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Alexandra Gavryushkina
Researcher at University of Otago
Publications - 12
Citations - 3087
Alexandra Gavryushkina is an academic researcher from University of Otago. The author has contributed to research in topics: Phylogenetic tree & Software design. The author has an hindex of 9, co-authored 12 publications receiving 1828 citations. Previous affiliations of Alexandra Gavryushkina include Swiss Institute of Bioinformatics & ETH Zurich.
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Journal ArticleDOI
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.
Remco R. Bouckaert,Remco R. Bouckaert,Timothy G. Vaughan,Timothy G. Vaughan,Joëlle Barido-Sottani,Joëlle Barido-Sottani,Sebastián Duchêne,Mathieu Fourment,Alexandra Gavryushkina,Joseph Heled,Graham Jones,Denise Kühnert,Nicola De Maio,Michael Matschiner,Fábio K. Mendes,Nicola F. Müller,Nicola F. Müller,Huw A. Ogilvie,Louis du Plessis,Alex Popinga,Andrew Rambaut,David A. Rasmussen,Igor Siveroni,Marc A. Suchard,Chieh-Hsi Wu,Dong Xie,Chi Zhang,Tanja Stadler,Tanja Stadler,Alexei J. Drummond +29 more
TL;DR: A series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release are described.
Journal ArticleDOI
Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration
TL;DR: A Bayesian Markov Chain Monte Carlo algorithm is developed and implemented to infer sampled ancestor trees, that is, trees in which sampled individuals can be direct ancestors of other sampled individuals, and applies its phylogenetic inference accounting for sampled ancestors to epidemiological data.
Journal ArticleDOI
Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins
Alexandra Gavryushkina,Tracy A. Heath,Daniel T. Ksepka,Tanja Stadler,David Welch,Alexei J. Drummond +5 more
TL;DR: The FBD model and a model of morphological trait evolution are incorporated into a Bayesian total‐evidence approach to dating species phylogenies and it is shown that including stem‐fossil diversity can greatly improve the estimates of the divergence times of crown taxa.
Posted ContentDOI
BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis
Remco R. Bouckaert,Timothy G. Vaughan,Joëlle Barido-Sottani,Sebastián Duchêne,Mathieu Fourment,Alexandra Gavryushkina,Joseph Heled,Graham Jones,Denise Kühnert,Nicola De Maio,Michael Matschiner,Fábio K. Mendes,Nicola F. Müller,Huw A. Ogilvie,Louis du Plessis,Alex Popinga,Andrew Rambaut,David A. Rasmussen,Igor Siveroni,Marc A. Suchard,Chieh-Hsi Wu,Dong Xie,Chi Zhang,Tanja Stadler,Alexei J. Drummond +24 more
TL;DR: The full range of new tools and models available on the BEAST 2.5 platform are described, which expand joint evolutionary inference in many new directions, especially for joint inference over multiple data types, non-tree models and complex phylodynamics.
Journal ArticleDOI
Sources of HIV infection among men having sex with men and implications for prevention
Oliver Ratmann,Ard van Sighem,Daniela Bezemer,Alexandra Gavryushkina,Suzanne Jurriaans,Annemarie M. J. Wensing,Frank de Wolf,Peter Reiss,Christophe Fraser,Athena observational cohort +9 more
TL;DR: Making ART for pre-exposure prophylaxis available worldwide, and especially in countries with high retention in care and high ART coverage among infected MSM, is supported.