Dr Andrew Page

Head of Informatics

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Informatics and bioinformatics support

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Biography

Recent Publications

I am the Head of Informatics at the Quadram Institute with an interest in high performance computing and high throughput bioinformatics sequence analysis pipelines.

I have BSc in Software Engineering and a PhD in Computer Science on the topic of Distributed Computing Systems. I was a Post-Doctoral research fellow at the National College of Ireland working on machine learning. After moving to the Wellcome Trust Sanger Institute, I worked on Laboratory Information Systems.

In 2011 I became the Principal Computer Programmer in the Pathogen Informatics group supporting the Infection Genomics group at Sanger. My work focused on building and managing bioinformatics sequence analysis pipelines for pathogenic organisms using both short and long read sequencing technologies. As part of this work I developed multiple novel software applications for analyzing bacterial genomic data including Roary for pan-genome analysis, Gubbins for recombination detection, SNP-sites for SNP analysis and PlasmidTron for assembling mobile genetic elements.

In 2018 I moved to the Quadram Institute where my group provides support for Informatics and Bioinformatics.

Key Publications

Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T.G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill (2015), “Roary: rapid large-scale prokaryote pan genome analysis”, Bioinformatics 31 (22), 3691-3693
https://doi.org/10.1093/bioinformatics/btv421Nicholas J Croucher, Andrew J Page, Thomas R Connor, Aidan J Delaney, Jacqueline A Keane, Stephen D Bentley, Julian Parkhill, Simon R Harris (2014), “Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins”, Nucleic acids research 43 (3), e15-e15
https://doi.org/10.1093/nar/gku1196

Andrew J. Page, Nishadi De Silva, Martin Hunt, Michael A. Quail, Julian Parkhill, Simon R. Harris, Thomas D. Otto, Jacqueline A. Keane (2016), “Robust high throughput prokaryote de novo assembly and improvement pipeline for Illumina data”, Microbial Genomics 2 (8)
https://dx.doi.org/10.1099/mgen.0.000083

Andrew J Page, Ben Taylor, Aidan J Delaney, Jorge Soares, Torsten Seemann, Jacqueline A Keane, Simon R Harris (2016), “SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments”, Microbial Genomics 2 (4)
https://dx.doi.org/10.1099/mgen.0.000056

Andrew J Page, Nabil-Fareed Alikhan, Heather A Carleton, Torsten Seemann, Jacqueline A Keane, Lee S Katz (2017), “Comparison of classical multi-locus sequence typing software for next-generation sequencing data”, Microbial genomics 3 (8)
https://dx.doi.org/10.1099/mgen.0.000124

Webber M., Yasir M., Turner K., Bastkowski S., Baker D., Page A., Telatin A., Savva G., Charles I.. (2020)

TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance.

Genome Research, 30, 239-249

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Gold Lock

Turner AK,Yasir M,Bastkowski S,Telatin A,Page AJ,Charles IG,Webber MA. (2020)

A genome-wide analysis of Escherichia coli responses to fosfomycin using TraDIS-Xpress reveals novel roles for phosphonate degradation and phosphate transport systems.

The Journal of antimicrobial chemotherapy

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Gold Lock

Salter S. J., Scott P., Page A., Tracey A., de Goffau M. C., Cormie C., Ochoa-Montaño B., Ling C. L., Tangmanakit J., Turner P., Parkhill J.. (2019)

'Candidatus Ornithobacterium hominis': insights gained from draft genomes obtained from nasopharyngeal swabs.