Tanja Stadler

According to our database, Tanja Stadler authored at least 18 papers between 2012 and 2024.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2024

Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates.

Adrian Lison, Sam Abbott, Jana S. Huisman, Tanja Stadler

PLoS Comput. Biol., 2024

EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering.

Ciara E. Judge, Timothy G. Vaughan, Timothy Russell, Sam Abbott, Louis du Plessis, Tanja Stadler, Oliver Brady, Sarah Hill

PLoS Comput. Biol., 2024

2023

estimateR: an R package to estimate and monitor the effective reproductive number.

Jérémie Scire, Jana S. Huisman, Ana Grosu, Daniel C. Angst, Adrian Lison, Jinzhou Li, Marloes H. Maathuis, Sebastian Bonhoeffer, Tanja Stadler

BMC Bioinform., December, 2023

LAPIS is a fast web API for massive open virus sequencing data.

Chaoran Chen, Alexander Taepper, Fabian Engelniederhammer, Jonas Kellerer, Cornelius Roemer, Tanja Stadler

BMC Bioinform., December, 2023

Why are different estimates of the effective reproductive number so different? A case study on COVID-19 in Germany.

Elisabeth K. Brockhaus, Daniel Wolffram, Tanja Stadler, Michael Osthege, Tanmay Mitra, Jonas M. Littek, Ekaterina A. Krymova, Anna J. Klesen, Jana S. Huisman, Stefan Heyder, Laura Marie Helleckes, Matthias an der Heiden, Sebastian Funk, Sam Abbott, Johannes Bracher

PLoS Comput. Biol., November, 2023

GenSpectrum Chat: Data Exploration in Public Health Using Large Language Models.

Chaoran Chen, Tanja Stadler

CoRR, 2023

2022

CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants.

Chaoran Chen, Sarah Nadeau, Michael Yared, Philippe Voinov, Ning Xie, Cornelius Roemer, Tanja Stadler

Bioinform., 2022

2021

Correction: Practical considerations for measuring the effective reproductive number, Rt.

Katelyn M. Gostic, Lauren McGough, Edward B. Baskerville, Sam Abbott, Keya Joshi, Christine Tedijanto, Rebecca Kahn, Rene Niehus, James A. Hay, Pablo M. De Salazar, Joel Hellewell, Sophie Meakin, James D. Munday, Nikos I. Bosse, Katharine Sherratt, Robin N. Thompson, Laura F. White, Jana S. Huisman, Jérémie Scire, Sebastian Bonhoeffer, Tanja Stadler, Jacco Wallinga, Sebastian Funk, Marc Lipsitch, Sarah Cobey

PLoS Comput. Biol., 2021

2020

Practical considerations for measuring the effective reproductive number, Rt.

Katelyn M. Gostic, Lauren McGough, Edward B. Baskerville, Sam Abbott, Keya Joshi, Christine Tedijanto, Rebecca Kahn, Rene Niehus, James A. Hay, Pablo M. De Salazar, Joel Hellewell, Sophie Meakin, James D. Munday, Nikos I. Bosse, Katharine Sherratt, Robin N. Thompson, Laura F. White, Jana S. Huisman, Jérémie Scire, Sebastian Bonhoeffer, Tanja Stadler, Jacco Wallinga, Sebastian Funk, Marc Lipsitch, Sarah Cobey

PLoS Comput. Biol., 2020

2019

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

PLoS Comput. Biol., 2019

2018

MASCOT: parameter and state inference under the marginal structured coalescent approximation.

Nicola F. Müller, David A. Rasmussen, Tanja Stadler

Bioinform., 2018

2017

Phylodynamics on local sexual contact networks.

David A. Rasmussen, Roger D. Kouyos, Huldrych F. Günthard, Tanja Stadler

PLoS Comput. Biol., 2017

Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim).

Alexander Yermanos, Victor Greiff, Nike Julia Krautler, Ulrike Menzel, Andreas Dounas, Enkelejda Miho, Annette Oxenius, Tanja Stadler, Sai T. Reddy

Bioinform., 2017

2014

Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration.

Alexandra Gavryushkina, David Welch, Tanja Stadler, Alexei J. Drummond

PLoS Comput. Biol., 2014

Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models.

Veronika Boskova, Sebastian Bonhoeffer, Tanja Stadler

PLoS Comput. Biol., 2014

2012

A Characterization of the Set of Species Trees that Produce Anomalous Ranked Gene Trees.

James H. Degnan, Noah A. Rosenberg, Tanja Stadler

IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Inferring Epidemic Contact Structure from Phylogenetic Trees.

Gabriel E. Leventhal, Roger D. Kouyos, Tanja Stadler, Viktor von Wyl, Sabine Yerly, Jürg Böni, Cristina Cellerai, Thomas Klimkait, Huldrych F. Günthard, Sebastian Bonhoeffer

PLoS Comput. Biol., 2012

A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree.

Tanja Stadler, James H. Degnan

Algorithms Mol. Biol., 2012