Spectral gene selection methods and models for host/parasite co-phylogeny

Date

Oct 16, 2025

Time

3:00 PM - 3:45 PM

Speaker

Renee Hoekzema

Affiliation

Vrije Universiteit Amsterdam

Language

en

Main Topic

Biologie

Host

Organisers: Nikola Sadovek, Maximilian Wiesmann, Giulio Zucal

Description

I will talk about two disjoint projects. Firstly, I will talk about an application of spectral graph theory to the study of single cell transcriptomics, in particular the problem of feature selection of relevant genes in such experiments. Single cell transcriptomics is a powerful technique in biology that allows for the measurement of gene expression levels in many individual cells simultaneously. Current methods for analysis assume that cell types are discrete. However, in practice there is also continuous variation between cells: subtypes of subtypes, differentiation pathways, responses to environment or treatment, et cetera. We propose topologically-inspired data analysis methods that identify coherent gene expression patterns considering discrete and continuous patterns on equal footing. This is joint work with Lewis Marsh, Otto Sumray, Thomas Carroll, Xin Lu, Helen Byrne and Heather Harrington. Secondly, I will talk about ongoing work with Gillian Grindstaff on models for co-evolution of “nested’’ systems, such as parasite/host systems, individuals within a species, or “phylosymbiosis” – the coupled evolution of the microbiome and its hosts. We create a space of nested phylogenetic trees and study its intricate geometry. In particular we show that this space is CAT(0) – in analogy with the influential work of Billera, Holmes and Vogtmann (2001) – implying the existence of unique averages over nested trees.

Last modified: Oct 16, 2025, 7:35:47 AM