Tanja Stadler

19 papers Journal 19
YearRankTypeTitle / Venue / Authors
2025 J jnl
Artificial intelligence for modelling infectious disease epidemics.
Nat.
Moritz U. G. Kraemer, Joseph L.-H. Tsui, Serina Chang, Spyros Lytras, Mark P. Khurana, Samantha Vanderslott, Sumali Bajaj, Neil Scheidwasser, Jacob Liam Curran-Sebastian, Elizaveta Semenova, Mengyan Zhang, H. Juliette T. Unwin, Oliver J. Watson, Cathal Mills, Abhishek Dasgupta, Luca Ferretti, Samuel V. Scarpino, Etien Koua, Oliver Morgan, Houriiyah Tegally, Ulrich Paquet, Loukas Moutsianas, Christophe Fraser, Neil M. Ferguson, Eric J. Topol, David A. Duchêne, Tanja Stadler, Patricia Kingori, Michael J. Parker, Francesca Dominici, Nigel Shadbolt, Marc A. Suchard, Oliver Ratmann, Seth R. Flaxman, Edward C. Holmes, Manuel Gomez-Rodriguez, Bernhard Schölkopf, Christl A. Donnelly, Oliver G. Pybus, Simon Cauchemez, Samir Bhatt
2024 J jnl
EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering.
PLoS Comput. Biol.
Ciara E. Judge, Timothy G. Vaughan, Timothy Russell, Sam Abbott, Louis du Plessis, Tanja Stadler, Oliver Brady, Sarah Hill
2024 J jnl
Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates.
PLoS Comput. Biol.
Adrian Lison, Sam Abbott, Jana S. Huisman, Tanja Stadler
2023 J jnl
GenSpectrum Chat: Data Exploration in Public Health Using Large Language Models.
CoRR
Chaoran Chen, Tanja Stadler
2023 J jnl
LAPIS is a fast web API for massive open virus sequencing data.
BMC Bioinform.
Chaoran Chen, Alexander Taepper, Fabian Engelniederhammer, Jonas Kellerer, Cornelius Roemer, Tanja Stadler
2023 J jnl
Why are different estimates of the effective reproductive number so different? A case study on COVID-19 in Germany.
PLoS Comput. Biol.
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
2023 J jnl
estimateR: an R package to estimate and monitor the effective reproductive number.
BMC Bioinform.
Jérémie Scire, Jana S. Huisman, Ana Grosu, Daniel C. Angst, Adrian Lison, Jinzhou Li, Marloes H. Maathuis, Sebastian Bonhoeffer, Tanja Stadler
2022 J jnl
CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants.
Bioinform.
Chaoran Chen, Sarah Nadeau, Michael Yared, Philippe Voinov, Ning Xie, Cornelius Roemer, Tanja Stadler
2021 J jnl
Correction: Practical considerations for measuring the effective reproductive number, Rt.
PLoS Comput. Biol.
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
2020 J jnl
Practical considerations for measuring the effective reproductive number, Rt.
PLoS Comput. Biol.
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
2019 J jnl
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.
PLoS Comput. Biol.
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
2018 J jnl
MASCOT: parameter and state inference under the marginal structured coalescent approximation.
Bioinform.
Nicola F. Müller, David A. Rasmussen, Tanja Stadler
2017 J jnl
Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim).
Bioinform.
Alexander Yermanos, Victor Greiff, Nike Julia Krautler, Ulrike Menzel, Andreas Dounas, Enkelejda Miho, Annette Oxenius, Tanja Stadler, Sai T. Reddy
2017 J jnl
Phylodynamics on local sexual contact networks.
PLoS Comput. Biol.
David A. Rasmussen, Roger D. Kouyos, Huldrych F. Günthard, Tanja Stadler
2014 J jnl
Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration.
PLoS Comput. Biol.
Alexandra Gavryushkina, David Welch, Tanja Stadler, Alexei J. Drummond
2014 J jnl
Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models.
PLoS Comput. Biol.
Veronika Boskova, Sebastian Bonhoeffer, Tanja Stadler
2012 J jnl
A Characterization of the Set of Species Trees that Produce Anomalous Ranked Gene Trees.
IEEE ACM Trans. Comput. Biol. Bioinform.
James H. Degnan, Noah A. Rosenberg, Tanja Stadler
2012 J jnl
A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree.
Algorithms Mol. Biol.
Tanja Stadler, James H. Degnan
2012 J jnl
Inferring Epidemic Contact Structure from Phylogenetic Trees.
PLoS Comput. Biol.
Gabriel E. Leventhal, Roger D. Kouyos, Tanja Stadler, Viktor von Wyl, Sabine Yerly, Jürg Böni, Cristina Cellerai, Thomas Klimkait, Huldrych F. Günthard, Sebastian Bonhoeffer