Short read sequence typing (SRST): multi-locus sequence types from short reads

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

(2012) M. V. Larsen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

Multilocus sequence typing of IncN plasmids

(2011) Aurora García-Fernández et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

(2011) Ankur Mutreja et al.   NATURE

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

Rapid Pneumococcal Evolution in Response to Clinical Interventions

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

Salmonella bongori Provides Insights into the Evolution of the Salmonellae

(2011) Maria Fookes et al.   PLoS Pathogens

Bacterial epidemiology and biology - lessons from genome sequencing

(2011) Julian Parkhill et al.   GENOME BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Evolution and Population Structure of Salmonella enterica Serovar Newport

(2010) V. Sangal et al.   JOURNAL OF BACTERIOLOGY

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Complete Nucleotide Sequences of Plasmids pEK204, pEK499, and pEK516, Encoding CTX-M Enzymes in Three Major Escherichia coli Lineages from the United Kingdom, All Belonging to the International O25:H4-ST131 Clone

(2009) N. Woodford et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Phylogenetic understanding of clonal populations in an era of whole genome sequencing

(2009) Talima Pearson et al.   INFECTION GENETICS AND EVOLUTION

Variation in Salmonella enterica Serovar Typhi IncHI1 Plasmids during the Global Spread of Resistant Typhoid Fever

(2008) M.-D. Phan et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Multilocus sequence typing of IncI1 plasmids carrying extended-spectrum β-lactamases in Escherichia coli and Salmonella of human and animal origin

(2008) Aurora García-Fernández et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY