Global phylogeography and evolutionary history of Shigella dysenteriae type 1

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

(2015) Vanessa K Wong et al.   NATURE GENETICS

The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource

(2015) Kate S. Baker et al.   Genome Medicine

Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri

(2015) Thomas R Connor et al.   eLife

Enteric Bacterial Pathogens in Children with Diarrhea in Niger: Diversity and Antimicrobial Resistance

(2015) Céline Langendorf et al.   PLoS One

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Genomic analysis of the emergence of 20th century epidemic dysentery

(2014) Laurence Rohmer et al.   BMC GENOMICS

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

(2013) L. Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

(2012) Kathryn E Holt et al.   NATURE GENETICS

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

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

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

A novel methodology for large-scale phylogeny partition

(2011) Mattia C.F. Prosperi et al.   Nature Communications

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study

(2010) Karthikeyan K Kumarasamy et al.   LANCET INFECTIOUS DISEASES

Chromosomal Integration of the Extended-Spectrum  -Lactamase Gene blaCTX-M-15 in Salmonella enterica Serotype Concord Isolates from Internationally Adopted Children

(2009) L. Fabre et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Safety and immunogenicity of SC599, an oral live attenuated Shigella dysenteriae type-1 vaccine in healthy volunteers: Results of a Phase 2, randomized, double-blind placebo-controlled trial

(2009) Odile Launay et al.   VACCINE

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

(2008) Tim Carver et al.   BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

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

Safety and immunogenicity of WRSd1, a live attenuated Shigella dysenteriae type 1 vaccine candidate

(2008) Robin McKenzie et al.   VACCINE