List of works - Tanja Stadler

Inferring Epidemiological Parameters on the Basis of Allele Frequencies

scientific article published on 05 May 2011

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

Social meets molecular: Combining phylogenetic and latent class analyses to understand HIV-1 transmission in Switzerland

scientific article published on 12 May 2014

Quantifying Age-dependent Extinction from Species Phylogenies

scientific article

Estimating Speciation and Extinction Rates for Phylogenies of Higher Taxa

scientific article published on 25 October 2012

The probability distribution of ranked gene trees on a species tree

scientific article published on 31 October 2011

Distribution of branch lengths and phylogenetic diversity under homogeneous speciation models

scientific article published on 01 December 2011

The fossilized birth-death model for the analysis of stratigraphic range data under different speciation modes

scientific article published on 14 March 2018

Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics

scientific article published on 20 February 2018

Exact vs. approximate computation: reconciling different estimates of Mycobacterium tuberculosis epidemiological parameters

scientific article published on 04 February 2014

Inferring epidemiological dynamics with Bayesian coalescent inference: the merits of deterministic and stochastic models

scientific article

The influence of phylodynamic model specifications on parameter estimates of the Zika virus epidemic

scientific article

Impact of the tree prior on estimating clock rates during epidemic outbreaks

scientific article published on 2 April 2018

Getting to the root of epidemic spread with phylodynamic analysis of genomic data

scientific article

Phylodynamics on local sexual contact networks

scientific article

Closing the gap between palaeontological and neontological speciation and extinction rate estimates

scientific article published in Nature Communications

Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim).

scientific article published on 31 August 2017

Transmission of ESBL-producing Enterobacteriaceae and their mobile genetic elements-identification of sources by whole genome sequencing: study protocol for an observational study in Switzerland.

scientific article published on 17 February 2018

How well can the exponential-growth coalescent approximate constant-rate birth-death population dynamics?

scientific article

UNEXPECTEDLY MANY EXTINCT HOMININS

scientific article

Bayesian phylogenetic estimation of fossil ages

scientific article

A characterization of the set of species trees that produce anomalous ranked gene trees.

scientific article published in November 2012

A Practical Guide to Estimating the Heritability of Pathogen Traits

scientific article published on 9 January 2018

Tuberculosis outbreak investigation using phylodynamic analysis

scholarly article published by David Stucki in 2018

Does Gene Tree Discordance Explain the Mismatch between Macroevolutionary Models and Empirical Patterns of Tree Shape and Branching Times?

scientific article

Estimating shifts in diversification rates based on higher-level phylogenies

scientific article

Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics

scientific article published on 4 March 2014

Tracing Antibody Repertoire Evolution by Systems Phylogeny

scholarly article by Alexander Dimitri Yermanos et al published 2 October 2018 in Frontiers in Immunology

A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree

scientific article published on 30 April 2012

On the statistical analysis of single cell lineage trees.

scientific article published on 2 December 2017

Origins of Biodiversity--Response

scientific article

Finding the best resolution for the Kingman-Tajima coalescent: theory and applications

scientific article published on 14 May 2014

Automatic generation of evolutionary hypotheses using mixed Gaussian phylogenetic models

scientific article published on 02 August 2019

Detection of HIV transmission clusters from phylogenetic trees using a multi-state birth-death model

article

Analyzing and reconstructing reticulation networks under timing constraints

scientific article published in November 2010

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

scientific article published on 01 July 2019

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

scientific article published on 15 August 2019

Earlier Initiation of Antiretroviral Treatment Coincides With an Initial Control of the HIV-1 Sub-Subtype F1 Outbreak Among Men-Having-Sex-With-Men in Flanders, Belgium

article

Swapping Birth and Death: Symmetries and Transformations in Phylodynamic Models

scientific article published on 01 September 2019

TreeSimGM: Simulating phylogenetic trees under general Bellman-Harris models with lineage-specific shifts of speciation and extinction in R.

scientific article

Mathematical and computational evolutionary biology (2013).

