European Conference on Mathematical and Theoretical Biology (ECMTB 2026)

Inferring and modeling stochastic biochemical processes at the single-cell level

Not scheduled

20m

University of Graz

Minisymposium Systems Biology and Biochemical Networks Inferring and designing stochastic biochemical processes at the single-cell level

Speakers

Alexandra Loudieres (Université Paris-Saclay) Juan David Marmolejo Lozano (University of Edinburgh) Valentine Brulard (Inria Saclay) William Hilton (Imperial College London)

Description

Biochemical processes inside cells are fundamentally stochastic. Inferring parameters of stochastic models describing these processes from collected single-cell data poses mathematical and computational problems. This minisymposium brings together international speakers who will present recent methodological advances on modeling and inference with different types of single-cell data. Juan David Marmolejo-Lozano (Uni. of Edinburgh) will present a general stochastic framework showing how DNA replication–induced gene dosage changes shape the timing and variability of threshold-crossing events in transcriptional networks, with implications for single-cell inference. Valentine Brulard (Inria Saclay) will present an age-structured model that connects stochastic intracellular plasmid replication and segregation dynamics to population-level plasmid copy number distributions. William Hilton (Imperial College London) will focus on inferring gene regulatory networks from single-cell RNA sequencing data by utilizing moment equations of interacting random telegraph models. Alexandra Loudieres (Paris-Saclay Uni.) will propose a model of phage mediated communication between bacteria that shows the importance of stochastic modeling for the design of bacterial communication systems \cite{c,d,e}. Together, the talks address important challenges in learning and modeling stochastic processes at the single-cell level and propose innovative mathematical solutions to deal with computational challenges in stochastic modeling and statistical inference.

Bibliography

@article{c,
title={Phage-mediated intercellular CRISPRi for biocomputation in bacterial consortia},
author={Pujar, Abhinav and Pathania, Amit and Hopper, Corbin and Pandi, Amir and Calder{\'o}n, Cristian Ruiz and F{\"u}gger, Matthias and Nowak, Thomas and Kushwaha, Manish},
journal={Nucleic Acids Research},
volume={53},
number={3},
year={2025},
publisher={Oxford University Press}
}

@article{d,
title={An M13 phagemid toolbox for engineering tuneable DNA communication in bacterial consortia},
author={Pujar, Abhinav and Sharma, Anchita and Jbara, Hadi and Kushwaha, Manish},
journal={bioRxiv},
pages={2025--06},
year={2025},
publisher={Cold Spring Harbor Laboratory}
}

@article{e,
title={Distributed computation with continual population growth},
author={Cho, Da-Jung and F{\"u}gger, Matthias and Hopper, Corbin and Kushwaha, Manish and Nowak, Thomas and Soubeyran, Quentin},
journal={Distributed Computing},
volume={35},
number={6},
pages={547--569},
year={2022},
publisher={Springer}
}