D
Denise Kühnert
Researcher at Max Planck Society
Publications - 60
Citations - 10257
Denise Kühnert is an academic researcher from Max Planck Society. The author has contributed to research in topics: Population & Viral phylodynamics. The author has an hindex of 25, co-authored 52 publications receiving 7373 citations. Previous affiliations of Denise Kühnert include ETH Zurich & University of Zurich.
Papers
More filters
Journal ArticleDOI
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
Remco R. Bouckaert,Joseph Heled,Denise Kühnert,Timothy G. Vaughan,Chieh-Hsi Wu,Dong Xie,Marc A. Suchard,Andrew Rambaut,Alexei J. Drummond +8 more
TL;DR: BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform.
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
Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)
TL;DR: A model, the Bayesian birth–death skyline plot, is introduced, which explicitly estimates the rate of transmission, recovery, and sampling and thus allows inference of the effective reproductive number directly from genetic data.
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
The contrasting phylodynamics of human influenza B viruses
Dhanasekaran Vijaykrishna,Edward C. Holmes,Udayan Joseph,Mathieu Fourment,Yvonne C. F. Su,Rebecca A. Halpin,Raphael T.C. Lee,Yi-Mo Deng,Vithiagaran Gunalan,Xudong Lin,Timothy B. Stockwell,Nadia Fedorova,Bin Zhou,Natalie Spirason,Denise Kühnert,Veronika Boskova,Tanja Stadler,Anna-Maria Costa,Dominic E. Dwyer,Q. Sue Huang,Lance C. Jennings,William D. Rawlinson,Sheena G. Sullivan,Aeron C. Hurt,Sebastian Maurer-Stroh,David E. Wentworth,Gavin J. D. Smith,Ian G. Barr,Ian G. Barr +28 more
TL;DR: Fundamental differences in the phylodynamics of the two co-circulating lineages of influenza B virus are revealed, showing that their individual dynamics are determined by a complex relationship between virus transmission, age of infection, and receptor binding preference.