Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks

Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial

(2022) Pengyu Liu et al.   SYSTEMATIC BIOLOGY

Unifying Phylogenetic Birth–Death Models in Epidemiology and Macroevolution

(2021) Ailene MacPherson et al.   SYSTEMATIC BIOLOGY

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Predicting clustered weather patterns: A test case for applications of convolutional neural networks to spatio-temporal climate data

(2020) Ashesh Chattopadhyay et al.   Scientific Reports

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

Bayesian phylodynamic inference with complex models

(2018) Erik M. Volz et al.   PLoS Computational Biology

GISAID: Global initiative on sharing all influenza data – from vision to reality

(2017) Yuelong Shu et al.   Eurosurveillance

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

A Metric on Phylogenetic Tree Shapes

(2017) C. Colijn et al.   SYSTEMATIC BIOLOGY

Phylodynamics on local sexual contact networks

(2017) David A. Rasmussen et al.   PLoS Computational Biology

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

(2017) Emma Saulnier et al.   PLoS Computational Biology

Life expectancy in HIV-positive persons in Switzerland

(2016) Aysel Gueler et al.   AIDS

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

(2016) Denise Kühnert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Characterizing and Comparing Phylogenies from their Laplacian Spectrum

(2015) Eric Lewitus et al.   SYSTEMATIC BIOLOGY

Fast Dating Using Least-Squares Criteria and Algorithms

(2015) Thu-Hien To et al.   SYSTEMATIC BIOLOGY

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

(2014) S. K. Gire et al.   SCIENCE

Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models

(2014) Veronika Boskova et al.   PLoS Computational Biology

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

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

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

Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods

(2013) T. Stadler et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Estimating the Basic Reproductive Number from Viral Sequence Data

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

Molecular Epidemiology Reveals Long‐Term Changes in HIV Type 1 Subtype B Transmission in Switzerland

(2010) Roger D. Kouyos et al.   JOURNAL OF INFECTIOUS DISEASES

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

Cohort Profile: The Swiss HIV Cohort Study

(2009) et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY