Matt Thomson

California Institute of Technology — United States

Biochemistry, Genetics and Molecular Biology · Life Sciences

17h-index1.8kcitations90works7.42yr avg
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Research Topics

Single-cell and spatial transcriptomics(21), Gene Regulatory Network Analysis(17), Cell Image Analysis Techniques(10), Cellular Mechanics and Interactions(7), Pluripotent Stem Cells Research(6)

Publications90 total

1131 Spatially-guided therapy predictions with morpheus
Regular and Young Investigator Award Abstracts·2025Open Access
Pretrained protein language models choose between sequence novelty and structural completeness
2025Open Access
Geometry-dependent defect merging induces bifurcated dynamics in active networks
Physical Review Research·2025· 1 citedOpen Access
Boundaries Program Deformation in Isolated Active Networks
arXiv (Cornell University)·2025Open Access
Rapid discovery of new-to-nature protein domains by novelty-first forcing of language models
2025Open Access
Designing signaling environments to modulate neural progenitor cell differentiation with regulatory network models
2025Open Access
Reverse Engineering the Evolutionary Logic of Cytoskeletal Dynamics
2025Open Access
Force Propagation in Active Cytoskeletal Networks
2025Open Access
Designing biochemical circuits with tree search
2025Open Access
Author response: Designing biochemical circuits with tree search
2025Open Access
Designing biochemical circuits with tree search
2025Open Access
Revealing a coherent cell state landscape across single cell datasets with CONCORD
2025Open Access
Identifying perturbations that boost T-cell infiltration into tumours via counterfactual learning of their spatial proteomic profiles
Nature Biomedical Engineering·2025· 6 citedOpen Access
Dynamic flow control through active matter programming language
Nature Materials·2025· 10 citedOpen Access
Designing biochemical circuits with tree search
2025Open Access
Benchmarking protein language models for protein crystallization
Scientific Reports·2025· 8 citedOpen Access
Designing Signaling Environments To Modulate Neural Progenitor Cell Differentiation With Regulatory Network Modelss
SSRN Electronic Journal·2025Open Access
Control of spatio-temporal patterning via cell growth in a multicellular synthetic gene circuit
Nature Communications·2024· 9 citedOpen Access
Engineering flexible machine learning systems by traversing functionally invariant paths
Nature Machine Intelligence·2024· 8 citedOpen Access
Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease
Nature Communications·2024· 39 citedOpen Access
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Frequent Co-authors

Sisi Chen(8), Jake Cornwall-Scoones(4), David A. Sivak(4), Paul Rivaud(4), Alexander Viloria Winnett(4), Reid Akana(4), Natasha Shelby(4), Hannah Davich(4), Saharai Caldera(4), Taikun Yamada(4), John Raymond B. Reyna(4), Anna E. Romano(4), Alyssa M. Carter(4), Mi Kyung Kim(4), Colten Tognazzini(4), Matthew Feaster(4), Ying-Ying Goh(4), Yap Ching Chew(4), Rustem F. Ismagilov(4), Vasudha Srivastava(3)