Search filters

List of works by Tanja Stadler

A Practical Guide to Estimating the Heritability of Pathogen Traits

scientific article published on 9 January 2018

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

scientific article published in November 2012

A method for investigating relative timing information on phylogenetic trees

scientific article

A new method for handling missing species in diversification analysis applicable to randomly or nonrandomly sampled phylogenies

scientific article

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

scientific article published on 30 April 2012

A transmissible cancer shifts from emergence to endemism in Tasmanian devils

scientific article published on 01 December 2020

Age-dependent speciation can explain the shape of empirical phylogenies

scientific article

Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity

scientific article (publication date: 12 November 2010)

Analyzing and reconstructing reticulation networks under timing constraints

scientific article published in November 2010

Assessment of Overlap of Phylogenetic Transmission Clusters and Communities in Simple Sexual Contact Networks: Applications to HIV-1.

scientific article published on 10 February 2016

Automatic generation of evolutionary hypotheses using mixed Gaussian phylogenetic models

scientific article published on 02 August 2019

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

scientific article published on 08 April 2019

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

scientific article published on 21 October 2019

Bayesian Inference of Species Networks from Multilocus Sequence Data

scientific article

Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins. ⬇️

scientific article

Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration ⬇️

scientific article

Bayesian phylogenetic estimation of fossil ages

scientific article

Birth-death models and coalescent point processes: the shape and probability of reconstructed phylogenies

scientific article published on 21 October 2013

Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV) ⬇️

scientific article published on December 17, 2012

Branch lengths on birth-death trees and the expected loss of phylogenetic diversity.

scientific article published on 24 August 2011

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

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

scientific article published on 15 August 2019

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

article

Distribution of branch lengths and phylogenetic diversity under homogeneous speciation models

scientific article published on 01 December 2011

Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record

scientific article (publication date: 7 April 2012)

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

scientific article

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

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

scientific article published on 27 November 2020

Epiphytic leafy liverworts diversified in angiosperm-dominated forests

scientific article

Estimating Speciation and Extinction Rates for Phylogenies of Higher Taxa

scientific article published on 25 October 2012

Estimating epidemic incidence and prevalence from genomic data

article

Estimating shifts in diversification rates based on higher-level phylogenies

scientific article

Estimating the basic reproductive number from viral sequence data.

scientific article

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

scientific article published on 04 February 2014

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

scientific article published on 14 May 2014

Fossils and a large molecular phylogeny show that the evolution of species richness, generic diversity, and turnover rates are disconnected.

scientific article

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

scientific article

How Can We Improve Accuracy of Macroevolutionary Rate Estimates? ⬇️

scientific article published on 08 September 2012

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

scientific article

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

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

scientific article published on 2 April 2018

Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification

scientific article

Inference of epidemiological dynamics based on simulated phylogenies using birth-death and coalescent models

scientific article

Inferring Epidemiological Parameters on the Basis of Allele Frequencies ⬇️

scientific article published on 05 May 2011

Inferring epidemic contact structure from phylogenetic trees

scientific article published on 8 March 2012

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

scientific article

Inferring speciation and extinction processes from extant species data ⬇️

scientific article (publication date: 27 September 2011)

Inferring speciation and extinction rates under different sampling schemes

scientific article published on 11 April 2011

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

scientific article published on 01 July 2019

LAPIS is a fast web API for massive open virus sequencing data

scientific article published in 2023

Lineages-through-time plots of neutral models for speciation.

scientific article published on 27 September 2008

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

Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix

scientific article published in 2012

Mammalian phylogeny reveals recent diversification rate shifts ⬇️

scientific article (publication date: 12 April 2011)

Mathematical and computational evolutionary biology (2013).

scientific article published in January 2015

On age and species richness of higher taxa

scientific article

On incomplete sampling under birth-death models and connections to the sampling-based coalescent

scientific article

On the need for mechanistic models in computational genomics and metagenomics

scientific article (publication date: 2013)

On the statistical analysis of single cell lineage trees.

scientific article published on 2 December 2017

Origin, imports and exports of HIV-1 subtype C in South Africa: A historical perspective

scientific article published on 12 July 2016

Origins of Biodiversity--Response

scientific article

Outbreak investigation for toxigenic Corynebacterium diphtheriae wound infections in refugees from Northeast Africa and Syria in Switzerland and Germany by whole genome sequencing

scientific article

Phylodynamics of Enterovirus A71-Associated Hand, Foot, and Mouth Disease in Viet Nam.

scientific article published on 17 June 2015

Phylodynamics on local sexual contact networks

scientific article

Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data

scientific article

Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.

scientific article published on 07 October 2016

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

scientific article published on 4 March 2014

Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load

scientific article published on 30 September 2010

Practical considerations for measuring the effective reproductive number, Rt

scientific article published on 10 December 2020

Quantifying Age-dependent Extinction from Species Phylogenies

scientific article

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

scientific article published on 20 February 2018

Recovering speciation and extinction dynamics based on phylogenies ⬇️

scientific article published on May 13, 2013

Response to Comment on "Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification"

scientific article published in Science

Robust Phylodynamic Analysis of Genetic Sequencing Data from Structured Populations

scientific article published in 2022

Sampling trees from evolutionary models

scientific article published on 28 May 2010

Sampling-through-time in birth-death trees

scientific article

Simulating Trees with a Fixed Number of Extant Species ⬇️

scientific article published on April 11, 2011

Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model

scientific article published on 26 February 2014

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

scientific article published on 12 May 2014

Species-specific diversification

scientific article published on 01 July 2019

Swapping Birth and Death: Symmetries and Transformations in Phylodynamic Models

scientific article published on 01 September 2019

Taming the BEAST - A community teaching material resource for BEAST 2.

scientific article

Testing the spatial and temporal framework of speciation in an ancient lake species flock: the leech genus Dina (Hirudinea: Erpobdellidae) in Lake Ohrid

article

The Structured Coalescent and its Approximations

scientific article

The abrupt climate change at the Eocene-Oligocene boundary and the emergence of South-East Asia triggered the spread of sapindaceous lineages

scientific article (publication date: July 2013)

The contrasting phylodynamics of human influenza B viruses.

scientific article

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

scientific article published on 14 March 2018

The fossilized birth-death process for coherent calibration of divergence-time estimates

scientific article

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

scientific article

The probability distribution of ranked gene trees on a species tree

scientific article published on 31 October 2011

The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology

article

Total-Evidence Dating under the Fossilized Birth-Death Process

scientific article

Tracing Antibody Repertoire Evolution by Systems Phylogeny

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

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

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

scientific article

Tuberculosis outbreak investigation using phylodynamic analysis

scholarly article published by David Stucki in 2018

UNEXPECTEDLY MANY EXTINCT HOMININS

scientific article

Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods ⬇️

scientific article (publication date: 19 March 2013)

Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission

scientific article (publication date: 2014)

Vaccination of dogs in an African city interrupts rabies transmission and reduces human exposure

scientific article published in December 2017

Paulina is supported by:

About Paulina

Help