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

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

(2015) Matthew Hall et al.   PLoS Computational Biology

New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation

(2015) Nicola De Maio et al.   PLoS Genetics

Genome Sequencing of an Extended Series of NDM-Producing Klebsiella pneumoniae Isolates from Neonatal Infections in a Nepali Hospital Characterizes the Extent of Community- versus Hospital-Associated Transmission in an Endemic Setting

(2014) N. Stoesser et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

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

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

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

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

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

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

Complex Population Dynamics and the Coalescent Under Neutrality

(2011) Erik M. Volz   GENETICS

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

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

Sequential Bottlenecks Drive Viral Evolution in Early Acute Hepatitis C Virus Infection

(2011) Rowena A. Bull et al.   PLoS Pathogens

Reconstructing disease outbreaks from genetic data: a graph approach

(2010) T Jombart et al.   HEREDITY

Intra- and Interhost Evolutionary Dynamics of Equine Influenza Virus

(2010) P. R. Murcia et al.   JOURNAL OF VIROLOGY

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection

(2009) Jesus F. Salazar-Gonzalez et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Evolutionary analysis of the dynamics of viral infectious disease

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

Genetic Diversity in the SIR Model of Pathogen Evolution

(2009) Isabel Gordo et al.   PLoS One

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

Transmission Pathways of Foot-and-Mouth Disease Virus in the United Kingdom in 2007

(2008) Eleanor M. Cottam et al.   PLoS Pathogens