetic inference package version 3.5c. Distributed over the Internet , 1993 .
[49] Robert M. Miura,et al. Some mathematical questions in biology : DNA sequence analysis , 1986 .
[50] J. Felsenstein. Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.
[51] David A. Matthews,et al. Real-time, portable genome sequencing for Ebola surveillance , 2016, Nature.
[52] S. Tavaré. Some probabilistic and statistical problems in the analysis of DNA sequences , 1986 .
[53] Daniel L. Ayres,et al. BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics , 2019, Systematic biology.
[54] Daniel L. Ayres,et al. BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics , 2011, Systematic biology.
[55] Michael Worobey,et al. A synchronized global sweep of the internal genes of modern avian influenza virus , 2014, Nature.
[56] Daniel J. Wilson,et al. Sequential Monte Carlo with transformations , 2016, Statistics and Computing.
[57] Michael I. Jordan,et al. Phylogenetic Inference via Sequential Monte Carlo , 2012, Systematic biology.
[58] E. Virginia Armbrust,et al. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree , 2010, BMC Bioinformatics.
[59] Vu C. Dinh,et al. Online Bayesian Phylogenetic Inference: Theoretical Foundations via Sequential Monte Carlo , 2016, Systematic biology.
[60] Daniel L. Ayres,et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 , 2018, Virus evolution.
[61] Guy Baele,et al. Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST , 2017, Bioinform..
[62] Mandev S. Gill,et al. Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. , 2013, Molecular biology and evolution.