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“Simultaneous Reconstruction of Evolutionary History and Epidemiological Dynamics from Viral Sequences with the Birth–death SIR Model.” Journal of The Royal Society Interface 11 (94): 20131106. “Efficient Bayesian Inference under the Structured Coalescent.” Bioinformatics, April, btu201. Gavryushkina, Alexandra, David Welch, and Alexei J. “BEAST 2: A Software Platform for Bayesian Evolutionary Analysis.” PLo S Comput Biol 10 (4): e1003537. Davies, Neil, Dawn Field, Linda Amaral-Zettler, Mesude Bicak, Sarah Bourlat, Jonathan Coddington, John Deck, et al. “Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012.” Standards in Genomic Sciences 9 (3). Davies, Neil, Dawn Field, Linda Amaral-Zettler, Melody S Clark, John Deck, Alexei Drummond, Daniel P Faith, et al. “The Founding Charter of the Genomic Observatories Network.” Giga Science 3 (March): 2. “Recursive Algorithms for Phylogenetic Tree Counting.” Algorithms for Molecular Biology 8 (1): 26. Bahl, Justin, Scott Krauss, Denise Kühnert, Mathieu Fourment, Garnet Raven, S. Wu, Chieh-Hsi, Marc A Suchard, and Alexei J Drummond. “Bayesian Selection of Nucleotide Substitution Models and Their Site Assignments.” Molecular Biology and Evolution 30 (3): 669–88. “A Stochastic Simulator of Birth-Death Master Equations with Application to Phylodynamics.” Molecular Biology and Evolution 30 (6): 1480–93. Bouckaert, Remco, Philippe Lemey, Michael Dunn, Simon J Greenhill, Alexander V Alekseyenko, Alexei J Drummond, Russell D Gray, Marc A Suchard, and Quentin D Atkinson. “Mapping the Origins and Expansion of the Indo-European Language Family. Kearse, Matthew, Richard Moir, Amy Wilson, Steven Stones-Havas, Matthew Cheung, Shane Sturrock, Simon Buxton, et al. “Geneious Basic: An Integrated and Extendable Desktop Software Platform for the Organization and Analysis of Sequence Data.” Bioinformatics (Oxford, England) 28 (12): 1647–49. @alexeidrummond Google Citations Alexei completed his BSc (1996) and Ph D in Bioinformatics (2002) at the University of Auckland. “b Model Test: Bayesian Phylogenetic Site Model Averaging and Model Comparison.” BMC Evolutionary Biology 17 (1): 42. He then spent 3 years at the University of Oxford doing post-doctoral research in the Department of Statistics and the Department of Zoology before returning to the University of Auckland in 2005 to take up a Lecturership in Bioinformatics in the Department of Computer Science. “How Well Can the Exponential-Growth Coalescent Approximate Constant-Rate Birth-Death Population Dynamics? Biological Sciences / The Royal Society 282 (1806): 20150420. Popinga, Alex, Tim Vaughan, Tanja Stadler, and Alexei J.
“Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics.” Molecular Biology and Evolution 30 (2): 239–43. Stadler, Tanja, Denise Kühnert, Sebastian Bonhoeffer, and Alexei J Drummond. “Birth-Death Skyline Plot Reveals Temporal Changes of Epidemic Spread in HIV and Hepatitis C Virus (HCV).” Proceedings of the National Academy of Sciences of the United States of America 110 (1): 228–33. “Model Averaging and Bayes Factor Calculation of Relaxed Molecular Clocks in Bayesian Phylogenetics.” Molecular Biology and Evolution 29 (2): 751–61.
“Guided Tree Topology Proposals for Bayesian Phylogenetic Inference.” Systematic Biology 61 (1): 1–11.
“Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation.” Systematic Biology 61 (1): 138–49. Kühnert, Denise, Chieh-Hsi Wu, and Alexei J Drummond. “Phylogenetic and Epidemic Modeling of Rapidly Evolving Infectious Diseases.” Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases 11 (8): 1825–41. Shapiro, Beth, Simon Y W Ho, Alexei J Drummond, Marc A Suchard, Oliver G Pybus, and Andrew Rambaut. “A Bayesian Phylogenetic Method to Estimate Unknown Sequence Ages.” Molecular Biology and Evolution 28 (2): 879–87. Drummond, Peter D, Timothy G Vaughan, and Alexei J Drummond. “Extinction Times in Autocatalytic Systems.” The Journal of Physical Chemistry.
“The Space of Ultrametric Phylogenetic Trees.”ar Xiv:1410.3544 [math, Stat], October.
Vaughan, Timothy G., Denise Kühnert, Alex Popinga, David Welch, and Alexei J. Bouckaert, Remco, Joseph Heled, Denise Kühnert, Tim Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A.
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“Bayesian Random Local Clocks, or One Rate to Rule Them All.” BMC Biology 8: 114.