outbreaker2: a modular platform for outbreak reconstruction

Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks

(2017) Xavier Didelot et al.   MOLECULAR BIOLOGY AND EVOLUTION

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks

(2017) Don Klinkenberg et al.   PLoS Computational Biology

Reconstructing transmission trees for communicable diseases using densely sampled genetic data

(2016) Colin J. Worby et al.   Annals of Applied Statistics

Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees

(2016) Eben Kenah et al.   PLoS Computational Biology

SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent

(2016) Nicola De Maio et al.   PLoS Computational Biology

Ebola superspreading

(2015) Christian L Althaus   LANCET INFECTIOUS DISEASES

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

Genetic diversity and evolutionary dynamics of Ebola virus in Sierra Leone

(2015) Yi-Gang Tong et al.   NATURE

West African Ebola Epidemic after One Year — Slowing but Not Yet under Control

(2015)   NEW ENGLAND JOURNAL OF MEDICINE

A Systematic Bayesian Integration of Epidemiological and Genetic Data

(2015) Max S. Y. Lau et al.   PLoS Computational Biology

Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set

(2015) Matthew Hall et al.   PLoS Computational Biology

Bayesian Inference of Infectious Disease Transmission from Whole-Genome Sequence Data

(2014) Xavier Didelot et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014)   NEW ENGLAND JOURNAL OF MEDICINE

Two-phase importance sampling for inference about transmission trees

(2014) E. Numminen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Bayesian approach for inferring the dynamics of partially observed endemic infectious diseases from space-time-genetic data

(2014) N. Mollentze et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2014) S. K. Gire et al.   SCIENCE

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

(2014) Thibaut Jombart et al.   PLoS Computational Biology

Relating Phylogenetic Trees to Transmission Trees of Infectious Disease Outbreaks

(2013) Rolf J. F. Ypma et al.   GENETICS

Infectious disease transmission as a forensic problem: who infected whom?

(2013) P. Teunis et al.   Journal of the Royal Society Interface

Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods

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

ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R

(2012) Andrei-Alin Popescu et al.   BIOINFORMATICS

A Bayesian Inference Framework to Reconstruct Transmission Trees Using Epidemiological and Genetic Data

(2012) Marco J. Morelli et al.   PLoS Computational Biology

Modelling the spread of infectious salmon anaemia among salmon farms based on seaway distances between farms and genetic relationships between infectious salmon anaemia virus isolates

(2011) M. Aldrin et al.   Journal of the Royal Society Interface

Unravelling transmission trees of infectious diseases by combining genetic and epidemiological data

(2011) R. J. F. Ypma et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Reconstructing disease outbreaks from genetic data: a graph approach

(2010) T Jombart et al.   HEREDITY

Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus

(2008) E. M Cottam et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES