Day 1 (Mon 25-Oct) will feature talks on Imaging from Prof. Tri Phan (Garvan Institute) and Dr. Joanna Groom (WEHI), Single-cell analysis from A/Prof. Fabio Luciani (UNSW) and Prof. Wei Shi (ONJCRI), and COVID-19/respiratory immunology from Prof. Stephanie Gras (La Trobe University) and Prof. Katherine Kedzierska.
Day 2 (Tue 26-Oct) will consist of an online workshop where we will apply high-dimensional analysis approaches to profile the immune responses to COVID-19 in the blood and respiratory tract, reproducing the types of analysis used in Koustakous et al. 2021 and Zhang et al. 2021. This workshop will be led by researchers from the University of Sydney, The University of NSW, The Dohert Institute, and The University of Melbourne; including Thomas Ashhurst, Givanna Putri, Felix Marsh-Wakefield, Wuji Zhang, and Jennifer Habel.
Workshop (Tue 26-Oct) sessions
Tuesday will consist of a series of online hands-on workshop sessions.
Session #1: Getting started with cytometry analysis using Spectre and R
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
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
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.|