Thomson, Matt

Combined from CaltechAUTHORS

• Polonsky, Michal and Gerhardt, Louisa M. S., et el. (2024) Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease; Nature Communications; Vol. 15; No. 1; 7010; PMCID PMC11377535; 10.1038/s41467-024-51186-z
• Garibyan, Mher and Hoffman, Tyler, et el. (2024) Engineering programmable material-to-cell pathways via synthetic notch receptors to spatially control differentiation in multicellular constructs; Nature Communications; Vol. 15; 5891; PMCID PMC11246427; 10.1038/s41467-024-50126-1
• Huycke, Tyler R. and Häkkinen, Teemu J., et el. (2024) Patterning and folding of intestinal villi by active mesenchymal dewetting; Cell; Vol. 187; No. 12; 3072-3089.e20; 10.1016/j.cell.2024.04.039
• Shadkhoo, Shahriar and Thomson, Matt (2024) Theoretical limits of energy extraction in active fluids; Physical Review Research; Vol. 6; No. 2; 023195; 10.1103/physrevresearch.6.023195
• Gornet, James A. and Thomson, Matt (2024) Automated construction of cognitive maps with predictive coding; bioRxiv; 2023.09.18.558369; 10.1101/2023.09.18.558369
• Vasquez Ayala, Adriana and Hsu, Chia-Yun, et el. (2024) Commensal bacteria promote type I interferon signaling to maintain immune tolerance in mice; Journal of Experimental Medicine; Vol. 221; No. 1; e20230063; PMCID PMC10716256; 10.1084/jem.20230063
• Subramanian, Arjuna M. and Thomson, Matt (2023) Unexplored regions of the protein sequence-structure map revealed at scale by a library of foldtuned language models; PMCID PMC10769378; 10.1101/2023.12.22.573145
• Polonsky, Michal and Gerhardt, Louisa M. S., et el. (2023) Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and disease; bioRxiv; 10.1101/2023.11.22.568217
• Martinez, Zachary A and Murray, Richard M., et el. (2023) TRILL: Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable Protein Analysis and Engineering; bioRxiv; 2023.10.24.563881; PMCID PMC10659302; 10.1101/2023.10.24.563881
• Pool, Allan-Hermann and Poldsam, Helen, et el. (2023) Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references; Nature Methods; 10.1038/s41592-023-02003-w
• Bao, Min and Cornwall-Scoones, Jake, et el. (2023) Stem cell-derived synthetic embryos self-assemble by exploiting cadherin codes and cortical tension; Nature Cell Biology; Vol. 24; No. 9; 1341-2349; PMCID PMC9481465; 10.1038/s41556-022-00984-y
• Srivastava, Vasudha and Hu, Jennifer L., et el. (2023) Configurational entropy is an intrinsic driver of tissue structural heterogeneity; PMCID PMC10327153; 10.1101/2023.07.01.546933
• Winnett, Alexander Viloria and Akana, Reid, et el. (2023) Daily SARS-CoV-2 Nasal Antigen Tests Miss Infected and Presumably Infectious People Due to Viral Load Differences among Specimen Types; Microbiology Spectrum; Vol. 11; No. 4; e01295-23; PMCID PMC10434058; 10.1128/spectrum.01295-23
• Jiang, Jialong and Chen, Sisi, et el. (2023) D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response; PMCID PMC10153191; 10.1101/2023.04.19.537364
• Lemma, Linnea M. and Varghese, Minu, et el. (2023) Spatio-temporal patterning of extensile active stresses in microtubule-based active fluids; PNAS Nexus; Vol. 2; No. 5; Art. No. pgad130; PMCID PMC10165807; 10.1093/pnasnexus/pgad130
• Santorelli, Marco and Bhamidipati, Pranav S., et el. (2023) Control of spatio-temporal patterning via cell density in a multicellular synthetic gene circuit; 10.1101/2022.10.04.510900
• Winnett, Alexander Viloria and Akana, Reid, et el. (2023) Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods; PNAS Nexus; Vol. 2; No. 3; pgad033; PMCID PMC10013338; 10.1093/pnasnexus/pgad033
• Banks, Rachel A. and Galstyan, Vahe, et el. (2023) Motor processivity and speed determine structure and dynamics of microtubule-motor assemblies; eLife; Vol. 12; Art. No. e79402; PMCID PMC10014072; 10.7554/elife.79402
• Thomson, Matt (2023) Spin glasses, error correcting codes, and synchronization of human stem cell organoids; Cell; Vol. 186; No. 3; 461-463; 10.1016/j.cell.2023.01.006
• Abdel-Haq, Reem and Schlachetzki, Johannes C. M., et el. (2022) A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice; eLife; Vol. 11; Art. No. e81453; PMCID PMC9668333; 10.7554/elife.81453
