925 citations · 2.4k across the 15 of their papers we have counts for
16 papers
Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates
Adrian Lison, Sam Abbott, Jana Huisman +1
The time-varying effective reproduction number is a widely used indicator of transmission dynamics during infectious disease outbreaks. Timely estimates of can be obtai…
GenSpectrum Chat: Data Exploration in Public Health Using Large Language Models
Chaoran Chen, Tanja Stadler
Introduction: The COVID-19 pandemic highlighted the importance of making epidemiological data and scientific insights easily accessible and explorable for public health agencies, t…
LAPIS is a fast web API for massive open virus sequencing databases
Chaoran Chen, Alexander Taepper, Fabian Engelniederhammer +3
Background: Recent epidemic outbreaks such as the SARS-CoV-2 pandemic and the mpox outbreak in 2022 have demonstrated the value of genomic sequencing data for tracking the origin a…
CoV-Spectrum: Analysis of globally shared SARS-CoV-2 data to Identify and Characterize New Variants
Chaoran Chen, Sarah Nadeau, Michael Yared +4
Summary: The CoV-Spectrum website supports the identification of new SARS-CoV-2 variants of concern and the tracking of known variants. Its flexible amino acid and nucleotide mutat…
Fast likelihood evaluation for multivariate phylogenetic comparative methods: the PCMBase R package
Venelin Mitov, Krzysztof Bartoszek, Georgios Asimomitis +1
We introduce an R package, PCMBase, to rapidly calculate the likelihood for multivariate phylogenetic comparative methods. The package is not specific to particular models but offe…
Bayesian phylogenetic estimation of fossil ages
Alexei J. Drummond, Tanja Stadler
Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of…
Bayesian total evidence dating reveals the recent crown radiation of penguins
Alexandra Gavryushkina, Tracy A. Heath, Daniel T. Ksepka +3
The total-evidence approach to divergence-time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence t…
Inferring epidemiological dynamics with Bayesian coalescent inference: The merits of deterministic and stochastic models
Alex Popinga, Tim Vaughan, Tanja Stadler +1
Estimation of epidemiological and population parameters from molecular sequence data has become central to the understanding of infectious disease dynamics. Various models have bee…
Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration
Alexandra Gavryushkina, David Welch, Tanja Stadler +1
Phylogenetic analyses which include fossils or molecular sequences that are sampled through time require models that allow one sample to be a direct ancestor of another sample. As…
The Fossilized Birth-Death Process: A Coherent Model of Fossil Calibration for Divergence Time Estimation
Tracy A. Heath, John P. Huelsenbeck, Tanja Stadler
Time-calibrated species phylogenies are critical for addressing a wide range of questions in evolutionary biology, such as those that elucidate historical biogeography or uncover p…
Macro-evolutionary models and coalescent point processes: The shape and probability of reconstructed phylogenies
Amaury Lambert, Tanja Stadler
Forward-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow "vertically" as time goes by. Pruning the extinct lineages out of such…
Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model
Denise Kühnert, Tanja Stadler, Timothy G. Vaughan +1
The evolution of RNA viruses such as HIV, Hepatitis C and Influenza virus occurs so rapidly that the viruses' genomes contain information on past ecological dynamics. Hence, we dev…
Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics
Amaury Lambert, Helen K. Alexander, Tanja Stadler
The reconstruction of phylogenetic trees based on viral genetic sequence data sequentially sampled from an epidemic provides estimates of the past transmission dynamics, by fitting…
A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree
Tanja Stadler, James H. Degnan
In this paper, we provide a polynomial time algorithm to calculate the probability of a {\it ranked} gene tree topology for a given species tree, where a ranked tree topology is a…
Distribution of branch lengths and phylogenetic diversity under homogeneous speciation models
Tanja Stadler, Mike Steel
The constant rate birth--death process is a popular null model for speciation and extinction. If one removes extinct and non-sampled lineages, this process induces `reconstructed t…
Branch lengths on Yule trees and the expected loss of phylogenetic diversity
Arne Mooers, Olivier Gascuel, Tanja Stadler +2
Diversification is nested, and early models suggested this could lead to a great deal of evolutionary redundancy in the Tree of Life. This result is based on a particular set of br…