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)

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 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)

Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models. - Veronika Boskova; Sebastian Bonhoeffer; Tanja Stadler (PLoS Comput. Biol., 2014)

Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration. - Alexandra Gavryushkina; David Welch 003; Tanja Stadler; Alexei J. Drummond (PLoS Comput. Biol., 2014)

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)

Phylodynamics on local sexual contact networks. - David A. Rasmussen; Roger D. Kouyos; Huldrych F. Günthard; Tanja Stadler (PLoS Comput. Biol., 2017)

MASCOT: parameter and state inference under the marginal structured coalescent approximation. - Nicola F. Müller; David A. Rasmussen; Tanja Stadler (Bioinform., 2018)

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; et al. (PLoS Comput. Biol., 2019)

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; et al. (PLoS Comput. Biol., 2020)

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; et al. (PLoS Comput. Biol., 2021)

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)

GenSpectrum Chat: Data Exploration in Public Health Using Large Language Models. - Chaoran Chen; Tanja Stadler (CoRR, 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; et al. (PLoS Comput. Biol., 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., 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., 2023)

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)

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)

Artificial intelligence for modelling infectious disease epidemics. - 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; et al. (Nat., 2025)