A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes

Neisseria Adhesin A Variation and Revised Nomenclature Scheme

(2014) Stefania Bambini et al.   Clinical and Vaccine Immunology

Implications of Differential Age Distribution of Disease-Associated Meningococcal Lineages for Vaccine Development

(2014) Carina Brehony et al.   Clinical and Vaccine Immunology

Using MLST to study bacterial variation: prospects in the genomic era

(2014) Keith A Jolley et al.   Future Microbiology

MLST revisited: the gene-by-gene approach to bacterial genomics

(2013) Martin C. J. Maiden et al.   NATURE REVIEWS MICROBIOLOGY

Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology

(2013) Sandra Reuter et al.   JAMA Internal Medicine

SEQuel: improving the accuracy of genome assemblies

(2012) R. Ronen et al.   BIOINFORMATICS

Evolutionary and genomic insights into meningococcal biology

(2012) Holly B Bratcher et al.   Future Microbiology

Whole-Genome Sequences of Bacillus subtilis and Close Relatives

(2012) A. M. Earl et al.   JOURNAL OF BACTERIOLOGY

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

Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain

(2012) K. A. Jolley et al.   MICROBIOLOGY-SGM

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

(2012) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Persistence of Hyperinvasive Meningococcal Strain Types during Global Spread as Recorded in the PubMLST Database

(2012) Eleanor R. Watkins et al.   PLoS One

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

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies

(2011) Joshua Wetzel et al.   BMC BIOINFORMATICS

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Virulence Evolution of the Human Pathogen Neisseria meningitidis by Recombination in the Core and Accessory Genome

(2011) Biju Joseph et al.   PLoS One

Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination

(2011) S. Budroni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data

(2010) Yukari Nishito et al.   BMC GENOMICS

Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06

(2010) Julia S Bennett et al.   BMC GENOMICS

De novo assembly of short sequence reads

(2010) K. Paszkiewicz et al.   BRIEFINGS IN BIOINFORMATICS

Complete Genome Sequence of Corynebacterium pseudotuberculosis I19, a Strain Isolated from a Cow in Israel with Bovine Mastitis

(2010) A. Silva et al.   JOURNAL OF BACTERIOLOGY

Comparative Genome Biology of a Serogroup B Carriage and Disease Strain Supports a Polygenic Nature of Meningococcal Virulence

(2010) B. Joseph et al.   JOURNAL OF BACTERIOLOGY

De Novo Assembly of the Complete Genome of an Enhanced Electricity-Producing Variant of Geobacter sulfurreducens Using Only Short Reads

(2010) Harish Nagarajan et al.   PLoS One

Genome Sequencing Reveals Widespread Virulence Gene Exchange among Human Neisseria Species

(2010) Pradeep Reddy Marri et al.   PLoS One

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

Genealogical typing of Neisseria meningitidis

(2009) X. Didelot et al.   MICROBIOLOGY-SGM

Variation of the factor H-binding protein of Neisseria meningitidis

(2009) C. Brehony et al.   MICROBIOLOGY-SGM

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

(2009) Iwanka Kozarewa et al.   NATURE METHODS

Whole Genome Amplification and De novo Assembly of Single Bacterial Cells

(2009) Sébastien Rodrigue et al.   PLoS One

Genome Project Standards in a New Era of Sequencing

(2009) P. S. G. Chain et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies

(2008) Jean-Marc Aury et al.   BMC GENOMICS

De novoassembly of thePseudomonas syringaepv.syringaeB728a genome using Illumina/Solexa short sequence reads

(2008) Rhys A. Farrer et al.   FEMS MICROBIOLOGY LETTERS

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer

(2008) D. Hernandez et al.   GENOME RESEARCH

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

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

A large genome center's improvements to the Illumina sequencing system

(2008) Michael A Quail et al.   NATURE METHODS

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

Association of a Bacteriophage with Meningococcal Disease in Young Adults

(2008) Emmanuelle Bille et al.   PLoS One

Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis

(2008) C. Schoen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA