Bioinformatics Seminar
Time: 11AM
Venue: Davis Auditorium and Slido
29 March 2022
This is a WEHI internal seminarAnalysing immunological data at two extreme scales
Kristen FeherWEHI Bioinformatics
Macroscopic phenomena are the emergent properties of countless molecular interactions, however there is no single experimental technique that captures exactly how molecular interactions coalesce on the nanometre scale into a person on the metre scale. I will present two methods I have developed in an immunological context that characterises variation over a set of biological samples at two very different scales.
The first method is the analysis of a set of single molecule localisation microscopy (SMLM) images of T cells (with a TCR staining), which I carried out in the lab of the late Kat Gaus, who was Australia's pioneer in SMLM. I will introduce how I consider the images as a composition of local neighbourhoods (K-neighbourhood analysis). I use this method to compare TCR phosphorylation patterns in T cells compared to CAR T cells.
The second method introduces a method to obtain a patient-centric overview of a large number of flow cytometry samples. This is done in such a way that most traditional gating is avoided, apart from FSC/SSC and doublet gating. The method embeds the samples in a latent space and provides 'explanatory components' (EC) or interpretation. The ECs can be derived from quantities such as pseudobulk measurements of log-odds ratios of marker pairs, extracted from the flow samples, or from external covariates such as cytokine concentration.