Bacterial genomes in epidemiology--present and future

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Nepalese origin of cholera epidemic in Haiti

(2012) R.R. Frerichs et al.   CLINICAL MICROBIOLOGY AND INFECTION

Resolution of a Meningococcal Disease Outbreak from Whole-Genome Sequence Data with Rapid Web-Based Analysis Methods

(2012) K. A. Jolley et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Pneumococcal genome sequencing tracks a vaccine escape variant formed through a multi-fragment recombination event

(2012) Tanya Golubchik et al.   NATURE GENETICS

Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing

(2012) Simon R Harris et al.   NATURE GENETICS

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

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

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

(2012) Y. H. Grad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A High-Resolution View of Genome-Wide Pneumococcal Transformation

(2012) Nicholas J. Croucher et al.   PLoS Pathogens

BIGSdb: Scalable analysis of bacterial genome variation at the population level

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

Origins of theE. coliStrain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany

(2011) David A. Rasko et al.   NEW ENGLAND JOURNAL OF MEDICINE

Open-Source Genomic Analysis of Shiga-Toxin–ProducingE. coliO104:H4

(2011) Holger Rohde et al.   NEW ENGLAND JOURNAL OF MEDICINE

Epidemic Profile of Shiga-Toxin–ProducingEscherichia coliO104:H4 Outbreak in Germany

(2011) Christina Frank et al.   NEW ENGLAND JOURNAL OF MEDICINE

German Outbreak ofEscherichia coliO104:H4 Associated with Sprouts

(2011) Udo Buchholz et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

Detection of recombination events in bacterial genomes from large population samples

(2011) Pekka Marttinen et al.   NUCLEIC ACIDS RESEARCH

Rapid Pneumococcal Evolution in Response to Clinical Interventions

(2011) N. J. Croucher et al.   SCIENCE

Population Genetics of Vibrio cholerae from Nepal in 2010: Evidence on the Origin of the Haitian Outbreak

(2011) R. S. Hendriksen et al.   mBio

Measuring the temporal structure in serially sampled phylogenies

(2011) Rebecca R. Gray et al.   Methods in Ecology and Evolution

Inference of Homologous Recombination in Bacteria Using Whole-Genome Sequences

(2010) X. Didelot et al.   GENETICS

The Origin of the Haitian Cholera Outbreak Strain

(2010) Chen-Shan Chin et al.   NEW ENGLAND JOURNAL OF MEDICINE

Automated use of WHONET and SaTScan to detect outbreaks of Shigella spp. using antimicrobial resistance phenotypes

(2009) J. STELLING et al.   EPIDEMIOLOGY AND INFECTION

Evolution, Population Structure, and Phylogeography of Genetically Monomorphic Bacterial Pathogens

(2008) Mark Achtman   Annual Review of Microbiology