ASI IgV Masterclass 2021 - workshop on high-dimensional analysis of COVID-19

In 2021, the Immunology Group of Victoria (IgV) of the Australia and New Zealand Society for Immunology (ASI) are running a masterclass on ‘Quantitative Immunology’.


Workshop (Tue 26-Oct) sessions

Tuesday will consist of a series of online hands-on workshop sessions.


The workshop day (Tue 26-Oct) will start off with some opening remarks on COVID-19 and respiratory immunology from Thomas Ashhurst, Oanh Nguyen, and Katherine Kedzierska.

Session #1: Getting started with cytometry analysis using Spectre and R

Lead instructors: Givanna Putri, Felix Marsh-Wakefield

In this session, instructors will introduce attendees to methods of high-dimensional analysis with R/RStudio. Specifically we will use the R package Spectre, and will explore computational approaches such as clustering (e.g. using FlowSOM) and dimensionality reduction (e.g. using tSNE or UMAP).

Session #2: High-dimensional analysis of immune responses to COVID-19 in perhiperhal blood

Lead instructors: Felix Marsh-Wakefield, Jennifer Habel

In this session we will be investigating the immune response to COVID-19 in perihperal blood. We will compare immune responses in healthy controls, convalescent patients, and patients with mild COVID-19 or severe COVID-19.

Session #3: High-dimensional analysis of immune responses to COVID-19 in the respiratory tract

Lead instructors: Givanna Putri, Wuji Zhang

In this session we will be investigating the immune response to COVID-19 in the respiratory tract, from samples acquired via an endotracheal tube. In particular we will explore a variety of myeloid cells that infiltrate the respiratory tract via the blood, including macrophages and neutrophils, and how they compare to similar cells in the blood.

Workshop instructor profiles

Thomas Ashhurst is a high-dimensional cytometry specialist with the Sydney Cytometry Core Research Facility, and an Honorary Research Fellow with the School of Medical Sciences at The University of Sydney. His work is focused on the development and application of high-dimensional single-cell and imaging methods, as well as advanced computational approaches, to comprehensively map the dynamic immune responses to inflammation and infectious diseases.
Givanna Putri is a postdoctoral research fellow at the Lowy Cancer Research Centre. Her research focuses on developing and applying computational approaches to analyse high dimensional single-cell data.
Felix Marsh-Wakefield is a post-doctoral researcher interrogating the immune landscape in hepatocellular carcinoma. He uses bioinformatics to assist in the analysis of high dimensional data, including cytometry, transcriptomic and spatial data.
Wuji Zhang is a PhD candidate from the Kedzierska lab at the Peter Doherty Institute. Wuji's PhD project involves investigating immune responses towards influenza and SARS-CoV-2 infections and vaccinations.
Jennifer Habel is a PhD candidate in the Kedzierska Laboratory at the University of Melbourne/Peter Doherty Institute for Infection and Immunity. Her work focuses on defining immune responses to respiratory viral infections in pregnant women to better understand how immunomodulation during pregnancy can affect disease severity.