Overview

I am a Senior Cytometry Scientist with the Sydney Cytometry Core Research Facility, an Honorary Research Fellow with the Infection, Immunity, and Inflammation theme and Sydney Infectious Disease Institute, and co-leader of the Single Cell and Spatial Biology Research Node with the Charles Perkins Centre at the University of Sydney. In these roles I specialise in the use of cutting edge high-dimensional cytometry, single-cell, and spatial multiomics technologies for interrogating cellular systems. My work involves the development of new computational and experimental methods to better understand immune development and pathology across the human lifespan, with a particular interest in the pathogenesis of severe respiratory and neuroinvasive infectious diseases.

I received my Ph.D in Medicine (Immunology) from the University of Sydney, where I used Australia’s first mass cytometry system to discover a role for inflammatory haematopoiesis in the pathogenesis of viral encephalitis. Subsequently I served as a high-dimensional cytometry specialist with the Sydney Cytometry Core Research Facility, and held visiting scientist positions with Stanford University and the Francis Crick Institute in London. Across these roles I developed and implemented multiple new techniques for cytometry, single-cell, and spatial analysis, helping to discover key determinants of host protection and pathology in important diseases including COVID-19.

My work

High-dimensional cytometry, single-cell, and spatial multiomics

  • Through the Sydney Cytometry Core Research Facility, I provide a range of services in assay design, sample preparation, sample acquisition, and data analysis for high-dimensional cytometry, single-cell, and spatial multiomics technologies.
  • Details of these services can be found through the Sydney Cytometry website.

Systems immunology method development

  • My work involves developing new laboratory and computational methods for cellular and spatial analysis. We apply these methods to study the development of the immune system over the human lifetime in health and disease.
  • Details of this work can be found through the Immune Dynamics website.

Interests

High dimensional cytometry - Platforms for high-throughput immune profiling, including high-dimensional flow, mass, and spectral cytometry.
Single cell and spatial multiomics - Deep cellular profiling through single-cell and spatial genomics technologies.
Computational data analysis - Developing tools for scalable integration and analysis of high-dimensional cytometry and spatial data.
Respiratory and neuroinvasive infectious disease - Undestanding the determinats of immune mediated protection and pathology in viral encephalitis and COVID-19.
Adult and paediatric immunology - Development of the immune system over the human lifetime, and consequences for responses to infectious challenges.

Resources

Sydney Cytometry Website - Resources and services for cytometry, single-cell, and spatial multiomics
Spectre - A computational toolkit for high-dimensional cytometry and spatial analysis.
SuperCellCyto - Scalable cytometry analysis of large datasets using SuperCells.
TrackSOM - TrackSOM is an algorithm for investigating how the dynamic immune response evolves over time and/or disease severity.

Publications

Selected publications. Full list on Google Scholar

  • A high‐dimensional cytometry atlas of peripheral blood over the human life span
  • S Jalali, CM Harpur, AT Piers, M Auladell, L Perriman, S Li, K An, ...
    Immunology and Cell Biology 100 (10), 805-821, 2022
  • SARS-CoV-2 infection results in immune responses in the respiratory tract and peripheral blood that suggest mechanisms of disease severity
  • W Zhang, BY Chua, KJ Selva, L Kedzierski, TM Ashhurst, ER Haycroft, ...
    Nature Communications 13 (1), 2774, 2022
  • Integrated immune dynamics define correlates of COVID-19 severity and antibody responses
  • M Koutsakos, LC Rowntree, L Hensen, BY Chua, CE Van De Sandt, ...
    Cell Reports Medicine 2 (3), 2021
  • Integration, exploration, and analysis of high‐dimensional single-cell data using Spectre
  • TM Ashhurst, F Marsh‐Wakefield, GH Putri, AG Spiteri, D Shinko, ...
    Cytometry Part A 101 (3), 237-253, 2022
  • An updated guide for the perplexed - cytometry in the high-dimensional era
  • T Liechti, LM Weber, TM Ashhurst, N Stanley, M Prlic, S Van Gassen, ...
    Nature Immunology 22 (10), 1190-1197, 2021
  • Evaluating spectral cytometry for immune profiling in viral disease
  • P Niewold, TM Ashhurst, AL Smith, NJC King
    Cytometry Part A 97 (11), 1165-1179, 2020
  • Mass Cytometry - Methods and Protocols
  • HM McGuire, T Ashhurst (eds)
    Methods in Molecular Biology, 2019

    Training & Experience

    Senior Cytometry Scientist

    2022 - Present
    Sydney Cytometry Core Research Facility, The University of Sydney

    Achievements

    Roles:

    • Visiting Scientist, Francis Crick Institute, London (2024)
    • Honorary Research Fellow, Infectious Disease and Immunology
    • Co-lead, Single Cell and Spatial Biology Research Node

    Cytometry Specialist

    2017 - 2022
    Sydney Cytometry Core Research Facility, The University of Sydney

    Achievements:

    • Management of high-dimensional flow and mass cytometry (CyTOF)
    • Introduced Australia’s first Imaging Mass Cytometer, and the University of Sydney’s first spectral cytometry systems
    • Aided important discoveries in the immune response against COVID-19
    • Introduced the Spectre computational toolkit for high-dimensional cytometry analysis
    • Co-founded the Single Cell and Spatial Biology Research Node of the Charles Perkins Centre
    • Published the first 27-colour flow cytometry panels

    Roles:

    • Honorary Research Fellow, Infectious Disease and Immunology (2021-present)
    • Co-lead, Single Cell and Spatial Biology Research Node (2021-present)
    • Systems Cytometry and NSW representative, Systems Immunology specialist interest group of the Australia and New Zealand Society for Immunology (2020 – 2023)
    • International Society for the Advancement of Cytometry (ISAC) Marylou Ingram Scholar (2017-2022)

    Ph.D in Medicine (Immunology)

    2012 - 2017
    Discipline of Pathology, The University of Sydney

    Achievements:

    • Thesis: “Mobilisation of the murine haematopoietic system in the bone marrow during viral encephalitis”
    • Mapping inflammatory changes to haematopoiesis during viral encephalitis in Australia’s first CyTOF experiments

    Roles:

    • Visiting Scientist, Stanford University (2014) supported by a Sydney Medical School travelling fellowship

    Bachelor of Science (hons)

    2008 - 2011
    The University of Sydney
    • Majors: Immunobiology, Virology
    • Honours: Cell Pathology