Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks

Reconstructing transmission trees for communicable diseases using densely sampled genetic data

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

Estimating the Effective Sample Size of Tree Topologies from Bayesian Phylogenetic Analyses

(2016) Robert Lanfear et al.   Genome Biology and Evolution

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

Next-Generation Sequencing and Comparative Analysis of Sequential Outbreaks Caused by Multidrug-Resistant Acinetobacter baumannii at a Large Academic Burn Center

(2015) Hajime Kanamori et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Whole-Genome Sequencing in Outbreak Analysis

(2015) Carol A. Gilchrist et al.   CLINICAL MICROBIOLOGY REVIEWS

Tracking Nosocomial Klebsiella pneumoniae Infections and Outbreaks by Whole-Genome Analysis: Small-Scale Italian Scenario within a Single Hospital

(2015) Raffaella Onori et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Semiparametric Relative-Risk Regression for Infectious Disease Transmission Data

(2015) Eben Kenah   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Measurably evolving pathogens in the genomic era

(2015) Roman Biek et al.   TRENDS IN ECOLOGY & EVOLUTION

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

Time Clustered Sampling Can Inflate the Inferred Substitution Rate in Foot-And-Mouth Disease Virus Analyses

(2015) Casper-Emil T. Pedersen et al.   PLoS One

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

Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host

(2014) Andrew Varble et al.   Cell Host & Microbe

The Distribution of Pairwise Genetic Distances: A Tool for Investigating Disease Transmission

(2014) Colin J. Worby et al.   GENETICS

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

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

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

Whole-genome sequencing to control antimicrobial resistance

(2014) Claudio U. Köser et al.   TRENDS IN GENETICS

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

(2014) Thibaut Jombart et al.   PLoS Computational Biology

Contribution of Seasonality in Transmission of Mycobacterium tuberculosis to Seasonality in Tuberculosis Disease: A Simulation Study

(2013) Lucia C. Soetens et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Relating Phylogenetic Trees to Transmission Trees of Infectious Disease Outbreaks

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

MRSA Transmission on a Neonatal Intensive Care Unit: Epidemiological and Genome-Based Phylogenetic Analyses

(2013) Ulrich Nübel et al.   PLoS One

Viral Phylodynamics

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

Genetic Data Provide Evidence for Wind-Mediated Transmission of Highly Pathogenic Avian Influenza

(2012) Rolf J.F. Ypma et al.   JOURNAL OF INFECTIOUS DISEASES

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

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease

(2012) B. C. Young et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Within-farm transmission dynamics of foot and mouth disease as revealed by the 2001 epidemic in Great Britain

(2012) Irina Chis Ster et al.   Epidemics

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

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

Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

(2011) Christopher B Ford 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

Evolutionary Analysis of Inter-Farm Transmission Dynamics in a Highly Pathogenic Avian Influenza Epidemic

(2011) Arnaud Bataille et al.   PLoS Pathogens

A Timescale for Evolution, Population Expansion, and Spatial Spread of an Emerging Clone of Methicillin-Resistant Staphylococcus aureus

(2010) Ulrich Nübel et al.   PLoS Pathogens

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

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

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