Bayesian reconstruction of transmission within outbreaks using genomic variants

Donor-Recipient Identification in Para- and Poly-phyletic Trees Under Alternative HIV-1 Transmission Hypotheses Using Approximate Bayesian Computation

(2017) Ethan O. Romero-Severson et al.   GENETICS

The Bacterial Sequential Markov Coalescent

(2017) Nicola De Maio et al.   GENETICS

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks

(2017) Don Klinkenberg et al.   PLoS Computational Biology

Donor-Recipient Identification in Para- and Poly-phyletic Trees Under Alternative HIV-1 Transmission Hypotheses Using Approximate Bayesian Computation

(2017) Ethan O. Romero-Severson et al.   GENETICS

The Bacterial Sequential Markov Coalescent

(2017) Nicola De Maio et al.   GENETICS

Reversible polymorphism-aware phylogenetic models and their application to tree inference

(2016) Dominik Schrempf et al.   JOURNAL OF THEORETICAL BIOLOGY

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

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

'SEEDY' (Simulation of Evolutionary and Epidemiological Dynamics): An R Package to Follow Accumulation of Within-Host Mutation in Pathogens

(2015) Colin J. Worby et al.   PLoS One

PoMo: An Allele Frequency-Based Approach for Species Tree Estimation

(2015) Nicola De Maio et al.   SYSTEMATIC 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

Timing and Order of Transmission Events Is Not Directly Reflected in a Pathogen Phylogeny

(2014) Ethan Romero-Severson et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data

(2014) Colin J. Worby et al.   PLoS Computational Biology

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

(2014) Thibaut Jombart et al.   PLoS Computational Biology

Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007–12, with whole pathogen genome sequences: an observational study

(2014) Timothy M Walker et al.   Lancet Respiratory Medicine

Selected insights from application of whole-genome sequencing for outbreak investigations

(2013) Vien Thi Minh Le et al.   Current Opinion in Critical Care

Relating Phylogenetic Trees to Transmission Trees of Infectious Disease Outbreaks

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

Linking Great Apes Genome Evolution across Time Scales Using Polymorphism-Aware Phylogenetic Models

(2013) Nicola De Maio et al.   MOLECULAR BIOLOGY AND EVOLUTION

Diverse Sources of C. difficile Infection Identified on Whole-Genome Sequencing

(2013) David W. Eyre et al.   NEW ENGLAND JOURNAL OF MEDICINE

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

(2012) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

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

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

Insights from Genomics into Bacterial Pathogen Populations

(2012) Daniel J. Wilson   PLoS Pathogens

Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology

(2012) Claudio U. Köser et al.   PLoS Pathogens

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

Contribution of Intra- and Interhost Dynamics to Norovirus Evolution

(2011) R. A. Bull et al.   JOURNAL OF VIROLOGY

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

(2011) Tami D Lieberman et al.   NATURE GENETICS

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

Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting

(2011) Yun Yu et al.   SYSTEMATIC BIOLOGY

Reconstructing disease outbreaks from genetic data: a graph approach

(2010) T Jombart et al.   HEREDITY

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Evolutionary analysis of the dynamics of viral infectious disease

(2009) Oliver G. Pybus et al.   NATURE REVIEWS GENETICS

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