Dr Jacqueline A Keane | Senior Scientific Manager

Keane, Jacqueline A

Jacqui Keane has a PhD in Software Engineering from the National University of Irelane, Maynooth and joined the Pathogen group at the Wellcome Trust Sanger Institute as a postdoctoral fellow in 2008. In 2010, she took on the role of managing the Pathogen Informatics team whose main responsibilities are to develop sequence analysis pipelines and provide informatics support to the Infection Genomics programme.

Publications

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

    Page AJ, De Silva N, Hunt M, Quail MA, Parkhill J et al.

    Microbial genomics 2016;2;8;e000083

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

    Barquist L, Mayho M, Cummins C, Cain AK, Boinett CJ et al.

    Bioinformatics (Oxford, England) 2016;32;7;1109-11

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

    Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T et al.

    Microbial genomics 2016;2;4;e000056

  • Circlator: automated circularization of genome assemblies using long sequencing reads.

    Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA and Harris SR

    Genome biology 2015;16;294

  • Roary: rapid large-scale prokaryote pan genome analysis.

    Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al.

    Bioinformatics (Oxford, England) 2015;31;22;3691-3

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

    Wong VK, Baker S, Pickard DJ, Parkhill J, Page AJ et al.

    Nature genetics 2015;47;6;632-9

  • IVA: accurate de novo assembly of RNA virus genomes.

    Hunt M, Gall A, Ong SH, Brener J, Ferns B et al.

    Bioinformatics (Oxford, England) 2015;31;14;2374-6

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

    Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA et al.

    Nucleic acids research 2015;43;3;e15

  • Epithelial IL-22RA1-mediated fucosylation promotes intestinal colonization resistance to an opportunistic pathogen.

    Pham TA, Clare S, Goulding D, Arasteh JM, Stares MD et al.

    Cell host & microbe 2014;16;4;504-16

  • The genomes of four tapeworm species reveal adaptations to parasitism.

    Tsai IJ, Zarowiecki M, Holroyd N, Garciarrubio A, Sánchez-Flores A et al.

    Nature 2013;496;7443;57-63

  • BamView: visualizing and interpretation of next-generation sequencing read alignments.

    Carver T, Harris SR, Otto TD, Berriman M, Parkhill J and McQuillan JA

    Briefings in bioinformatics 2013;14;2;203-12

  • Optimal enzymes for amplifying sequencing libraries.

    Quail MA, Otto TD, Gu Y, Harris SR, Skelly TF et al.

    Nature methods 2011;9;1;10-1

  • Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.

    Carver T, Harris SR, Berriman M, Parkhill J and McQuillan JA

    Bioinformatics (Oxford, England) 2012;28;4;464-9

  • GeneDB--an annotation database for pathogens.

    Logan-Klumpler FJ, De Silva N, Boehme U, Rogers MB, Velarde G et al.

    Nucleic acids research 2012;40;Database issue;D98-108

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

    Page AJ, De Silva N, Hunt M, Quail MA, Parkhill J et al.

    Microbial genomics 2016;2;8;e000083

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

    Barquist L, Mayho M, Cummins C, Cain AK, Boinett CJ et al.

    Bioinformatics (Oxford, England) 2016;32;7;1109-11

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

    Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T et al.

    Microbial genomics 2016;2;4;e000056

  • Circlator: automated circularization of genome assemblies using long sequencing reads.

    Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA and Harris SR

    Genome biology 2015;16;294

  • Roary: rapid large-scale prokaryote pan genome analysis.

    Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al.

    Bioinformatics (Oxford, England) 2015;31;22;3691-3

  • IVA: accurate de novo assembly of RNA virus genomes.

    Hunt M, Gall A, Ong SH, Brener J, Ferns B et al.

    Bioinformatics (Oxford, England) 2015;31;14;2374-6

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

    Wong VK, Baker S, Pickard DJ, Parkhill J, Page AJ et al.

    Nature genetics 2015;47;6;632-9

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

    Yeung AT, Hale C, Xia J, Tate PH, Goulding D et al.

    Scientific reports 2015;5;8908

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

    Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA et al.

    Nucleic acids research 2015;43;3;e15

  • Epithelial IL-22RA1-mediated fucosylation promotes intestinal colonization resistance to an opportunistic pathogen.

    Pham TA, Clare S, Goulding D, Arasteh JM, Stares MD et al.

    Cell host & microbe 2014;16;4;504-16

  • The genomes of four tapeworm species reveal adaptations to parasitism.

    Tsai IJ, Zarowiecki M, Holroyd N, Garciarrubio A, Sánchez-Flores A et al.

    Nature 2013;496;7443;57-63

  • BamView: visualizing and interpretation of next-generation sequencing read alignments.

    Carver T, Harris SR, Otto TD, Berriman M, Parkhill J and McQuillan JA

    Briefings in bioinformatics 2013;14;2;203-12

  • Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species.

    Jackson AP, Berry A, Aslett M, Allison HC, Burton P et al.

    Proceedings of the National Academy of Sciences of the United States of America 2012;109;9;3416-21

  • Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.

    Carver T, Harris SR, Berriman M, Parkhill J and McQuillan JA

    Bioinformatics (Oxford, England) 2012;28;4;464-9

  • GeneDB--an annotation database for pathogens.

    Logan-Klumpler FJ, De Silva N, Boehme U, Rogers MB, Velarde G et al.

    Nucleic acids research 2012;40;Database issue;D98-108

  • Optimal enzymes for amplifying sequencing libraries.

    Quail MA, Otto TD, Gu Y, Harris SR, Skelly TF et al.

    Nature methods 2011;9;1;10-1

  • A deep sequencing approach to comparatively analyze the transcriptome of lifecycle stages of the filarial worm, Brugia malayi.

    Choi YJ, Ghedin E, Berriman M, McQuillan J, Holroyd N et al.

    PLoS neglected tropical diseases 2011;5;12;e1409

  • The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis.

    Jackson AP, Sanders M, Berry A, McQuillan J, Aslett MA et al.

    PLoS neglected tropical diseases 2010;4;4;e658

  • Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans.

    Jackson AP, Gamble JA, Yeomans T, Moran GP, Saunders D et al.

    Genome research 2009;19;12;2231-44

Keane, Jacqueline A
Jacqueline's Timeline
2010

Became Pathogen Informatics team leader

2008

PhD, NUI Maynooth

Joined Sanger Institute

2000

BSc (Hons), NUI Maynooth