Dr. Khalil Abudahab

Principal Software Developer


Engineers software for data visualisation and integration.

Learn more about my work

After completing my PhD in belief rule-based knowledge modelling from Manchester Business School (https://mbs.ac.uk), I joined the CGPS as a software enginner. I develop and maintain various software including Microreact (https://microreact.org/), PhyloCanvas (http://phylocanvas.org/), Pathogen.watch (https://pathogen.watch/), and Data-flo (https://data-flo.io/).


  • Phandango: an interactive viewer for bacterial population genomics
    J Hadfield, NJ Croucher, RJ Goater, K Abudahab, DM Aanensen, et al.
    Bioinformatics 34 (2), 292-293
  • Microreact: visualizing and sharing data for genomic epidemiology and phylogeography
    S Argimón, K Abudahab, RJE Goater, A Fedosejev, J Bhai, C Glasner, et al.
    Microbial Genomics 2 (11)
  • Public health surveillance of multidrug-resistant clones of Neisseria gonorrhoeae in Europe: a genomic survey
    SR Harris, MJ Cole, G Spiteri, L Sánchez-Busó, D Golparian, et al.
    The Lancet Infectious Diseases
  • Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread
    S David, S Reuter, SR Harris, C Glasner, T Feltwell, S Argimon, et al.
    Nature microbiology, 1-11
  • Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection
    A McNally, T Kallonen, C Connor, K Abudahab, DM Aanensen, C Horner, et al.
    mBio 10 (2), e00644-19
  • PANINI: Pangenome Neighbor Identification for Bacterial Populations
    K Abudahab, JM Prada, Z Yang, SD Bentley, NJ Croucher, J Corander, et al.
    bioRxiv, 174409

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

Big Data Institute logoOxford University logoWellcome Trust logo
Wellcome Sanger Institute logoWellcome Genome Campus logo

Ⓒ 2019 Centre for Genomic Pathogen Surveillance