J. Keane

发表

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.

Circlator: automated circularization of genome assemblies using long sequencing reads

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

Circlator: automated circularization of genome assemblies using long sequencing reads

J. Parkhill, S. Harris, T. Otto, 2015, bioRxiv.

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.

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.

PlasmidTron: assembling the cause of phenotypes from NGS data

G. Dougan, N. Thomson, A. Page, 2017, bioRxiv.

Phylogenetic Analysis of Klebsiella pneumoniae from Hospitalized Children, Pakistan

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

template PlasmidTron : assembling the cause of phenotypes 1 from NGS data 2

G. Dougan, N. Thomson, A. Page, 2017 .

Identifying the best PCR enzyme for library amplification in NGS

M. Quail, Craig Corton, Yong Gu, 2022, bioRxiv.

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

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

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

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

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

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

Circlator: automated circularization of genome assemblies using long sequencing reads

J. Parkhill, N. D. Silva, S. Harris, 2015, bioRxiv.

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

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

IVA: accurate de novo assembly of RNA virus genomes

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

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.

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

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

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

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

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.

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.

Multilocus sequence typing by blast from de novo assemblies against PubMLST

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

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.

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

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

TriTrypDB : A web based resource offering the improvement of structural gene models of pathogenic kinetoplastids through community annotation using Apollo.

Brian P. Brunk, Omar S. Harb, Susanne Warrenfeltz, 2019 .

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

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

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.

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

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