Dr Nicole Wheeler | Data Scientist

Wheeler, Nicole

Nicole is a Data Scientist at the Centre for Genomic Pathogen Surveillance. Her focus is on developing high-throughput computational methods for understanding adaptation in bacterial pathogens. She combines a background in biochemistry and genetics with experience in statistics and machine learning to find new ways to gain insight from genome sequence data.

During my PhD I developed a bioinformatic method which weights mutations in protein coding genes based on their predicted impact on protein function. I then collaborated with a variety of groups to apply this method to the study of the genomic changes that occur during niche adaptation in bacterial pathogens.

My current work is focussed on linking genotype to phenotype in bacterial pathogens using comparative genomics, genome-wide association studies and machine learning. This work is a balance of developing new methods and applying them to questions regarding the evolution of virulence in a range of bacterial species. I am particularly interested in understanding the ways bacteria enter new pathogenic niches, and how they adapt to their new environment. I’ve been applying these insights to the development of ways to recognise emerging pathogens using genome sequence data.


  • Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica.

    Wheeler NE, Gardner PP and Barquist L

    PLoS genetics 2018;14;5;e1007333

  • Breaking the code of antibiotic resistance.

    Lo SW, Kumar N and Wheeler NE

    Nature reviews. Microbiology 2018;16;5;262

  • Genomic, Transcriptomic, and Phenotypic Analyses of <i>Neisseria meningitidis</i> Isolates from Disease Patients and Their Household Contacts.

    Ren X, Eccles DA, Greig GA, Clapham J, Wheeler NE et al.

    mSystems 2017;2;6

  • A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes.

    Wheeler NE, Barquist L, Kingsley RA and Gardner PP

    Bioinformatics (Oxford, England) 2016;32;23;3566-3574

  • Why so narrow: Distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems.

    Coray DS, Wheeler NE, Heinemann JA and Gardner PP

    RNA biology 2017;14;3;275-280

  • Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling.

    Lindgreen S, Umu SU, Lai AS, Eldai H, Liu W et al.

    PLoS computational biology 2014;10;10;e1003907

Wheeler, Nicole
Nicole's Timeline

Joined the Centre for Genomic Pathogen Surveillance


Joined the Parkhill group

PhD in Biochemistry, University of Canterbury, New Zealand


New Zealand Federation for Graduate Women Sadie Balkind Award


Research Assistant, University of Otago, New Zealand