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

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

Genomic analysis to improve the management of outbreaks of bacterial infection

(2013) Xavier Didelot   Expert Review of Anti-Infective Therapy

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

Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage

(2013) Tanya Golubchik et al.   PLoS One

Genomic evolution and transmission ofHelicobacter pyloriin two South African families

(2013) Xavier Didelot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How the Dynamics and Structure of Sexual Contact Networks Shape Pathogen Phylogenies

(2013) Katy Robinson et al.   PLoS Computational Biology

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

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

Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study

(2012) Simon R Harris et al.   LANCET INFECTIOUS DISEASES

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

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

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

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

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

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

Microevolutionary analysis of Clostridium difficile genomes to investigate transmission

(2012) Xavier Didelot et al.   GENOME BIOLOGY

Estimating the Basic Reproductive Number from Viral Sequence Data

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

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

(2011) Tami D Lieberman et al.   NATURE GENETICS

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

(2011) Christopher B Ford et al.   NATURE GENETICS

Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak

(2011) Jennifer L. Gardy et al.   NEW ENGLAND JOURNAL OF MEDICINE

Helicobacter pylori genome evolution during human infection

(2011) L. Kennemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of donor genital tract HIV-1 diversity in the transmission bottleneck

(2011) D. I. Boeras et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Reconstructing disease outbreaks from genetic data: a graph approach

(2010) T Jombart et al.   HEREDITY

Epidemiological and clinical consequences of within-host evolution

(2010) Samuel Alizon et al.   TRENDS IN MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Evolutionary analysis of the dynamics of viral infectious disease

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

Inflammatory Genital Infections Mitigate a Severe Genetic Bottleneck in Heterosexual Transmission of Subtype A and C HIV-1

(2009) Richard E. Haaland et al.   PLoS Pathogens

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection

(2008) B. F. Keele et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Accounting for Phylogenetic Uncertainty in Biogeography: A Bayesian Approach to Dispersal-Vicariance Analysis of the Thrushes (Aves: Turdus)

(2008) Johan A. A. Nylander et al.   SYSTEMATIC BIOLOGY

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

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

Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty

(2007) Joe Parker et al.   INFECTION GENETICS AND EVOLUTION