T. Stadler

Integrating Transmission Dynamics and Pathogen Evolution Through a Bayesian Approach

This paper introduces the Transmission Tree (TnT) model to improve understanding of epidemic dynamics by integrating pathogen gene sequences and clinical data through a Bayesian approach.

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

EpiFusion improves estimation of outbreak dynamics by integrating phylodynamic and epidemiological data using particle filtering, enhancing accuracy and efficiency in large, poorly sampled epidemics.

HIV co-infection is associated with reduced Mycobacterium tuberculosis transmissibility in sub-Saharan Africa

This study uses genomic data and a Bayesian phylodynamic model to show HIV co-infection reduces Mycobacterium tuberculosis transmissibility in sub-Saharan Africa.

Skyline fossilized birth-death model is robust to violations of sampling assumptions in total-evidence dating

This paper shows that the skyline FBD model provides more robust age estimates in total-evidence dating by reducing deep root attraction effects caused by sampling biases.

Robust phylodynamic analysis of genetic sequencing data from structured populations

The paper improves the bdmm algorithm in BEAST 2 to handle larger genetic datasets, enabling more precise phylodynamic analysis of structured populations.

Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus H5N8 in Europe

This study uses phylodynamic analysis of H5N8 virus sequences to quantify transmission dynamics between poultry farms and wild birds in Europe during the 2016-17 epidemic and identifies key drivers of cross-border spread.

Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales

This paper introduces a new evolutionary model, FBD-MSC, that integrates genealogical and fossilization processes to improve divergence time estimates in Caninae.

Joint inference of migration and reassortment patterns for viruses with segment genomes

This paper extends the structured coalescent to account for reassortment in segmented viruses, showing it leads to different estimates of population sizes, migration, and clock rates compared to models without reassortment.

Joint inference of species histories and gene flow

The paper introduces a method to infer species trees while accounting for gene flow, showing improved accuracy in species history reconstruction for mosquitoes.

A skyline birth-death process for inferring the population size from a reconstructed tree with occurrences

This paper introduces a skyline birth-death process to infer population size changes over time using occurrence data and phylogenetic trees, applied to epidemiology and macroevolution.

Characterising the epidemic spread of Influenza A/H3N2 within a city through phylogenetics

The paper uses genetic sequence data and patient metadata to analyze local influenza transmission dynamics in Basel, Switzerland, finding that temperature trends correlate with transmission and that elderly and school children drive different transmission networks.

High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters

This study maps influenza transmission in a city at high resolution, finding socioeconomic factors like income influence infection patterns and vaccination rates, independent of population density.

Mouse-specific but infection-unspecific IgM repertoire fingerprint following viral infection

This study compares IgM antibody repertoires in blood and bone marrow plasma cells of mice after viral infection, finding that they are mouse-specific but not infection-specific.

Clinical extended-spectrum beta-lactamase antibiotic resistance plasmids have diverse transfer rates and can spread in the absence of antibiotic selection

This study quantifies the conjugative transfer dynamics of ESBL plasmids in vitro and in vivo, showing variation in transfer efficiency and potential for predicting plasmid spread.

Ignoring fossil age uncertainty leads to inaccurate topology and divergence times in time calibrated tree inference

This study shows that ignoring fossil age uncertainty leads to less accurate tree topologies and divergence times, especially with high character sampling.

Improved multi-type birth-death phylodynamic inference in BEAST 2

The paper improves the multi-type birth-death model in BEAST 2 to handle larger datasets and reports results on Influenza A virus migration and seasonal dynamics.

The ancestral population size conditioned on the reconstructed phylogenetic tree with occurrence data

The paper derives the conditional probability distribution of ancestral population size given a reconstructed phylogenetic tree and occurrence data, with applications in epidemiology and macroevolution.

Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses

This study uses Bayesian inference to analyze reassortment networks in human influenza viruses, finding that reassortment events occur more frequently on fitter parts of the network.

The probability distribution of the reconstructed phylogenetic tree with occurrence data

The paper derives a probability distribution for phylogenetic trees with occurrence data, enabling parameter estimation in epidemiology and macroevolution.

Coupling adaptive molecular evolution to phylodynamics using fitness-dependent birth-death models

The paper introduces a new birth-death model that links molecular evolution to phylodynamics by estimating lineage fitness and mutation effects from phylogenetic branching patterns.

Swapping Birth and Death: Symmetries and Transformations in Phylodynamic Models

This paper identifies and formalizes symmetries in birth-death models by swapping birth and death rates, showing their preservation under sampling and relevance to phylodynamic inference methods.

Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth-death process

This study shows that ignoring stratigraphic age uncertainty in fossil data leads to biased divergence time estimates under the fossilized birth-death process, and recommends explicitly incorporating age uncertainty.

BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis

The paper describes new developments in the BEAST 2.5 software platform for Bayesian evolutionary analysis, expanding joint inference over multiple data types and complex phylodynamics.

Parallel Likelihood Calculation for Phylogenetic Comparative Models: the SPLITT C++ Library

The paper introduces SPLITT, a C++ library for parallelizing phylogenetic comparative model inference, achieving significant speed-ups in likelihood calculations for Gaussian models.

A Multi-State Birth-Death model for Bayesian inference of lineage-specific birth and death rates

The paper introduces a multi-state birth-death model to estimate lineage-specific speciation and extinction rates without requiring prior trait hypotheses, showing its effectiveness on simulated and empirical datasets.

Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations

The paper introduces a method to infer time-dependent migration and coalescence patterns in structured populations using predictors and applies it to Ebola virus data.

Adaptive Reduction of Male Gamete Number in a Selfing Species

The paper uses GWAS to show polygenic selection on pollen number in Arabidopsis thaliana, identifies a gene affecting pollen number, and validates its causal role using CRISPR-Cas9 mutants.

The Structured Coalescent and its Approximations

The paper presents an exact solution to the structured coalescent and improves approximations for phylogeographic analysis without inferring ancestral migration histories.

Bayesian Inference of Species Networks from Multilocus Sequence Data

This paper introduces a Bayesian method to infer species networks and gene trees from multilocus sequence data, demonstrating its ability to detect reticulate evolution in spruce species.

MASCOT: Parameter and state inference under the marginal structured coalescent approximation

The paper introduces MASCOT, an algorithm that improves parameter and state inference under the structured coalescent approximation, enabling analysis of larger datasets with more states.