Nicholas J. McKenzie

Melbourne, VIC, Australia | GitHub | LinkedIn | Email:

Education

Monash University
Melbourne
Australia
Doctor of Philosophy 2018–2023
Biochemistry and Molecular Biology, Department of Biochemistry, Faculty of Medicine Nursing and Health Sciences
Thesis: Identifying the function of JARID2 and AEBP2 in nucleic acid binding
Monash University
Melbourne
Australia
Bachelor of Science (First Class Honours) 2017
Specialisation: Biochemistry
Thesis: Identifying an RNA-binding site within the histone methyltransferase PRC2
Monash University
Melbourne
Australia
Bachelor of Science and Bachelor of Arts (Double Degree) 2013–2016
Double Major in Biochemistry and Molecular Biology, Major in Japanese, Major in Asian Studies

Experience

Australian National University (ANU) Canberra
Australia
Bioinformatician (Postdoctoral Researcher) 2022–2023
  • Python Nextflow pipelines for CRISPR screen data
  • RNA-seq analyses; custom R analyses
Monash University Melbourne
Australia
PhD Candidate Researcher 2018–2023
  • 100% research based. Responsibilities were the same as that of an employed researcher, with the additional responsibility of writing a doctoral thesis.
  • Laboratory work, data analysis, scientific presentations, technical writing (scientific papers and a dissertation)
  • Investigated PRC2–DNA/RNA interactions and recruitment
  • Developed RBDmap Lite (R Shiny app for XL-MS data)
  • Protein expression/purification protocols (PRC2–AEBP2–JARID2)
Monash University Melbourne
Australia
Honours Student Researcher 2017
  • Majority research based.
  • Adapted RBDmap to identify RNA-binding residues in vitro
Monash University Melbourne
Australia
Undergraduate Research Opportunities Program (UROP) Research Assistant (Paid Internship) 2016–2017
  • Protein expression/purification, RNA transcription, molecular cloning
Monash University Melbourne
Australia
Research Assistant 2015
  • KLK-5 expression optimisation; epitope analysis of GAD65
Monash University Melbourne
Australia
Summer Research Scholarship Student (Paid Internship) 2014–2015
  • KLK-5 expression optimisation; epitope analysis of GAD65

Publications

  • *Mucha, M., *Lai, Z., *McKenzie, N.J., *Matrà, F., Boudes, M., Flanigan, S.F., Alejo-Vinogradova, M.T., Monger, C., Zhang, Q., Nimmo, D., Healy, E., Silva, A.J., Angelov, D., Reck, D.M., Holland, G., Atmaca, Z.E., King, H.E., Hamilton, M., Glancy, E., Nolan, J., Weatheritt, R.J., Bell, O., Vermeulen, M., Davidovich, C. & Bracken, A.P., 2025. Auto-inhibition of PRC2 by the broadly expressed long isoform of AEBP2. The EMBO Journal, 44(23), p.6979. [Link to paper]
  • Ohtomo, H., Ito, S., McKenzie, N.J., Uckelmann, M., Wakamori, M., Ehara, H., Furukawa, A., Tsunaka, Y., Shibata, M., Sekine, S., Umehara, T., Davidovich, C., Koseki, H. & Nishimura, Y., 2023. H2A Ubiquitination Alters H3-tail Dynamics on Linker-DNA to Enhance H3K27 Methylation. Journal of Molecular Biology, 435(4), p.167936. [Link to paper]
  • *Zhang, Q., *McKenzie, N.J., *Warneford-Thomson, R., Gail, E.H., Flanigan, S.F., Owen, B.M., Lauman, R., Levina, V., Garcia, B.A., Schittenhelm, R.B., Bonasio, R. & Davidovich, C., 2019. RNA exploits an exposed regulatory site to inhibit the enzymatic activity of PRC2. Nature Structural & Molecular Biology, 26(3), pp.237–247. [Link to paper]
Asterisk (*) denotes co-first authorship

Conference Presentations & Posters

  • 3rd Place Oral Presentation, Monash Biochemistry PhD Student Symposium 2019
  • Best Poster Award, meRNA 2018 Student Symposium 2018
  • Honours Student Speaker Award, meRNA Club 2017

Bioinformatics & Computational Skills

  • Languages: Python, R, Bash
  • Tools: Nextflow, R Shiny, Git/GitHub, HTML, Unix
  • Projects: RBDmap Lite, DNA complexity filter, RNA-seq/ChIP-seq pipelines, Japanese study tools

Certificates & Professional Development

  • Fundamentals of Computing Specialization (Coursera)
  • Finding Hidden Messages in DNA (Bioinformatics I, Coursera)
  • Conferences: Victorian Cancer Bioinformatics Symposium, BioC Asia, AMSI BioInfoSummer

Teaching & Mentoring

  • Co-supervisor, Undergraduate lab project, Monash University 2020
  • Teaching Associate, Molecular Biology and the Cell (MCB2011), Monash University 2019

Grants & Prizes

  • RTP Stipend 2018–2021
    Competitive stipend awarded to high-quality research candidates which funds PhD tuition and living expenses.
  • Charlee Ferrar Scholarship 2018–2021
    Top-up scholarship of AUD$5,000 per year from the Isabella and Marcus Pediatric Brainstem Tumour Fund to support my PhD at Monash University.
  • UROP CSL Stipend 2016
    A small grant for research consumables provided to the lab by biotechnology company CSL for undertaking an approved project during my placement in the Undergraduate Research Opportunities Program (UROP).
  • SCI2015 Best Blogger Award 2014
    Science communication award for the undergraduate unit "SCI2015 — Scientific practice and communication (advanced)" for weekly assessed blog posts. Received a H. pylori T-shirt as a prize from Nobel Prize-winning scientist Barry Marshall.
  • AsiaBound Scholarship (AUD$5,000) 2015
    Grant from the Australian Government to cover studying abroad at Nagoya University, Japan for one semester.
  • Australian-Asian Association of Victoria Inc. Award ($300) 2014
    Award for high achievement in Japanese language learning at Monash University.

Other Skills

  • Languages: English (native), Japanese (JLPT-N2)
  • CAD & 3D Printing: Fusion 360; designed lab equipment shared on Thingiverse and Printables