Dr. Khalil Abu-Dahab

Senior Web Software Engineer/Architect

I work as a Web Software Engineer/Architect for the Centre for Genomic Pathogen Surveillance at the Big Data Institute at the University of Oxford.I develop and maintain various software including Microreact (https://microreact.org.), Phylocanvas.gl (http://phylocanvas.gl.), Pathogenwatch (https://pathogen.watch.), and Data-flo (https://data-flo.io.).

Publications

Hadfield, J., Croucher, N. J., Goater, R. J., Abudahab, K., Aanensen, D. M., & Harris, S. R. (2018). Phandango: an interactive viewer for bacterial population genomics. Bioinformatics, 34(2), 292–293.

AbuDahab, K., Xu, D.-L., & Keane, J. (2012). Induction of belief decision trees from data. AIP Conference Proceedings, 1479, 2262–2265. AIP.

Abudahab, K., Prada, J. M., Yang, Z., Bentley, S. D., Croucher, N. J., Corander, J., & Aanensen, D. M. (2017). PANINI: Pangenome Neighbor Identification for Bacterial Populations. bioRxiv, 174409.

Harris, S. R., Cole, M. J., Spiteri, G., Sánchez-Busó, L., Golparian, D., Jacobsson, S., … Others. (2018). Public health surveillance of multidrug-resistant clones of Neisseria gonorrhoeae in Europe: a genomic survey. The Lancet Infectious Diseases, 18(7), 758–768.

Argimón, Silvia, Abudahab, K., Goater, R. J. E., Fedosejev, A., Bhai, J., Glasner, C., … Others. (2016). Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microbial Genomics, 2(11), e000093.

Dahab, K., & Belz, A. (2010). A Game-based Approach to Transcribing Images of Text. LREC.

AbuDahab, K., Xu, D.-L., & Chen, Y.-W. (2016). A new belief rule base knowledge representation scheme and inference methodology using the evidential reasoning rule for evidence combination. Expert Systems with Applications, 51, 218–230.

AbuDahab, K., Xu, D.-L., & Chen, Y.-W. (2013). Generic expert system and its application in knowledge modelling and inference. 2013 IEEE International Conference on Systems, Man, and Cybernetics, 1367–1372. IEEE.

McNally, A., Kallonen, T., Connor, C., Abudahab, K., Aanensen, D., Horner, C., … Corander, J. (2018). Signatures of negative frequency dependent selection in colonisation factors and the evolution of a multi-drug resistant lineage of Escherichia coli. bioRxiv, 400374.

Argimón, S., Abudahab, K., Goater, R. J., Fedosejev, A., Bhai, J., Glasner, C., & Others. (n.d.). Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microb Genom. 2016; 2 (11): e000093. Epub 2017/03/30. https://doi. org/10.1099/mgen. 0.000093 PMID: 28348833.

McNally, A., Kallonen, T., Connor, C., Abudahab, K., Aanensen, D. M., Horner, C., … Corander, J. (2019). Diversification of colonization factors in a multidrug-resistant Escherichia coli lineage evolving under negative frequency-dependent selection. MBio, 10(2), 10–1128.

Abudahab, K., Prada, J. M., Yang, Z., Bentley, S. D., Croucher, N. J., Corander, J., & Aanensen, D. M. (2019). PANINI: pangenome neighbour identification for bacterial populations. Microbial Genomics, 5(4), e000220.

David, S., Reuter, S., Harris, S. R., Glasner, C., Feltwell, T., Argimon, S., … Others. (2019). Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread. Nature Microbiology, 4(11), 1919–1929.

Argimón, Silvia, Masim, M. A. L., Gayeta, J. M., Lagrada, M. L., Macaranas, P. K. V., Cohen, V., … Others. (2020). Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines. Nature Communications, 11(1), 2719.

Alm, E., Broberg, E. K., Connor, T., Hodcroft, E. B., Komissarov, A. B., Maurer-Stroh, S., … Others. (2020). Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. Eurosurveillance, 25(32), 2001410.