Jacqueline A. Keane

发表

SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments

Aidan Delaney, Andrew J. Page, Simon R. Harris, 2016 .

The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries

Andrew J. Page, Lars Barquist, Julian Parkhill, 2016, Bioinform..

Comparison Of Multi-locus Sequence Typing software For next generation sequencing data

Torsten Seemann, Jacqueline A. Keane, Lee S. Katz, 2017, bioRxiv.

IVA: accurate de novo assembly of RNA virus genomes

Astrid Gall, Thomas D. Otto, Paul Kellam, 2015, Bioinform..

Roary: rapid large-scale prokaryote pan genome analysis

Andrew J. Page, Daniel Falush, Julian Parkhill, 2015, bioRxiv.

Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus

Andrew J. Page, Jacqueline A. Keane, 2018 .

Multilocus sequence typing by blast from de novo assemblies against PubMLST

Andrew J. Page, Jacqueline A. Keane, Ben Taylor, 2016, J. Open Source Softw..

GFF3toEMBL: Preparing annotated assemblies for submission to EMBL

Andrew J. Page, Sascha Steinbiss, Torsten Seemann, 2016, J. Open Source Softw..

SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data

Stephen D. Bentley, Jacqueline A. Keane, Rebecca A. Gladstone, 2017, bioRxiv.

SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments

Simon R. Harris, Torsten Seemann, Jacqueline A. Keane, 2016, bioRxiv.

SaffronTree: Fast, reference-free pseudo-phylogenomic trees from reads or contigs

Andrew J. Page, Martin Hunt, Torsten Seemann, 2017, J. Open Source Softw..

Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data

Julian Parkhill, Simon R. Harris, Martin Hunt, 2016, bioRxiv.

Comparison of classical multi-locus sequence typing software for next-generation sequencing data

Nabil-Fareed Alikhan, Torsten Seemann, Jacqueline A. Keane, 2017, Microbial genomics.

Roary: Rapid large-scale prokaryote pan genome analysis

Julian Parkhill, Martin Hunt, Jacqueline A. Keane, 2015, bioRxiv.

Robust high throughput prokaryote de novo assembly and improvement pipeline for Illumina data

Julian Parkhill, Simon R. Harris, Martin Hunt, 2016, bioRxiv.

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

Jacqueline A. Keane, Aidan J. Delaney, J. Parkhill, 2014, Nucleic acids research.

An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid

Jacqueline A. Keane, Richard Holliman, Thomas R Connor, 2016, Nature Communications.

Circlator: automated circularization of genome assemblies using long sequencing reads

Jacqueline A. Keane, J. Parkhill, N. D. Silva, 2015, Genome Biology.

The genomes of four tapeworm species reveal adaptations to parasitism

Jacqueline A. Keane, P. Holland, J. Parkinson, 2013, Nature.

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Julian Parkhill, Martin Hunt, Leonor Sánchez-Busó, 2017, bioRxiv.

Epithelial IL-22RA1-Mediated Fucosylation Promotes Intestinal Colonization Resistance to an Opportunistic Pathogen

Jacqueline A. Keane, Daniel J. Gaffney, S. Clare, 2014, Cell host & microbe.

Transcriptome of the parasitic flatworm Schistosoma mansoni during intra-mammalian development

Anna V. Protasio, Jacqueline A. Keane, N. Holroyd, 2019, bioRxiv.

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

Paul Turner, Julian Parkhill, Jacqueline A. Keane, 2015, Nature Genetics.

A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch

Richard J. Goater, Jacqueline A. Keane, S. Nair, 2020, Nature Communications.

Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus

Jacqueline A. Keane, Andrew J Page, Jacqueline A Keane, 2018, bioRxiv.

Phylogenetic Analysis of Klebsiella pneumoniae from Hospitalized Children, Pakistan

Jacqueline A. Keane, G. Dougan, T. Lithgow, 2017, Emerging infectious diseases.

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa

Andrew J. Page, Jacqueline A. Keane, Christine J. Boinett, 2018, Nature Communications.

Conditional-ready mouse embryonic stem cell derived macrophages enable the study of essential genes in macrophage function

Jacqueline A. Keane, G. Dougan, J. Xia, 2015, Scientific Reports.

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Jacqueline A. Keane, Julian Parkhill, Leonor Sánchez-Busó, 2017, bioRxiv.

PlasmidTron: assembling the cause of phenotypes and genotypes from NGS data

Jacqueline A. Keane, G. Dougan, N. Thomson, 2018, Microbial genomics.

Circlator: automated circularization of genome assemblies using long sequencing reads

Jacqueline A. Keane, J. Parkhill, N. D. Silva, 2015, Genome Biology.

Phylogenetic Analysis of Klebsiella pneumoniae from Hospitalized Children, Pakistan

Jacqueline A. Keane, G. Dougan, T. Lithgow, 2017, Emerging infectious diseases.

NCTC3000: a century of bacterial strain collecting leads to a rich genomic data resource

Jacqueline A. Keane, J. Korlach, M. Quail, 2023, Microbial genomics.

IVA: accurate de novo assembly of RNA virus genomes

Jacqueline A. Keane, S. Ong, B. Ferns, 2015, Bioinform..