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Polypolish: Short-read polishing of long-read bacterial genome assemblies

PLoS computational biology, 2022-01, Vol.18 (1), p.e1009802-e1009802

2022

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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

PLoS computational biology, 2017-06, Vol.13 (6), p.e1005595-e1005595

2017

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Performance of neural network basecalling tools for Oxford Nanopore sequencing

Genome Biology, 2019-06, Vol.20 (1), p.129-129, Article 129

2019

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The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development

Cell host & microbe, 2015-05, Vol.17 (5), p.704-715

2015

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Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae

PLoS genetics, 2019-04, Vol.15 (4), p.e1008114-e1008114

2019

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Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens

Science (American Association for the Advancement of Science), 2018-05, Vol.360 (6390), p.733-738

2018

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Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing

PLoS computational biology, 2023-03, Vol.19 (3), p.e1010905

2023

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Population genomics of Klebsiella pneumoniae

Nature reviews. Microbiology, 2020-06, Vol.18 (6), p.344-359

2020

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Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria

Current opinion in microbiology, 2018-10, Vol.45, p.131-139

2018

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Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks

PLoS computational biology, 2018-11, Vol.14 (11), p.e1006583

2018

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Bandage: interactive visualization of de novo genome assemblies

Bioinformatics, 2015-10, Vol.31 (20), p.3350-3352

2015

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A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

Nature communications, 2021-07, Vol.12 (1), p.4188-4188, Article 4188

2021

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Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes

Journal of clinical microbiology, 2018-06, Vol.56 (6)

2018

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Trycycler: consensus long-read assemblies for bacterial genomes

Genome Biology, 2021-09, Vol.22 (1), p.266-266, Article 266

2021

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FastSpar: rapid and scalable correlation estimation for compositional data

Bioinformatics, 2019-03, Vol.35 (6), p.1064-1066

2019

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Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones

Trends in microbiology (Regular ed.), 2016-12, Vol.24 (12), p.944-956

2016

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Benchmarking of long-read assemblers for prokaryote whole genome sequencing [version 1; peer review: 4 approved]

F1000 research, 2019, Vol.8, p.2138

2019

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SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

Genome medicine, 2014-11, Vol.6 (11), p.90-90, Article 90

2014

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Impact of insertion sequences on convergent evolution of Shigella species

PLoS genetics, 2020-07, Vol.16 (7), p.e1008931-e1008931

2020

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Vitamin D over the first decade and susceptibility to childhood allergy and asthma

Journal of allergy and clinical immunology, 2017-02, Vol.139 (2), p.472-481.e9

2017

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Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease

Cell host & microbe, 2018-09, Vol.24 (3), p.341-352.e5

2018

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Five Years of GenoTyphi: Updates to the Global Salmonella Typhi Genotyping Framework

The Journal of infectious diseases, 2021-12, Vol.224 (Supplement_7), p.S775-S780

2021

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Novel Subclone of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 with Enhanced Virulence and Transmissibility, China

Emerging infectious diseases, 2020-02, Vol.26 (2), p.289-297

2020

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Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating

Trends in microbiology (Regular ed.), 2018-12, Vol.26 (12), p.1008-1021

2018

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hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus

Journal of clinical microbiology, 2019-06, Vol.57 (6)

2019

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Polypolish: Short-read polishing of long-read bacterial genome assemblies

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

Performance of neural network basecalling tools for Oxford Nanopore sequencing

The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae

Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens

Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing

Population genomics of Klebsiella pneumoniae

Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks

Bandage: interactive visualization of de novo genome assemblies

A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes

Trycycler: consensus long-read assemblies for bacterial genomes

FastSpar: rapid and scalable correlation estimation for compositional data

Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones

Benchmarking of long-read assemblers for prokaryote whole genome sequencing [version 1; peer review: 4 approved]

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

Impact of insertion sequences on convergent evolution of Shigella species

Vitamin D over the first decade and susceptibility to childhood allergy and asthma

Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease

Five Years of GenoTyphi: Updates to the Global Salmonella Typhi Genotyping Framework

Novel Subclone of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 with Enhanced Virulence and Transmissibility, China

Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating

hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus

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