Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics

(2013) Anne Cori et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Robust Reconstruction and Analysis of Outbreak Data: Influenza A(H1N1)v Transmission in a School-based Population

(2012) N. Hens et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Quantifying Transmission of Norovirus During an Outbreak

(2012) Janneke C. M. Heijne et al.   EPIDEMIOLOGY

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

Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak

(2012) Claudio U. Köser et al.   NEW ENGLAND JOURNAL OF MEDICINE

Unifying the spatial epidemiology and molecular evolution of emerging epidemics

(2012) O. G. Pybus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing

(2012) E. S. Snitkin et al.   Science Translational Medicine

A pilot study of rapid benchtop sequencing ofStaphylococcus aureusandClostridium difficilefor outbreak detection and surveillance

(2012) David W Eyre et al.   BMJ Open

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

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

Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection

(2012) Erik M. Volz et al.   PLoS Computational Biology

Methods to infer transmission risk factors in complex outbreak data

(2011) S. Cauchemez et al.   Journal of the Royal Society Interface

Evidence for several waves of global transmission in the seventh cholera pandemic

(2011) Ankur Mutreja et al.   NATURE

Role of social networks in shaping disease transmission during a community outbreak of 2009 H1N1 pandemic influenza

(2011) S. Cauchemez 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

Inference for Nonlinear Epidemiological Models Using Genealogies and Time Series

(2011) David A. Rasmussen et al.   PLoS Computational 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

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

Pandemic Potential of a Strain of Influenza A (H1N1): Early Findings

(2009) C. Fraser et al.   SCIENCE

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