The Thomson Lab is applying quantitative experimental and modeling approaches to gain programmatic control over cellular differentiation. He is developing mathematical models to ask how cellular regulatory networks generate the vast diversity of cell-types that exists in the human body. He is applying models to engineer and rewire cellular physiology and to synthesize new types of cells that do not exist in nature. He is also developing simplified cellular systems in which physical models can be applied to control the geometry and morphology of different cell types. He uses a combination of approaches including mathematical modeling, machine learning, statistical analysis of high-throughput gene expression data, and single cell RNA sequencing experiments. Recent accomplishments include: Engineering an all-optical differentiation system in which he could optically-deliver pulsed neural differentiation inputs to embryonic stem cells; creating new computational tools for deriving cell state trajectories from single cell RNA-Seq data; and developing a stochastic modeling framework for analyzing principles that enable robust self-organization of the mammary gland.
Publications
- Santorelli, Marco;Bhamidipati, Pranav S. et al. (2024) Control of spatio-temporal patterning via cell growth in a multicellular synthetic gene circuitNature Communications
- Polonsky, Michal;Gerhardt, Louisa M. S. et al. (2024) Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and diseaseNature Communications
- Garibyan, Mher;Hoffman, Tyler et al. (2024) Engineering programmable material-to-cell pathways via synthetic notch receptors to spatially control differentiation in multicellular constructsNature Communications
- Huycke, Tyler R.;Häkkinen, Teemu J. et al. (2024) Patterning and folding of intestinal villi by active mesenchymal dewettingCell
- Shadkhoo, Shahriar;Thomson, Matt (2024) Theoretical limits of energy extraction in active fluidsPhysical Review Research
- Gornet, James A.;Thomson, Matt (2024) Automated construction of cognitive maps with predictive codingbioRxiv
- Vasquez Ayala, Adriana;Hsu, Chia-Yun et al. (2024) Commensal bacteria promote type I interferon signaling to maintain immune tolerance in miceJournal of Experimental Medicine
- Subramanian, Arjuna M.;Thomson, Matt (2023) Unexplored regions of the protein sequence-structure map revealed at scale by a library of foldtuned language models
- Polonsky, Michal;Gerhardt, Louisa M. S. et al. (2023) Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and diseasebioRxiv
- Martinez, Zachary A;Murray, Richard M. et al. (2023) TRILL: Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable Protein Analysis and EngineeringbioRxiv