
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. I am also a visiting professor in the School of Computing Sciences at UEA.
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/btv421
Nicholas 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
Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016.
The Lancet regional health. Western Pacific
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Twin peaks: The Omicron SARS-CoV-2 BA.1 and BA.2 epidemics in England.
Science (New York, N.Y.)
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Tatajuba: exploring the distribution of homopolymer tracts.
NAR genomics and bioinformatics
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Genome sequencing SARS-CoV-2 plays a critical role in informing national and international COVID-19 public health responses