Chindelevitch L, van Dongen M, Graz H, Pedrotta A, Suresh A, Uplekar S, et al. Ten simple rules for the sharing of bacterial genotype-phenotype data on antimicrobial resistance. PLoS Comput Biol. 2023;19.

Ho, S.F.S. et al. (2021) ‘Gauge your phage: Benchmarking of tools to identify phages in metagenomic shotgun sequencing data’, Microbiome. doi:10.1186/s40168-023-01533-x

Hoffmann SA, Diggans J, Densmore D, Dai J, Knight T, Leproust E, et al. Safety by Design: Biosafety and Biosecurity in the Age of Synthetic Genomics. iScience. 2023; 106165.

Chindelevitch, L. et al. (2022) ‘Applying data technologies to combat AMR: current status, challenges, and opportunities on the way forward’, arXiv [cs.CY]. Available at: http://arxiv.org/abs/2208.04683

Argimon S, David S, Underwood A, Abrudan M. Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch. Clinical Infectious Diseases. 2021.

NIHR Global Health Research Unit on Genomic Surveillance of AMR. Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap. BMJ Global Health, 2020.

Ma, K.C., Mortimer, T.D., Hicks, A.L., Wheeler, N.E., Sánchez-Busó, L., ... Grad, Y.H. Adaptation to the cervical environment is associated with increased antibiotic susceptibility in Neisseria gonorrhoeae. Nature Communications, 2020.

Ma, K.C., Mortimer, T.D., Hicks, A.L., Wheeler, N.E., Sánchez-Busó, L., Grad, Y.H. ​Increased power from conditional bacterial genome-wide association identifies macrolide resistance mutations in Neisseria gonorrhoeae. Nature Communications, 2020.

Wheeler, N.E., Computer says....Significance, 2020.

Lees, J. A., Tien Mai, T., Galardini, M., Wheeler, N. E., & Corander, J. Improved prediction of bacterial genotype-phenotype associations using interpretablepangenome-spanning regressions. mBio, 2020.

Wheeler, N.E., Sánchez-Busó, L., Argimón, S. & Jeffrey, B. Lean, mean, learning machines. Nature Reviews Microbiology, 2020.

Bawn, M., Thilliez, G., Kirkwood, M., Wheeler, N., Petrovska, L., Dallman, T. J., ... & Kingsley, R. A.. Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation. PLoS Genetics, 2020.

Van Puyvelde, S., Pickard, D., Vandelannoote, K., Heinz, E., Barbé, B., de Block, T., Clare, S., Coomber, E. L., Harcourt, K., ... Wheeler, N. E., ... An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation. Nature Communications, 2019.

Wheeler, N. E., Reuter, S., Chewapreecha, C., Lees, J. A., Blane, B., Horner, C., … Peacock, S. J. Contrasting approaches to genome-wide association studies impact the detection of resistance mechanisms in Staphylococcus aureus. BioRxiv, 2019.

Hicks. A.L., Wheeler, N.E., Sanchez-Buso, L., Rakeman, J.L., Harris, S.R., Grad, Y.H. Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data. PLoS Computational Biology, 2019.

Lees, J.A., Ferwerda, B., Kremer, P.H.C., Wheeler, N.E., Valls Serón, M., Croucher, N.J., Gladstone, R.A., Bootsma, H., Rots, N., Z... Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis. Nature Communications, 2019.

Sackton, T.B., Grayson, P., Cloutier, A., Hu, Z., Liu, J.S., Wheeler, N.E., Gardner, P.P., Clarke, J.A., Baker, A.J., Clamp, M. and Edwards, S.V. Convergent regulatory evolution and the origin of flightlessness in palaeognathous birds. Science, 2019.

Wheeler, N.E. Tracing outbreaks with machine learning. Nature Reviews Microbiology, 2019.

Wheeler, N.E., Gardner, P.P., Barquist, L. Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica. PLoS Genetics, 2018.

Lo, S.W., Kumar, N., Wheeler, N.E. Breaking the code of antibiotic resistance. Nature Reviews Microbiology, 2018.

Wheeler, N.E., Barquist, L., Kingsley, R.A., Gardner, P.P. A profile-based method for identifying functional divergence of orthologous proteins in bacterial genomes. Bioinformatics, 2016.

Lindgreen, S., Umu, S.U., Lai, A.S.W., Eldai, H., Liu, W., McGimpsey, S., Wheeler, N.E., Biggs, P.J., Thomson, N.R., Barquist, L. and Poole, A.M. Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling. PLoS Computational Biology, 2014.