People
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) 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) 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) |
TipToft: detecting plasmids contained in uncorrected long read sequencing data
Journal of Open Source Software, 4, 1021
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Staphylococcus cornubiensis sp. nov., a member of the Staphylococcus intermedius Group (SIG).
International journal of systematic and evolutionary microbiology
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The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa.
Nature communications, 9, 5094
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