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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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Population genomics of Klebsiella pneumoniae

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

2020

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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-e1010905

2023

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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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Bandage: interactive visualization of de novo genome assemblies

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

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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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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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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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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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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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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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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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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The genomic signatures of Shigella evolution, adaptation and geographical spread

Nature reviews. Microbiology, 2016-04, Vol.14 (4), p.235-250

2016

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Mercury methylation by metabolically versatile and cosmopolitan marine bacteria

The ISME Journal, 2021-06, Vol.15 (6), p.1810-1825

2021

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Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients

Clinical infectious diseases, 2017-07, Vol.65 (2), p.208-215

2017

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Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination

Nature communications, 2018-07, Vol.9 (1), p.2703-10, Article 2703

2018

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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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Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health

Proceedings of the National Academy of Sciences - PNAS, 2015-07, Vol.112 (27), p.E3574-E3581

2015

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Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae

Genome medicine, 2018-10, Vol.10 (1), p.77-77, Article 77

2018

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Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam

Nature genetics, 2018-06, Vol.50 (6), p.849-856

2018

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Identification of Klebsiella capsule synthesis loci from whole genome data

Microbial genomics, 2016-12, Vol.2 (12), p.e000102-e000102

2016

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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

Population genomics of Klebsiella pneumoniae

Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing

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

Bandage: interactive visualization of de novo genome assemblies

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

Trycycler: consensus long-read assemblies for bacterial genomes

FastSpar: rapid and scalable correlation estimation for compositional data

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

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

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

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

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

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

The genomic signatures of Shigella evolution, adaptation and geographical spread

Mercury methylation by metabolically versatile and cosmopolitan marine bacteria

Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients

Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination

Impact of insertion sequences on convergent evolution of Shigella species

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health

Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae

Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam

Identification of Klebsiella capsule synthesis loci from whole genome data

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