Immune Dynamics collaborative team

Editor

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

Lead, senior, or corresponding author

1. Givanna H Putri, Jonathan Chung, Davis N Edwards, Felix Marsh‐Wakefield, Irena Koprinska, Suat Dervish, Nicholas JC King, Thomas M Ashhurst*, Mark N Read*. 2022. TrackSOM: mapping immune response dynamics through clustering of time‐course cytometry data. Cytometry Part A.

2. 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. Corresponding author.

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

4. 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

5. 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

6. 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.

7. 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

8. 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

Senior or co-senior author, or co-supervising role

1. 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).

2. 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. Research Square (pre-print).

3. 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.

4. 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

5. 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

Co-author

• 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.

• Niels JM Verstegen, Ruth R Hagen, Jet van den Dijssel, Lisan H Kuijper, Christine Kreher, Thomas Ashhurst, Laura YL Kummer, … Marieke SM van Ham, Anja ten Brinke, Carolien E van de Sandt, on behalf of the T2B! immunity against SARS-CoV-2 study group. 2022. Immune dynamics in SARS-CoV-2 experienced immunosuppressed rheumatoid arthritis or multiple sclerosis patients vaccinated with mRNA-1273. eLife.

• 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.

• 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.

• F Marsh‐Wakefield, T Ashhurst, S Trend, HM McGuire, P Juillard, A Zinger, … 202. 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

• 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

• 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

• 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.

• News items: ABC News, The Guardian.

• 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.

Protocols at protocols.io

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• TM Ashhurst, DA Cox, AL Smith, NJC King 2021. Cell counting with a haemocytometer (with mouse bone marrow example). protocols.io https://dx.doi.org/10.17504/protocols.io.btqgnmtw

Newsletters

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• 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.