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2020 – today
- 2024
[j17]Adrian Lison
, Sam Abbott, Jana S. Huisman, Tanja Stadler:
Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates. PLoS Comput. Biol. 20(4): 1012021 (2024)- [j16]Ciara E. Judge, Timothy G. Vaughan, Timothy Russell, Sam Abbott, Louis du Plessis, Tanja Stadler, Oliver Brady, Sarah Hill:
EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering. PLoS Comput. Biol. 20(11): 1012528 (2024) - 2023
- [j15]Chaoran Chen, Alexander Taepper, Fabian Engelniederhammer, Jonas Kellerer, Cornelius Roemer, Tanja Stadler:
LAPIS is a fast web API for massive open virus sequencing data. BMC Bioinform. 24(1): 232 (2023) - [j14]Jérémie Scire, Jana S. Huisman, Ana Grosu, Daniel C. Angst, Adrian Lison, Jinzhou Li, Marloes H. Maathuis, Sebastian Bonhoeffer, Tanja Stadler:
estimateR: an R package to estimate and monitor the effective reproductive number. BMC Bioinform. 24(1): 310 (2023) - [j13]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:
Why are different estimates of the effective reproductive number so different? A case study on COVID-19 in Germany. PLoS Comput. Biol. 19(11) (2023) - [i1]Chaoran Chen, Tanja Stadler:
GenSpectrum Chat: Data Exploration in Public Health Using Large Language Models. CoRR abs/2305.13821 (2023) - 2022
- [j12]Chaoran Chen, Sarah Nadeau, Michael Yared, Philippe Voinov, Ning Xie, Cornelius Roemer, Tanja Stadler:
CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants. Bioinform. 38(6): 1735-1737 (2022) - 2021
- [j11]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:
Correction: Practical considerations for measuring the effective reproductive number, Rt. PLoS Comput. Biol. 17(12) (2021) - 2020
- [j10]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:
Practical considerations for measuring the effective reproductive number, Rt. PLoS Comput. Biol. 16(12) (2020)
2010 – 2019
- 2019
- [j9]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:
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 15(4) (2019) - 2018
- [j8]Nicola F. Müller, David A. Rasmussen, Tanja Stadler:
MASCOT: parameter and state inference under the marginal structured coalescent approximation. Bioinform. 34(22): 3843-3848 (2018) - 2017
- [j7]Alexander Yermanos, Victor Greiff, Nike Julia Krautler, Ulrike Menzel, Andreas Dounas, Enkelejda Miho, Annette Oxenius, Tanja Stadler, Sai T. Reddy:
Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim). Bioinform. 33(24): 3938-3946 (2017) - [j6]David A. Rasmussen, Roger D. Kouyos, Huldrych F. Günthard, Tanja Stadler:
Phylodynamics on local sexual contact networks. PLoS Comput. Biol. 13(3) (2017) - 2014
- [j5]Veronika Boskova, Sebastian Bonhoeffer, Tanja Stadler:
Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models. PLoS Comput. Biol. 10(11) (2014) - [j4]Alexandra Gavryushkina, David Welch, Tanja Stadler, Alexei J. Drummond:
Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration. PLoS Comput. Biol. 10(12) (2014) - 2012
- [j3]Tanja Stadler, James H. Degnan:
A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree. Algorithms Mol. Biol. 7: 7 (2012) - [j2]Gabriel E. Leventhal, Roger D. Kouyos, Tanja Stadler, Viktor von Wyl, Sabine Yerly, Jürg Böni, Cristina Cellerai, Thomas Klimkait, Huldrych F. Günthard, Sebastian Bonhoeffer:
Inferring Epidemic Contact Structure from Phylogenetic Trees. PLoS Comput. Biol. 8(3) (2012) - [j1]James H. Degnan, Noah A. Rosenberg, Tanja Stadler:
A Characterization of the Set of Species Trees that Produce Anomalous Ranked Gene Trees. IEEE ACM Trans. Comput. Biol. Bioinform. 9(6): 1558-1568 (2012)
Coauthor Index
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