Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data
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Tanja Stadler | Alexei J. Drummond | Denise Kühnert | Timothy G. Vaughan | A. Drummond | T. Vaughan | T. Stadler | D. Kühnert
[1] Tanja Stadler,et al. Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods , 2013, Philosophical Transactions of the Royal Society B: Biological Sciences.
[2] T. Leitner,et al. Rapid epidemic spread of HIV type 1 subtype A1 among intravenous drug users in Latvia and slower spread of subtype B among other risk groups. , 2004, AIDS research and human retroviruses.
[3] Greg Ewing,et al. Estimating Population Parameters using the Structured Serial Coalescent with Bayesian MCMC Inference when some Demes are Hidden , 2006, Evolutionary bioinformatics online.
[4] Peter Beerli,et al. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[5] Geoff Nicholls,et al. Using Temporally Spaced Sequences to Simultaneously Estimate Migration Rates, Mutation Rate and Population Sizes in Measurably Evolving Populations , 2004, Genetics.
[6] C. Viboud,et al. Explorer The genomic and epidemiological dynamics of human influenza A virus , 2016 .
[7] S. Otto,et al. Linking the Investigations of Character Evolution and Species Diversification , 2012, The American Naturalist.
[8] S. Guindon,et al. How well can the exponential-growth coalescent approximate constant-rate birth–death population dynamics? , 2015, Proceedings of the Royal Society B: Biological Sciences.
[9] Marc A Suchard,et al. Three roads diverged? Routes to phylogeographic inference. , 2010, Trends in ecology & evolution.
[10] O. Pybus,et al. Unifying the Epidemiological and Evolutionary Dynamics of Pathogens , 2004, Science.
[11] M. Suchard,et al. Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2 , 2014, PLoS pathogens.
[12] Integrating genealogy and epidemiology: the ancestral infection and selection graph as a model for reconstructing host virus histories. , 2005, Theoretical population biology.
[13] D. Rabosky,et al. Model inadequacy and mistaken inferences of trait-dependent speciation. , 2014, Systematic biology.
[14] Graham Jones,et al. Calculations for Multi-type Age-dependent Binary Branching Processes , 2022 .
[15] R. Ribeiro,et al. Agent-based and phylogenetic analyses reveal how HIV-1 moves between risk groups: injecting drug users sustain the heterosexual epidemic in Latvia. , 2012, Epidemics.
[16] Forrest W. Crawford,et al. Unifying the spatial epidemiology and molecular evolution of emerging epidemics , 2012, Proceedings of the National Academy of Sciences.
[17] R. Durrett,et al. The Importance of Being Discrete (and Spatial) , 1994 .
[18] Tanja Stadler,et al. Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration , 2014, PLoS Comput. Biol..
[19] M. Pascual,et al. Global Migration Dynamics Underlie Evolution and Persistence of Human Influenza A (H3N2) , 2010, PLoS pathogens.
[20] Tanja Stadler,et al. Insights into the Early Epidemic Spread of Ebola in Sierra Leone Provided by Viral Sequence Data , 2014, PLoS currents.
[21] Alexei J. Drummond,et al. A Stochastic Simulator of Birth–Death Master Equations with Application to Phylodynamics , 2013, Molecular biology and evolution.
[22] R. Hudson. Gene genealogies and the coalescent process. , 1990 .
[23] Dong Xie,et al. BEAST 2: A Software Platform for Bayesian Evolutionary Analysis , 2014, PLoS Comput. Biol..
[24] Richard G FitzJohn,et al. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. , 2009, Systematic biology.
[25] J. Felsenstein,et al. Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. , 1999, Genetics.
[26] Nicola De Maio,et al. New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation , 2015, PLoS genetics.
[27] Alexei J. Drummond,et al. Bayesian Phylogeography Finds Its Roots , 2009, PLoS Comput. Biol..
[28] Marc A Suchard,et al. Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints , 2013, Philosophical Transactions of the Royal Society B: Biological Sciences.
[29] E. Goldberg,et al. TEMPO AND MODE IN PLANT BREEDING SYSTEM EVOLUTION , 2012, Evolution; international journal of organic evolution.
[30] Christian N. K. Anderson,et al. Serial SimCoal: A population genetics model for data from multiple populations and points in time , 2005, Bioinform..
[31] 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.
[32] C. Wilke,et al. Contact Heterogeneity and Phylodynamics: How Contact Networks Shape Parasite Evolutionary Trees , 2010, Interdisciplinary perspectives on infectious diseases.
[33] S. Ho,et al. Relaxed Phylogenetics and Dating with Confidence , 2006, PLoS biology.
[34] S. Jeffery. Evolution of Protein Molecules , 1979 .
[35] P. Midford,et al. Exploring power and parameter estimation of the BiSSE method for analyzing species diversification , 2013, BMC Evolutionary Biology.
[36] David Welch,et al. Efficient Bayesian inference under the structured coalescent , 2014, Bioinform..
[37] M. Notohara,et al. The coalescent and the genealogical process in geographically structured population , 1990, Journal of mathematical biology.
[38] T. Jukes. CHAPTER 24 – Evolution of Protein Molecules , 1969 .
[39] L. Partridge,et al. Oxford Surveys in Evolutionary Biology , 1991 .
[40] Tanja Stadler,et al. Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model , 2013, Journal of The Royal Society Interface.
[41] Peter E Midford,et al. Estimating a binary character's effect on speciation and extinction. , 2007, Systematic biology.
[42] Peter Beerli,et al. Unified Framework to Evaluate Panmixia and Migration Direction Among Multiple Sampling Locations , 2010, Genetics.