Dr Andrew Page

Head of Informatics

Contact via email

Informatics and bioinformatics support

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/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

Davies MR, Duchene S, Valcanis M, Jenkins AP, Jenney A, Rosa V, Hayes AJ, Strobel AG, McIntyre L, Lacey JA, Klemm EJ, Wong VK, Sahukhan A, Thomson H, Page A, Hocking D, Wang N, Tudravu L, Rafai E, Dougan G, Howden BP, Crump JA, Mulholland K, Strugnell R. (2022)

Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016.

The Lancet regional health. Western Pacific


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Merhi G, Trotter AJ, de Oliveira Martins L, Koweyes J, Le Viet T, Abou Naja, Al Buaini, Prosolek SJ, Alikhan NF, Lott M, Tohmeh T, Badran B, Jupp OJ, Gardner S, Felgate MW, Makin KA, Wilkinson JM, Stanley R, Sesay AK, Webber MA, Davidson RK, Ghosn N, Pallen M, Hasan H, Page AJ, Tokajian . (2022)

Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021.

Microbial genomics


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Chadeau-Hyam M, Eales O, Bodinier B, Wang H, Haw D, Whitaker M, Elliott J, Walters CE, Jonnerby J, Atchison C, Diggle PJ, Page A, Ashby D, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Donnelly CA, Elliott . (2022)

Breakthrough SARS-CoV-2 infections in double and triple vaccinated adults and single dose vaccine effectiveness among children in Autumn 2021 in England: REACT-1 study.

EClinicalMedicine


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Elliott P, Eales O, Steyn N, Tang D, Bodinier B, Wang H, Elliott J, Whitaker M, Atchison C, Diggle PJ, Page A, Trotter AJ, Ashby D, Barclay W, Taylor G, Ward H, Darzi A, Cooke GS, Donnelly CA, Chadeau-Hyam . (2022)

Twin peaks: The Omicron SARS-CoV-2 BA.1 and BA.2 epidemics in England.

Science (New York, N.Y.)


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Chadeau-Hyam M, Wang H, Eales O, Haw D, Bodinier B, Whitaker M, Walters CE, Ainslie KEC, Atchison C, Fronterre C, Diggle PJ, Page A, Trotter AJ, Ashby D, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Riley S, Donnelly CA, Elliott . (2022)

SARS-CoV-2 infection and vaccine effectiveness in England (REACT-1): a series of cross-sectional random community surveys.

The Lancet. Respiratory medicine


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de Oliveira Martins L, Bloomfield S, Stoakes E, Grant AJ, Page AJ, Mather A. (2022)

Tatajuba: exploring the distribution of homopolymer tracts.

NAR genomics and bioinformatics


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Eales O, Walters CW, Wang H, Haw D, Ainslie KEC, Atchison CJ, Page AJ, Prosolek S, Trotter AJ, Le Viet, Alikhan N, Jackson LM, Ludden C, Ashby D, Donnelly CA, Cooke G, Barclay W, Ward H, Darzi A, Elliott P, Riley . (2022)

Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2 [version 1; peer review: awaiting peer review]

Wellcome open research


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Elliott P, Bodinier B, Eales O, Wang H, Haw D, Elliott J, Whitaker M, Jonnerby J, Tang D, Walters CE, Atchison C, Diggle PJ, Page A, Trotter AJ, Ashby D, Barclay W, Taylor G, Ward H, Darzi A, Cooke GS, Chadeau-Hyam M, Donnelly C. (2022)

Rapid increase in Omicron infections in England during December 2021: REACT-1 study.

Science (New York, N.Y.)


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