Uses statistics and machine learning to gain novel insights from data.
Learn more about my work
Nicole's work involves mining and modelling pathogen phenotypic, genomic and epidemiological data for the identification and surveillance of high-risk strains of bacterial pathogens. She aims to develop intelligent alerting systems for flagging the emergence of high-risk strains of bacteria, and guide the subsequent use of whole-genome sequencing (WGS) to investigate outbreaks.
Nicole has also recently joined OUTBREAK, a world-first surveillance system designed to combat the growing threat of antimicrobial resistance in Australia and across the world. Powered by artificial intelligence, OUTBREAK will use new sensor technologies and huge data sets to track, trace and tackle antibiotic-resistant infections, helping us to save lives.
Wheeler, N.E., Sánchez-Busó, L., Argimón, S. & Jeffrey, B. Lean, mean, learning machines. Nature Reviews Microbiology, 2020. Read Me
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. Read Me
Lees, J. A., Tien Mai, T., Galardini, M., Wheeler, N. E., & Corander, J. Improved inference and prediction of bacterial genotype-phenotype associations using pangenome-spanning regressions. BioRxiv, 2019. Read Me
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. Read Me
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. Read Me
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. Read Me
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. Read Me
Wheeler, N.E., Gardner, P.P., Barquist, L. Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica. PLoS Genetics, 2018. Read Me
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. Read Me