scientific article published in January 2015

Practical considerations for measuring the effective reproductive number, Rt

scientific article published on 10 December 2020

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

scientific article published on 21 October 2019

Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020

scientific article published on 27 November 2020

The origin and early spread of SARS-CoV-2 in Europe

Identification of influenza urban transmission patterns by geographical, epidemiological and whole genome sequencing data: protocol for an observational study

scientific article published on 20 August 2019

Bayesian phylodynamic inference of multi-type population trajectories using genomic data

Integrating Transmission Dynamics and Pathogen Evolution Through a Bayesian Approach

A transmissible cancer shifts from emergence to endemism in Tasmanian devils

scientific article published on 01 December 2020

List of works by Tanja Stadler

Inferring Epidemiological Parameters on the Basis of Allele Frequencies

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

Social meets molecular: Combining phylogenetic and latent class analyses to understand HIV-1 transmission in Switzerland

Quantifying Age-dependent Extinction from Species Phylogenies

Estimating Speciation and Extinction Rates for Phylogenies of Higher Taxa

The probability distribution of ranked gene trees on a species tree

Distribution of branch lengths and phylogenetic diversity under homogeneous speciation models

The fossilized birth-death model for the analysis of stratigraphic range data under different speciation modes

Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics

Exact vs. approximate computation: reconciling different estimates of Mycobacterium tuberculosis epidemiological parameters

Inferring epidemiological dynamics with Bayesian coalescent inference: the merits of deterministic and stochastic models

The influence of phylodynamic model specifications on parameter estimates of the Zika virus epidemic

Impact of the tree prior on estimating clock rates during epidemic outbreaks

Getting to the root of epidemic spread with phylodynamic analysis of genomic data

Phylodynamics on local sexual contact networks

Closing the gap between palaeontological and neontological speciation and extinction rate estimates

Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim).

Transmission of ESBL-producing Enterobacteriaceae and their mobile genetic elements-identification of sources by whole genome sequencing: study protocol for an observational study in Switzerland.

How well can the exponential-growth coalescent approximate constant-rate birth-death population dynamics?

UNEXPECTEDLY MANY EXTINCT HOMININS

Bayesian phylogenetic estimation of fossil ages

A characterization of the set of species trees that produce anomalous ranked gene trees.

A Practical Guide to Estimating the Heritability of Pathogen Traits

Tuberculosis outbreak investigation using phylodynamic analysis

Does Gene Tree Discordance Explain the Mismatch between Macroevolutionary Models and Empirical Patterns of Tree Shape and Branching Times?

Estimating shifts in diversification rates based on higher-level phylogenies

Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics

Tracing Antibody Repertoire Evolution by Systems Phylogeny

A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree

On the statistical analysis of single cell lineage trees.

Origins of Biodiversity--Response

Finding the best resolution for the Kingman-Tajima coalescent: theory and applications

Automatic generation of evolutionary hypotheses using mixed Gaussian phylogenetic models

Detection of HIV transmission clusters from phylogenetic trees using a multi-state birth-death model

Analyzing and reconstructing reticulation networks under timing constraints

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

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

Earlier Initiation of Antiretroviral Treatment Coincides With an Initial Control of the HIV-1 Sub-Subtype F1 Outbreak Among Men-Having-Sex-With-Men in Flanders, Belgium

Swapping Birth and Death: Symmetries and Transformations in Phylodynamic Models

TreeSimGM: Simulating phylogenetic trees under general Bellman-Harris models with lineage-specific shifts of speciation and extinction in R.

Mathematical and computational evolutionary biology (2013).

Practical considerations for measuring the effective reproductive number, Rt

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020

The origin and early spread of SARS-CoV-2 in Europe

Identification of influenza urban transmission patterns by geographical, epidemiological and whole genome sequencing data: protocol for an observational study

Bayesian phylodynamic inference of multi-type population trajectories using genomic data

Integrating Transmission Dynamics and Pathogen Evolution Through a Bayesian Approach

A transmissible cancer shifts from emergence to endemism in Tasmanian devils

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