Thomas Ashhurst - Profile About Research Publications Funding Community Talks

Thomas Ashhurst - Publications


My publications consist of 1 book, 1 current pre-print, and 29 published articles, with 732 citations since 2012 and an h-index of 15 (via Google Scholar). These publications include 1 as co-lead editor, 7 as lead or co-lead author, and 5 as senior or co-supervising author; with 2 as corresponding author. Online publication lists can be found on PubMed, Logo Google Scholar, Logo ORCID, Logo Loop, Logo Scopus, or Logo Publons. I have published 1 protocol with and 1 newsletter article with the Australia and New Zealand Society for Immunology. My software toolkit, Spectre, has been cited in 37 publications in prestigious journals such as Cell and Nature Immunology, and is a featured analysis package for the Human Cell Atlas project.


HM McGuire*, TM Ashhurst* (eds). 2019. Mass Cytometry: Methods and Protocols. Springer New York.

This book details a compilation of up-to-date and cutting-edge protocols in mass cytometry. Chapters guide readers through setting up a facility, panel design and reagent preparation, sample preparation, specific applications, and data analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Mass Cytometry: Methods and Protocols aims to ensure successful results in the further study of this vital field.

‘Mass Cytometry: Methods and Protocols’ has been downloaded over 57,000 times and cited 84 times. Protocols provided in this book have been cited in a wide variety of applications, including COVID-19 (Rodriguez et al. 2020, Koutsakos et al. 2021).


GH Putri, J Chung, DN Edwards, F Marsh-Wakefield, S Dervish, I Koprinska, NJC King, TM Ashhurst, MN Read. 2021. TrackSOM: mapping immune response dynamics through sequential clustering of time- and disease-course single-cell cytometry data. bioRxiv (pre-print).


W Zhang, B Chua, K Selva, L Kedzierski, T Ashhurst, E Haycroft, … Thi Nguyen, Katherine Kedzierska. 2022. SARS-CoV-2 infection results in immune responses in the respiratory tract and peripheral blood that suggest mechanisms of disease severity. Nature Communications.

Phillip K. West, Andrew N. McCorkindale, Boris Guennewig, Thomas M. Ashhurst, Barney Viengkhou, Emina Hayashida, So Ri Jung, Oleg Butovsky, Iain L. Campbell & Markus J. Hofer (2022). The cytokines interleukin-6 and interferon-α induce distinct microglia phenotypes. Journal of Neuroinflammation. 19, 96.

Felix Marsh-Wakefield, Pierre Juillard, Thomas M Ashhurst, Annette Juillard, Diana Shinko, Givanna H Putri, Mark N Read, Helen M McGuire, Scott N Byrne, Simon Hawke, Georges E Grau (2022). Peripheral B cell dysregulation is associated with relapse after long-term quiescence in multiple sclerosis patients. Immunology and Cell Biology. Online.

LuukWieske, Koos P Jvan Dam, Maurice Steenhuis, … Filip Eftimov on behalf of the T2B! Immunity against SARS-CoV-2 study group. Humoral responses after second and third SARS-CoV-2 vaccination in patients with immune-mediated inflammatory disorders on immunosuppressants: a cohort study. The Lancet Rheumatology. In press.

T Liechti, L Weber, TM Ashhurst, N Stanley, M Prlic, S Van Gassen, F Mair. (2021). An updated guide for the perplexed: cytometry in the high-dimensional era. Nature Immunology.

  • Featured on the Nature’s Immunology subject page.

AG Spiteri, RL Terry, CL Wishart, TM Ashhurst, IL Campbell, MJ Hofer, NJC King. 2021. High-parameter cytometry unmasks microglial cell spatio-temporal response kinetics in severe neuroinflammatory disease. J. Neuroinflammation, 18, 166.

TM Ashhurst*, F Marsh-Wakefield*, GH Putri*, AG Spiteri, D Shinko, … 2021. Integration, exploration, and analysis of high-dimensional single-cell cytometry data using Spectre. Cytometry A (accepted). Corresponding author.

F Marsh-Wakefield*, A Mitchell*, S Norton, TM Ashhurst, … HM McGuire, R Kemp. 2021. Making the most of high dimensional cytometry data. Immunology and Cellular Biology.

M Koutsakos, LC Rowntree, L Hensen, BY Chua, CE van de Sandt, JR Habel, W Zhang, X Jia, L Kedzierski, TM Ashhurst, … K Kedzierska. 2021. Integrated immune dynamics define correlates of COVID-19 severity and antibody responses. Cell Reports Medicine. Lead the computational analysis of COVID-19 blood samples, and supervised the development of TrackSOM for time-series tracking.

KC Ferrell, EL Stewart, C Counoupas, TM Ashhurst, WJ Britton, N Petrovsky, JA Triccas. 2021. Intrapulmonary vaccination with delta-inulin adjuvant stimulates non-polarised chemotactic signalling and diverse cellular interaction. Mucosal Immunology.

GH Putri, I Koprinska, TM Ashhurst, NJC King, MN Read. 2021. Using single-cell cytometry to illustrate integrated multi-perspective evaluation of clustering algorithms using Pareto fronts. Bioinformatics. Supervising role.

