SoftBio Theory Seminar: Physical modeling of embryonic transcriptomes identifies collective modes of gene expression

19 May 2025
Seminars and colloquia
Time
-
Venue
Simpkins Lee Seminar Room
Beecroft Building, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU
Speaker(s)

Dr Dominic Skinner, Flatiron Institute

Abstract

Starting from one totipotent cell, complex multicellular organisms form through a series of differentiation and morphogenetic events, culminating in a multitude of cell types arranged in a functional and intricate spatial pattern. To do so, cells coordinate with each other, resulting in dynamics which follow a precise developmental trajectory, constraining the space of possible embryo-to-embryo variation. Using recent single-cell sequencing data of early ascidian embryos, we study this natural variation at the level of a complete interconnected embryo. After developing a robust and biophysically motivated approach to classify cells into distinct transcriptomic states or cell types, a statistical analysis reveals correlations within embryos demonstrating the presence of collective variation. From these intra-embryo correlations, we infer minimal networks of cell-cell interactions using statistical physics models, and from these identify collective modes of gene expression.