Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study

Chains of transmission and control of Ebola virus disease in Conakry, Guinea, in 2014: an observational study

(2015) Ousmane Faye et al.   LANCET INFECTIOUS DISEASES

Phylodynamic Inference with Kernel ABC and Its Application to HIV Epidemiology

(2015) Art F.Y. Poon   MOLECULAR BIOLOGY AND EVOLUTION

How Ecology and Landscape Dynamics Shape Phylogenetic Trees

(2015) F. Gascuel et al.   SYSTEMATIC BIOLOGY

Eight challenges in phylodynamic inference

(2015) Simon D.W. Frost et al.   Epidemics

Four key challenges in infectious disease modelling using data from multiple sources

(2015) Daniela De Angelis et al.   Epidemics

Approximate Bayesian Computation of diversification rates from molecular phylogenies: introducing a new efficient summary statistic, the nLTT

(2015) Thijs Janzen et al.   Methods in Ecology and Evolution

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Exactvs.Approximate Computation: Reconciling Different Estimates ofMycobacterium tuberculosisEpidemiological Parameters

(2014) R. Zachariah Aandahl et al.   GENETICS

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

(2014) D. Kuhnert et al.   Journal of the Royal Society Interface

Ebola Virus Disease in West Africa — The First 9 Months of the Epidemic and Forward Projections

(2014)   NEW ENGLAND JOURNAL OF MEDICINE

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

(2014) S. K. Gire et al.   SCIENCE

Phylodynamic Inference for Structured Epidemiological Models

(2014) David A. Rasmussen et al.   PLoS Computational Biology

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics

(2013) Anne Cori et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Stabilizing the lasso against cross-validation variability

(2013) S. Roberts et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

Using an Epidemiological Model for Phylogenetic Inference Reveals Density Dependence in HIV Transmission

(2013) Gabriel E. Leventhal et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Stochastic Simulator of Birth-Death Master Equations with Application to Phylodynamics

(2013) T. G. Vaughan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Modelling tree shape and structure in viral phylodynamics

(2013) S. D. W. Frost et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Approximate Bayesian Computation

(2013) Mikael Sunnåker et al.   PLoS Computational Biology

Viral Phylodynamics

(2013) Erik M. Volz et al.   PLoS Computational Biology

A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation

(2012) S. Aeschbacher et al.   GENETICS

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

(2012) T. Stadler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

abc: an R package for approximate Bayesian computation (ABC)

(2012) Katalin Csilléry et al.   Methods in Ecology and Evolution

Phylodynamic Inference and Model Assessment with Approximate Bayesian Computation: Influenza as a Case Study

(2012) Oliver Ratmann et al.   PLoS Computational Biology

Inferring Epidemic Contact Structure from Phylogenetic Trees

(2012) Gabriel E. Leventhal et al.   PLoS Computational Biology

Digital Epidemiology

(2012) Marcel Salathé et al.   PLoS Computational Biology

Complex Population Dynamics and the Coalescent Under Neutrality

(2011) Erik M. Volz   GENETICS

Phylogenetic and epidemic modeling of rapidly evolving infectious diseases

(2011) Denise Kühnert et al.   INFECTION GENETICS AND EVOLUTION

Estimating the Basic Reproductive Number from Viral Sequence Data

(2011) Tanja Stadler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mammalian phylogeny reveals recent diversification rate shifts

(2011) T. Stadler   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inference for Nonlinear Epidemiological Models Using Genealogies and Time Series

(2011) David A. Rasmussen et al.   PLoS Computational Biology

Approximate Bayesian Computation in Evolution and Ecology

(2010) Mark A. Beaumont   Annual Review of Ecology Evolution and Systematics

Sampling-through-time in birth–death trees

(2010) Tanja Stadler   JOURNAL OF THEORETICAL BIOLOGY

Never mind the length, feel the quality: the impact of long-term epidemiological data sets on theory, application and policy

(2010) Pejman Rohani et al.   TRENDS IN ECOLOGY & EVOLUTION

Approximate Bayesian Computation (ABC) in practice

(2010) Katalin Csilléry et al.   TRENDS IN ECOLOGY & EVOLUTION

Phylodynamics of Infectious Disease Epidemics

(2009) Erik M. Volz et al.   GENETICS

Efficient Approximate Bayesian Computation Coupled With Markov Chain Monte Carlo Without Likelihood

(2009) Daniel Wegmann et al.   GENETICS

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

(2009) Tanja Stadler   JOURNAL OF THEORETICAL BIOLOGY

Non-linear regression models for Approximate Bayesian Computation

(2009) Michael G. B. Blum et al.   STATISTICS AND COMPUTING

Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems

(2008) T. Toni et al.   Journal of the Royal Society Interface

Lineages-through-time plots of neutral models for speciation

(2008) Tanja Stadler   MATHEMATICAL BIOSCIENCES