Twenty years of bacterial genome sequencing

Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis

(2015) Theoden Vigil-Stenman et al.   BMC GENOMICS

Genome assembly using Nanopore-guided long and error-free DNA reads

(2015) Mohammed-Amin Madoui et al.   BMC GENOMICS

Whole-Genome Sequencing for Outbreak Investigations of Methicillin-Resistant Staphylococcus aureus in the Neonatal Intensive Care Unit: Time for Routine Practice?

(2015) Taj Azarian et al.   INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY

Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes

(2015) Kim Judge et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

How to catch a cloud

(2015) Nadia Drake   NATURE

Pint-sized DNA sequencer impresses first users

(2015) Erika Check Hayden   NATURE

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

Successful test launch for nanopore sequencing

(2015) Nicholas J Loman et al.   NATURE METHODS

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission

(2015) Gavin K. Paterson et al.   Nature Communications

Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe

(2015) Gemma L. Kay et al.   Nature Communications

Scaffolding of a bacterial genome using MinION nanopore sequencing

(2015) E. Karlsson et al.   Scientific Reports

A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species

(2014) D. Ramasamy et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Prediction of Staphylococcus aureus Antimicrobial Resistance by Whole-Genome Sequencing

(2014) N. C. Gordon et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study

(2014) Yonatan H Grad et al.   LANCET INFECTIOUS DISEASES

Microbiology: Microbiome science needs a healthy dose of scepticism

(2014) William P. Hanage   NATURE

Dense genomic sampling identifies highways of pneumococcal recombination

(2014) Claire Chewapreecha et al.   NATURE GENETICS

Recent advances in genomic DNA sequencing of microbial species from single cells

(2014) Roger S. Lasken et al.   NATURE REVIEWS GENETICS

A brief history of synthetic biology

(2014) D. Ewen Cameron et al.   NATURE REVIEWS MICROBIOLOGY

Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing

(2014) Michael R. Wilson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Extensive Microbial and Functional Diversity within the Chicken Cecal Microbiome

(2014) Martin J. Sergeant et al.   PLoS One

Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences

(2014) W. Nasser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bexsero® chronicle

(2014) George Vernikos et al.   Pathogens and Global Health

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

(2014) Christopher W. Beitel et al.   PeerJ

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer

(2014) Joshua Quick et al.   GigaScience

A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4

(2013) Nicholas J. Loman et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

A Genomic Day in the Life of a Clinical Microbiology Laboratory

(2013) S. W. Long et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA

(2013) Nick Goldman et al.   NATURE

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

What has high-throughput sequencing ever done for us?

(2013) Julian Parkhill   NATURE REVIEWS MICROBIOLOGY

Diverse Sources of C. difficile Infection Identified on Whole-Genome Sequencing

(2013) David W. Eyre et al.   NEW ENGLAND JOURNAL OF MEDICINE

Identification of Novel Imidazo[1,2-a]pyridine Inhibitors Targeting M. tuberculosis QcrB

(2013) Katherine A. Abrahams et al.   PLoS One

Clonal Expansion within Pneumococcal Serotype 6C after Use of Seven-Valent Vaccine

(2013) Nicholas J. Loman et al.   PLoS One

Tetrahydropyrazolo[1,5-a]Pyrimidine-3-Carboxamide and N-Benzyl-6′,7′-Dihydrospiro[Piperidine-4,4′-Thieno[3,2-c]Pyran] Analogues with Bactericidal Efficacy against Mycobacterium tuberculosis Targeting MmpL3

(2013) Modesto J. Remuiñán et al.   PLoS One

Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter

(2013) S. K. Sheppard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

(2013) J. S. McLean et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The CRISPR Craze

(2013) E. Pennisi   SCIENCE

Exploitation of bacterial N-linked glycosylation to develop a novel recombinant glycoconjugate vaccine against Francisella tularensis

(2013) J. Cuccui et al.   Open Biology

After the gold rush

(2013) Neil Hall   GENOME BIOLOGY

Defining bacterial species in the genomic era: insights from the genus Acinetobacter

(2012) Jacqueline Z-M Chan et al.   BMC MICROBIOLOGY

Going beyond five bases in DNA sequencing

(2012) Jonas Korlach et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Oxford Nanopore announcement sets sequencing sector abuzz

(2012) Michael Eisenstein   NATURE BIOTECHNOLOGY

A hybrid approach for the automated finishing of bacterial genomes

(2012) Ali Bashir et al.   NATURE BIOTECHNOLOGY

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

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

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

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

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

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

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

Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy

(2011) Michael Hornsey et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Plasma nucleic acid analysis by massively parallel sequencing: pathological insights and diagnostic implications

(2011) YM Lo et al.   JOURNAL OF PATHOLOGY

The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

(2011) Mark A. Umbarger et al.   MOLECULAR CELL

A draft genome of Yersinia pestis from victims of the Black Death

(2011) Kirsten I. Bos et al.   NATURE

Probable Zoonotic Leprosy in the Southern United States

(2011) Richard W. Truman 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

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

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

Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation

(2011) D. A. Rasko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak

(2010) T. Lewis et al.   JOURNAL OF HOSPITAL INFECTION

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

The Origin of the Haitian Cholera Outbreak Strain

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

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

(2010) D. G. Gibson et al.   SCIENCE

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

(2009) Andrew L. Goodman et al.   Cell Host & Microbe

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

(2009) G. C. Langridge et al.   GENOME RESEARCH

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms

(2009) Tim van Opijnen et al.   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

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

(2008) Mark Achtman   Annual Review of Microbiology

High-Throughput Genotyping of Salmonella enterica Serovar Typhi Allowing Geographical Assignment of Haplotypes and Pathotypes within an Urban District of Jakarta, Indonesia

(2008) S. Baker et al.   JOURNAL OF CLINICAL MICROBIOLOGY

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

(2008) Kathryn E Holt et al.   NATURE GENETICS

Single-cell genomics

(2008) Alan Walker et al.   NATURE REVIEWS MICROBIOLOGY

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

(2008) Les Dethlefsen et al.   PLOS BIOLOGY