Dr. Anthony Underwood

Bioinformatics Implementation Manager


An advocate for translational bioinformatics, taking best practice approaches from research and implementing them in the public health domain. Focused on making reproducible open source pipelines accessible to all.

Learn more about my work

After completing an undergraduate degree in Microbiology at Bristol University and a PhD in molecular infectious disease at Oxford University I went on to research the molecular biology of parasitic worms at the Liverpool School of Tropical Medicine. This gave me a background in genomics that pivoted into the application of computational biology in an applied public health setting within Public Health England. After almost 20 years in PHE I decided to apply the experience I gained there of designing analytical pipelines in public health to implementation of open-access genomic analyses. Joining the CGPS team enabled me to work with partners across the globe to find ways of processing, interpreting, visualising and sharing pathogen genome data independent of place and working within the setting-specific resource boundaries.


Pathogen Pipelines



  • Coelho JM, Kapatai G, Jironkin A, Al-Shahib A, Daniel R, Dhami C, Laranjeira AM, Chambers T, Phillips S, Tewolde R, Underwood A, Chalker VJ. Genomic sequence investigation Streptococcus pyogenes clusters in England (2010–2015). Clin Microbiol Infect. 25(1):96-101
  • Fifer H, Cole M, Hughes G, Padfield S, Smolarchuk C, Woodford N, Wensley A, Mustafa N, Schaefer U, Myers R, Templeton K, Shepherd J, Underwood A. Sustained transmission of high-level azithromycin-resistant Neisseria gonorrhoeae in England: an observational study. Lancet Infect Dis. S1473-3099
  • Chalker V, Jironkin A, Coelho J, Al-Shahib A, Platt S, Kapatai G, Daniel R, Dhami C, Laranjeira M, Chambers T, Guy R, Lamagni T, Harrison T, Chand M, Johnson AP, Underwood A; Scarlet Fever Incident Management Team. Genome analysis following a national increase in Scarlet Fever in England 2014. BMC Genomics. 18(1):22
  • David S, Rusniok C, Mentasti M, Gomez-Valero L, Harris SR, Lechat P, Lees J, Ginevra C, Glaser P, Ma L, Bouchier C, Underwood A, Jarraud S, Harrison TG, Parkhill J, Buchrieser C. Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently. Genome Res. 26(11):1555-1564.
  • Kapatai G, Sheppard CL, Al-Shahib A, Litt DJ, Underwood AP, Harrison TG, Fry NK. Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline. PeerJ. 4:e2477

Our Research Alliances and Funders


Centers for Disease
Control and Prevention


European Centre for Disease Prevention and Control


Food and Agriculture Organisation
of the United Nations


National Institutes
for Health


National Institute for
Health Research


World Health Organisation

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Wellcome Sanger Institute logoWellcome Genome Campus logo

Ⓒ 2019 Centre for Genomic Pathogen Surveillance