P Niewold*, TM Ashhurst*, AL Smith, NJC King. 2020. Evaluating spectral cytometry for immune profiling in viral disease. Cytometry Part A.

  • ISAC webinar on spectral cytometry

F Marsh‐Wakefield, T Ashhurst, S Trend, HM McGuire, P Juillard, A Zinger, … 2020. IgG3+ B cells are associated with the development of multiple sclerosis. Clinical & Translational Immunology 9 (5), e01133

SR Jung, TM Ashhurst, PK West, B Viengkhou, NJC King, IL Campbell, … 2020. Contribution of STAT1 to innate and adaptive immunity during type I interferon-mediated lethal virus infection. PLoS Pathogens 16 (4), e1008525

GH Putri, MN Read, I Koprinska, TM Ashhurst, NJC King. 2019. Dimensionality Reduction for Clustering and Cluster Tracking of Cytometry Data. International Conference on Artificial Neural Networks, 624-640

GH Putri, MN Read, I Koprinska, D Singh, U Röhm, TM Ashhurst, NJC King. 2019. ChronoClust: Density-based clustering and cluster tracking in high-dimensional time-series data. Knowledge-Based Systems 174, 9-26

E Hayashida, ZL Ling, TM Ashhurst, B Viengkhou, SR Jung, … 2019. Zika virus encephalitis in immunocompetent mice is dominated by innate immune cells and does not require T or B cells. Journal of Neuroinflammation 16 (1), 1-15

R Salomon*, C Hall*, TM Ashhurst* (2019). Cytometry in the Era of the Human Cell Atlas (WS06). Part of: K Czechowsk et al. (2019). Cyt‐Geist: Current and future challenges in cytometry: Reports of the CYTO 2018 conference workshops. Cytometry Part A 95 (6), 598-644

TM Ashhurst, DA Cox, AL Smith, NJC King. 2019. Analysis of the murine bone marrow hematopoietic system using mass and flow cytometry. Mass Cytometry, 159-192

D Shinko, TM Ashhurst, HM McGuire, KA Charles. 2019. Staining of phosphorylated signalling markers protocol for mass cytometry. Mass Cytometry, 139-146

SR Jung, T Suprunenko, TM Ashhurst, NJC King, MJ Hofer. 2018. Collateral Damage: What Effect Does Anti-CD4 and Anti-CD8α Antibody–Mediated Depletion Have on Leukocyte Populations?. The Journal of Immunology 201 (7), 2176-2186

TM Campbell, BP McSharry, M Steain, TM Ashhurst, B Slobedman, … 2018. Varicella zoster virus productively infects human natural killer cells and manipulates phenotype. PLoS pathogens 14 (4), e1006999

TM Ashhurst, AL Smith, NJC King. 2017. High‐Dimensional Fluorescence Cytometry. Current Protocols in Immunology 119 (1), 5.8. 1-5.8. 38. Corresponding author.

  • In this paper we describe panel design strategies for panels up to 26 colours.
  • This is the first publication we are aware of describing a panel above 18 colours, following Dr. Pratip Chattodpahyay’s presentation of 25-colour flow at CYTO 2014.
  • Highly optimised panels of over 18 colours published around the same include Staser et al, 2017 and Mair & Prlic, 2018

M Huber, T Suprunenko, T Ashhurst, F Marbach, H Raifer, S Wolff, … 2017. IRF9 Prevents CD8+ T cell exhaustion in an extrinsic manner during acute Lymphocytic choriomeningitis virus infection. Journal of Virology 91 (22)

RL Terry, C Deffrasnes, DR Getts, C Minten, C Van Vreden, TM Ashhurst, … 2015. Defective inflammatory monocyte development in IRF8-deficient mice abrogates migration to the West Nile virus-infected brain. Journal of innate immunity 7 (1), 102-112

DR Getts, RL Terry, MT Getts, C Deffrasnes, M Müller, C van Vreden, TM Ashhurst … 2014. Therapeutic inflammatory monocyte modulation using immune-modifying microparticles. Science translational medicine 6 (219), 219ra7-219ra7.

TM Ashhurst*, C van Vreden*, P Niewold*, NJC King. 2014. The plasticity of inflammatory monocyte responses to the inflamed central nervous system. Cellular immunology 291 (1-2), 49-57

TM Ashhurst, C Van Vreden, L Munoz-Erazo, P Niewold, K Watabe, … 2013. Antiviral macrophage responses in flavivirus encephalitis. The Indian journal of medical research 138 (5), 632

DR Getts, RL Terry, MT Getts, M Müller, S Rana, C Deffrasnes, TM Ashhurst… 2012. Targeted blockade in lethal West Nile virus encephalitis indicates a crucial role for very late antigen (VLA)-4-dependent recruitment of nitric oxide-producing macrophages. Journal of Neuroinflammation 9 (1), 246.


TM Ashhurst, DA Cox, AL Smith, NJC King 2021. Cell counting with a haemocytometer (with mouse bone marrow example).


High-dimensional single cell mass cytometry (CyTOF) comes to Australia with the establishment of the Ramaciotti Facility for Human Systems Biology. 2015. T Ashhurst, N King, A Smith, BF de St Groth. ASI Newsletter.