Publications

2024

Theoretical Limits of Energy Extraction in Active Fluids

Shahriar Shadkhoo, Matt Thomson

2024, Physical Review Research

2023

Force Propagation in Active Cytoskeletal Networks

Shichen Liu, Rosalind Wenshan Pan, Heun Jin Lee, Shahriar Shadkhoo, Fan Yang, Chunhe Li, Zijie Qu, Matt Thomson

2024, arXiv preprint

TRILL: Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable Protein Analysis and Engineering

Zachary A Martinez, Richard M. Murray, Matt W. Thomson

2023, bioRxiv preprint

Unexplored regions of the protein sequence-structure map revealed at scale by a library of foldtuned language models

Arjuna M. Subramanian, Matt Thomson

2023, bioRxiv preprint

What's the Magic Word? A Control Theory of LLM Prompting

Aman Bhargava, Cameron Witkowski, Manav Shah, Matt Thomson

2023, arXiv preprint

Herd: Using multiple, smaller LLMs to match the performances of proprietary, large LLMs via an intelligent composer

Surya Narayanan Hari and Matt  Thomson

2023, arXiv preprint

Generating counterfactual explanations of tumor spatial proteomes to discover therapeutic strategies for enhancing immune infiltration

Zitong Jerry Wang, Alexander M. Xu, Aman Bhargava and Matt W. Thomson

2023, bioRxiv preprint

Automated construction of cognitive maps with predictive coding

James A. Gornet and Matt  Thomson

2023, bioRxiv preprint

Tryage: Real-time, intelligent routing of user prompts to large language models

Surya Narayanan Hari and Matt  Thomson

2023, arXiv preprint

Unraveling cell differentiation mechanisms through topological exploration of single-cell developmental trajectories

Emanuel Flores-Bautista, Matt Thomson

2023, bioRxiv preprint

Dynamic Flow Control Through Active Matter Programming Language

Fan Yang, Shichen Liu, Heun Jin Lee, Matt Thomson

2023, arXiv preprint

D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response

Jialong Jiang, Sisi Chen, Tiffany Tsou, Christopher S McGinnis, Tahmineh Khazaei, Qin Zhu, Jong H Park, Inna-Marie Strazhnik, John Hanna, Eric D Chow, David A Sivak, Zev J Gartner, Matt Thomson

2023, bioRxiv preprint

Connectedness of loss landscapes via the lens of Morse theory

Danil Akhtiamov, Matt Thomson

2023, Proceedings of the 1st NeurIPS Workshop on Symmetry and Geometry in Neural Representations

Motor processivity and speed determine structure and dynamics of microtubule-motor assemblies

Rachel A Banks, Vahe Galstyan, Heun Jin Lee, Soichi Hirokawa, Athena Ierokomos, Tyler D Ross, Zev Bryant, Matt Thomson, Rob Phillips
2023, eLife 12:e79402

Spin glasses, error correcting codes, and synchronization of human stem cell organoids

Matt Thomson

2023, Cell  (Preview Article)

2022

Stem cell-derived synthetic embryos self-assemble by exploiting cadherin codes and cortical tension

Min Bao, Jake Cornwall-Scoones, Estefania Sanchez-Vasquez, Dong-Yuan Chen, Joachim De Jonghe, Shahriar Shadkhoo, Florian Hollfelder, Matt Thomson, David M. Glover & Magdalena Zernicka-Goetz

2022, Nature Cell Biology

CloudPred: Predicting Patient Phenotypes From Single-cell RNA-seq

Bryan He, Matthew Thomson, Meena Subramaniam, Richard Perez, Chun Jimmie Ye & James Zou

2022, Pacific Symposium on Biocomputing

Generating counterfactual explanations of tumor spatial proteomes to discover effective, combinatorial therapies that enhance cancer immunotherapy

Zitong Jerry Wang and Matt Thomson

2022, NeurIPS AI for Science

Neural networks learn an environment's geometry in latent space by performing predictive coding on visual scenes

James Gornet and Matt Thomson

2022, NeurIPS Information-theoretic Principles in Cognitive Science

Control of spatio-temporal patterning via cell density in a multicellular synthetic gene circuit

Marco Santorelli, Pranav S. Bhamidipati, Dominik Schildknecht, Andriu Kavanagh, Victoria A. MacKrell, Trusha Sondkar, Matt Thomson & Leonardo Morsut

2022, bioRxiv

Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution

Lyndsay M. Murrow, Robert J. Weber, Joseph A. Caruso, Christopher S. McGinnis, Kiet Phong, Philippe Gascard, Gabrielle Rabadam, Alexander D. Borowsky, Tejal A. Desai, Matthew Thomson, Thea Tlsty, Zev J. Gartner

2022, Cell Systems

Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments

Zitong Jerry Wang and Matt Thomson

2022, Cell Systems

Minimal gene set discovery in single-cell mRNA-seq datasets with ActiveSVM

Xiaoqiao Chen, Sisi Chen & Matt Thomson

2022, Nature Computational Science

Reinforcement learning reveals fundamental limits on the mixing of active particles

Dominik Schildknecht, Anastasia N Popova, Jack Stellwagen & Matthew Thomson

2022, Soft Matter

A DNA repair pathway can regulate transcriptional noise to promote cell fate transitions

