<h1>Thomson, Matt</h1>
<h2>Monograph from <a href="https://authors.library.caltech.edu">CaltechAUTHORS</a></h2>
<ul>
<li>Gornet, James A. and Thomson, Matt (2024) <a href="https://authors.library.caltech.edu/records/e288m-hdm97">Automated construction of cognitive maps with predictive coding</a>; bioRxiv; 2023.09.18.558369; <a href="https://doi.org/10.1101/2023.09.18.558369">10.1101/2023.09.18.558369</a></li>
<li>Subramanian, Arjuna M. and Thomson, Matt (2023) <a href="https://authors.library.caltech.edu/records/sv6fh-01002">Unexplored regions of the protein sequence-structure map revealed at scale by a library of foldtuned language models</a>; PMCID PMC10769378; <a href="https://doi.org/10.1101/2023.12.22.573145">10.1101/2023.12.22.573145</a></li>
<li>Polonsky, Michal and Gerhardt, Louisa M. S., el al. (2023) <a href="https://authors.library.caltech.edu/records/hx122-ds441">Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and disease</a>; bioRxiv; <a href="https://doi.org/10.1101/2023.11.22.568217">10.1101/2023.11.22.568217</a></li>
<li>Martinez, Zachary A and Murray, Richard M., el al. (2023) <a href="https://authors.library.caltech.edu/records/0p6md-nzv84">TRILL: Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable Protein Analysis and Engineering</a>; bioRxiv; 2023.10.24.563881; PMCID PMC10659302; <a href="https://doi.org/10.1101/2023.10.24.563881">10.1101/2023.10.24.563881</a></li>
<li>Srivastava, Vasudha and Hu, Jennifer L., el al. (2023) <a href="https://authors.library.caltech.edu/records/7wsj9-9v221">Configurational entropy is an intrinsic driver of tissue structural heterogeneity</a>; PMCID PMC10327153; <a href="https://doi.org/10.1101/2023.07.01.546933">10.1101/2023.07.01.546933</a></li>
<li>Jiang, Jialong and Chen, Sisi, el al. (2023) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230628-257115000.23">D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response</a>; PMCID PMC10153191; <a href="https://doi.org/10.1101/2023.04.19.537364">10.1101/2023.04.19.537364</a></li>
<li>Santorelli, Marco and Bhamidipati, Pranav S., el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230322-366904000.5">Control of spatio-temporal patterning via cell density in a multicellular synthetic gene circuit</a>; <a href="https://doi.org/10.1101/2022.10.04.510900">10.1101/2022.10.04.510900</a></li>
<li>Winnett, Alexander Viloria and Akana, Reid, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220720-917402000">Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods</a>; <a href="https://doi.org/10.1101/2022.07.13.22277113">10.1101/2022.07.13.22277113</a></li>
<li>Winnett, Alexander Viloria and Akana, Reid, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220720-917093000">Why Daily SARS-CoV-2 Nasal Rapid Antigen Testing Poorly Detects Infected and Infectious Individuals</a>; <a href="https://doi.org/10.1101/2022.07.13.22277513">10.1101/2022.07.13.22277513</a></li>
<li>Abdel-Haq, Reem and Schlachetzki, Johannes C. M., el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220706-965670000">A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice</a>; <a href="https://doi.org/10.1101/2022.06.27.497828">10.1101/2022.06.27.497828</a></li>
<li>Raghavan, Guruprasad and Thomson, Matt (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220816-220025879">Engineering flexible machine learning systems by traversing functionally invariant paths in weight space</a>; <a href="https://doi.org/10.48550/arXiv.2205.00334">10.48550/arXiv.2205.00334</a></li>
<li>Pool, Allan-Hermann and Poldsam, Helen, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220505-806027100">Enhanced recovery of single-cell RNA-sequencing reads for missing gene expression data</a>; <a href="https://doi.org/10.1101/2022.04.26.489449">10.1101/2022.04.26.489449</a></li>
<li>Banks, Rachel A. and Galstyan, Vahe, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20211102-171349069">Motor processivity and speed determine structure and dynamics of microtubule-motor assemblies</a>; <a href="https://doi.org/10.1101/2021.10.22.465381">10.1101/2021.10.22.465381</a></li>
<li>Santorelli, Marco and Bhamidipati, Pranav, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220816-220022495">Cell density controls signal propagation waves in a multicellular synthetic gene circuit</a>; <a href="https://doi.org/10.48550/arXiv.2107.08116">10.48550/arXiv.2107.08116</a></li>
<li>Wang, Zitong Jerry and Thomson, Matt (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220816-220019094">Signaling receptor localization maximizes cellular information acquisition in spatially-structured, natural environments</a>; <a href="https://doi.org/10.48550/arXiv.2107.00806">10.48550/arXiv.2107.00806</a></li>
<li>Chen, Xiaoqiao and Chen, Sisi, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210622-154854635">Active feature selection discovers minimal gene sets for classifying cell types and disease states with single-cell mRNA-seq data</a>; <a href="https://doi.org/10.1101/2021.06.15.448478">10.1101/2021.06.15.448478</a></li>
<li>Qu, Zijie and Jiang, Jialong, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210217-132137942">Programming Boundary Deformation Patterns in Active Networks</a>; <a href="https://doi.org/10.48550/arXiv.2101.08464">10.48550/arXiv.2101.08464</a></li>
<li>Dobreva, Tatyana and Brown, David, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200727-093309639">Enabling out-of-clinic human immunity studies via single-cell profiling of capillary blood</a>; <a href="https://doi.org/10.1101/2020.07.25.210468">10.1101/2020.07.25.210468</a></li>
<li>Chen, Sisi and Park, Jong H., el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200102-083334191">Designing signaling environments to steer transcriptional diversity in neural progenitor cell populations</a></li>
<li>Jiang, Jialong and Sivak, David A., el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190520-085022351">Active Learning of Spin Network Models</a>; <a href="https://doi.org/10.48550/arXiv.1903.10474">10.48550/arXiv.1903.10474</a></li>
<li>Murrow, Lyndsay M. and Weber, Robert J., el al. (2018) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200121-074722672">Changes in epithelial proportions and transcriptional state underlie major premenopausal breast cancer risks</a>; <a href="https://doi.org/10.1101/430611">10.1101/430611</a></li>
</ul>