European Conference on Mathematical and Theoretical Biology (ECMTB 2026)

Making cells dance: modelling gene regulation and cell fate from transcriptomics

Not scheduled

20m

University of Graz

Minisymposium Systems Biology and Biochemical Networks Making cells dance: modelling gene regulation and cell fate from transcriptomics

Speakers

Dimitris Volteras (The Francis Crick Institute) Jack Soulsby (Imperial College London) Tara Chari (Eric and Wendy Schmidt Center at the Broad Institute of MIT and Harvard) Weixu Wang (ICB, Helmholtz Munich)

Description

Understanding how gene regulation gives rise to diverse cell states and cell fates during differentiation is a central question in biology. Single-cell RNA sequencing (scRNA-seq), as a rapidly developing and powerful methodology, provides both new insights into this problem and new challenges for mathematical modeling. While scRNA-seq enables measurement of genome-wide gene expression at single-cell resolution, it provides only snapshot data. This makes inference of dynamical processes and regulatory mechanisms difficult. How to fully exploit the rich gene expression information in the data while overcoming these inherent limitations remains a challenging open problem.

This minisymposium presents recent work that tackles these challenges from complementary perspectives. We will cover stochastic methods that utilize time-resolved single-cell transcriptomics \cite{Volteras} and perturbation \cite{Chari} to shed light on gene regulation, as well as approaches for inferring cell differentiation dynamics based on drift–diffusion Markov processes and deep learning models that encode gene regulatory relationships \cite{Wang}. These cutting edge methodologies provide distinct magnifying lenses on cellular dynamics. Their synergy through a shared emphasis on mathematical modeling and statistical inference will foster a timely discussion of both the limitations and opportunities in scRNA-seq–based modeling of gene regulation and cell fate.

Bibliography

@ARTICLE{Volteras,
title = "Global transcription regulation revealed from dynamical
correlations in time-resolved single-cell {RNA} sequencing",
author = "Volteras, Dimitris and Shahrezaei, Vahid and Thomas, Philipp",
journal = "Cell Syst.",
publisher = "Elsevier BV",
volume = 15,
pages = "694-708.e12",
year = 2024,
doi = "10.1016/j.cels.2024.07.002"
}
@ARTICLE{Wang,
title = "{RegVelo}: gene-regulatory-informed dynamics of single cells",
author = "Wang, Weixu and Hu, Zhiyuan and Weiler, Philipp and Mayes, Sarah
and Lange, Marius and Wang, Jingye and Xue, Zhengyuan and
Sauka-Spengler, Tatjana and Theis, Fabian J",
journal = "bioRxiv",
pages = "2024.12.11.627935",
year = 2024,
doi = "10.1101/2024.12.11.627935"
}
@ARTICLE{Chari,
title = "Stochastic modeling of biophysical responses to perturbation",
author = "Chari, Tara and Gorin, Gennady and Pachter, Lior",
journal = "bioRxivorg",
year = 2024,
doi = "10.1101/2024.07.04.602131"
}