Ravi V Desai, Xinyue Chen, Benjamin Martin, Sonali Chaturvedi, Dong Woo Hwang, Weihan Li, Chen Yu, Sheng Ding, Matt Thomson, Robert H Singer, Robert A Coleman, Maike MK Hansen, Leor S Weinberger

2022, Science

Engineering flexible machine learning systems by traversing functionally invariant paths in weight space

Guruprasad Raghavan and Matt Thomson

2022, arXiv preprint

2021

Deep parallel characterization of AAV tropism and AAV-mediated transcriptional changes via single-cell RNA sequencing

David Brown, Michael Altermatt, Tatyana Dobreva, Sisi Chen, Alexander Wang, Matt Thomson, Viviana Gradinaru
Frontiers in Immunology, 2021

Linear Transformations in Autoencoder Latent Space Predict Time Translations in Active Matter System

Enrique Amaya, Shahriar Shadkhoo, Dominik Schildknecht & Matt Thomson
NeurIPS AI for Science, 2021

Deep parallel characterization of AAV tropism and AAV-mediated transcriptional changes via single-cell RNA sequencing

David Brown, Michael Altermatt, Tatyana Dobreva, Sisi Chen, Alexander Wang, Matt Thomson, Viviana Gradinaru
bioRxiv pre-print, 2021

Phenomenological model of motility by spatiotemporal modulation of active interactions

Dominik Schildknecht, Matt Thomson
New Journal of Physics, 2021

Active feature selection discovers minimal gene-sets for classifying cell-types and disease states in single-cell mRNA-seq data

Xiaoqiao Chen, Sisi Chen, and Matt Thomson
arXiv preprint, 2021

Solving hybrid machine learning tasks by traversing weight space geodesics

Guruprasad Raghavan and Matt Thomson
arXiv preprint, 2021

Reinforcement Learning reveals fundamental limits on the mixing of active particles

Dominik Schildknecht, Anastasia N. Popova, Jack Stellwagen, and Matt Thomson
arXiv preprint, 2021 

2020

Single cell profiling of capillary blood enables out of clinic human immunity studies

Tatyana Dobreva, David Brown, Jong Hwee Park, and Matt Thomson
Scientific Reports, 2020

Dissecting heterogeneous cell populations across drug and disease conditions with PopAlign

Sisi Chen, Paul Rivaud, Jong H. Park, Tiffany Tsou, Emeric Charles, John R. Haliburton, Flavia Pichiorri, and Matt Thomson
PNAS, 2020

Self-organization of multi-layer spiking neural networks

Guruprasad Raghavan, Cong Lin, Matt Thomson
arXiv preprint, 2020

Geometric algorithms for predicting resilience and recovering damage in neural networks

Guruprasad Raghavan, Jiayi Li, Matt Thomson
arXiv preprint, 2020

Designing signaling environments to steer transcriptional diversity in neural progenitor cell populations

Jong H. Park, Tiffany Tsou, Paul Rivaud, Matt Thomson and Sisi Chen
bioRxiv, 2020 

2019 – 2008

Highly Multiplexed Single-Cell RNA-seq for Defining Cell Population and Transcriptional Spaces

Jase Gehring, Jong Hwee Park, Sisi Chen, Matthew Thomson and Lior Pachter
Nature Biotechnology volume 38, (35–38), 2019

Controlling Organization and Forces in Active Matter Through Optically-Defined Boundaries

Tyler D. Ross, Heun Jin Lee, Zijie Qu, Rachel A. Banks, Rob Phillips and Matt Thomson
Nature 572 224–229, 2019

Neural networks grown and self-organized by noise

Guruprasad Raghavan and Matt Thomson
NeurIPS, 2019

Diffusion as a Ruler: Modeling Kinesin Diffusion as a Lenth Sensor for Intraflagellar Transport

Nathan L. Hendel, Matt Thomson and Wallace F. Marshall
Biophysical Journal, 114 (3). 335A-336A. ISSN 0006-3495, 2018

Diffusion as a Ruler: Modeling Kinesin Diffusion as a Length Sensor for Intraflagellar Transport

Nathan L. Hendel, Matthew Thomson and Wallace F. Marshall
Biophysical Journal, 114 (3). pp. 663-674. ISSN 0006-3495, 2017

Diffusion as a ruler: Modeling kinesin diffusion as a length sensor for intraflagellar transport

N. L. Hendel, M. Thomson and W. F. Marshall
Molecular Biology of the Cell, 28 (26). Art. No. M196. ISSN 1059-1524, 2017

Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing

Graham Heimberg, Rajat Bhatnagar, Hana El-Samad and Matt Thomson
Cell Systems, 2 (4). pp. 239-250. ISSN 2405-4712. PMCID PMC4856162, 2016

Signaling Boundary Conditions Drive Self-Organization of Human “Gastruloids”.

Matthew Thomson
Developmental Cell, 39 (3). pp. 279-280. ISSN 1534-5807, 2016

The rational parameterisation theorem for multisite post-translational modification systems.

Matthew Thomson and Jeremy Gunawardena
Journal of Theoretical Biology, 261 (4). pp. 626-636. ISSN 0022-5193. PMCID PMC2800989, 2009