• Bao, Min and Cornwall-Scoones, Jake, et el. (2022) Stem cell-derived synthetic embryos self-assemble by exploiting cadherin codes and cortical tension; Nature Cell Biology; Vol. 24; No. 9; 1341-1349; PMCID PMC9481465; 10.1038/s41556-022-00984-y
• Wang, Zitong Jerry and Thomson, Matt (2022) Signaling receptor localization maximizes cellular information acquisition in spatially-structured, natural environments; 10.48550/arXiv.2107.00806
• Murrow, Lyndsay M. and Weber, Robert J., et el. (2022) Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution; Cell Systems; Vol. 13; No. 8; 644-664.e8; PMCID PMC9590200; 10.1016/j.cels.2022.06.005
• Raghavan, Guruprasad and Thomson, Matt (2022) Engineering flexible machine learning systems by traversing functionally invariant paths in weight space; 10.48550/arXiv.2205.00334
• Santorelli, Marco and Bhamidipati, Pranav, et el. (2022) Cell density controls signal propagation waves in a multicellular synthetic gene circuit; 10.48550/arXiv.2107.08116
• Winnett, Alexander Viloria and Akana, Reid, et el. (2022) Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods; 10.1101/2022.07.13.22277113
• Winnett, Alexander Viloria and Akana, Reid, et el. (2022) Why Daily SARS-CoV-2 Nasal Rapid Antigen Testing Poorly Detects Infected and Infectious Individuals; 10.1101/2022.07.13.22277513
• Wang, Zitong Jerry and Thomson, Matt (2022) Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments; Cell Systems; Vol. 13; No. 7; 530-546; 10.1016/j.cels.2022.05.004
• Abdel-Haq, Reem and Schlachetzki, Johannes C. M., et el. (2022) A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice; 10.1101/2022.06.27.497828
• Chen, Xiaoqiao and Chen, Sisi, et el. (2022) Minimal gene set discovery in single-cell mRNA-seq datasets with ActiveSVM; Nature Computational Science; Vol. 2; No. 6; 387-398; 10.1038/s43588-022-00263-8
• Pool, Allan-Hermann and Poldsam, Helen, et el. (2022) Enhanced recovery of single-cell RNA-sequencing reads for missing gene expression data; 10.1101/2022.04.26.489449
• Duarte, Ana I. and Jin Lee, Heun, et el. (2022) Measuring energy consumption through space and time in an active matter system of cytoskeletal motors and filaments; Biophysical Journal; Vol. 121; No. 3; 521a-522a; 10.1016/j.bpj.2021.11.2745
• Larios, David A. and Phillips, Rob, et el. (2022) Reconstituting the nonequilibrium biophysics of the LECA cytoskeleton in active matter; Biophysical Journal; Vol. 121; No. 3; 521a; 10.1016/j.bpj.2021.11.2744
• Schildknecht, Dominik and Popova, Anastasia N., et el. (2022) Reinforcement learning reveals fundamental limits on the mixing of active particles; Soft Matter; Vol. 18; No. 3; 617-625; 10.1039/d1sm01400e
• Banks, Rachel A. and Galstyan, Vahe, et el. (2021) Motor processivity and speed determine structure and dynamics of microtubule-motor assemblies; 10.1101/2021.10.22.465381
• Brown, David and Altermatt, Michael, et el. (2021) Deep Parallel Characterization of AAV Tropism and AAV-Mediated Transcriptional Changes via Single-Cell RNA Sequencing; Frontiers in Immunology; Vol. 12; Art. No. 730825; PMCID PMC8574206; 10.3389/fimmu.2021.730825
• Qu, Zijie and Schildknecht, Dominik, et el. (2021) Persistent fluid flows defined by active matter boundaries; Communications Physics; Vol. 4; Art. No. 198; 10.1038/s42005-021-00703-3
• Desai, Ravi V. and Chen, Xinyue, et el. (2021) A DNA repair pathway can regulate transcriptional noise to promote cell fate transitions; Science; Vol. 373; No. 6557; Art. No. eabc6506; PMCID PMC8667278; 10.1126/science.abc6506
• Schildknecht, Dominik and Thomson, Matt (2021) Phenomenological model of motility by spatiotemporal modulation of active interactions; New Journal of Physics; Vol. 23; No. 8; Art. No. 083001; 10.1088/1367-2630/ac1144
• Chen, Xiaoqiao and Chen, Sisi, et el. (2021) Active feature selection discovers minimal gene sets for classifying cell types and disease states with single-cell mRNA-seq data; 10.1101/2021.06.15.448478
• Qu, Zijie and Jiang, Jialong, et el. (2021) Programming Boundary Deformation Patterns in Active Networks; 10.48550/arXiv.2101.08464
• Srivastava, Vasudha and Hu, Jennifer L., et el. (2021) Identifying Enthalpic Barriers to Entropically-Driven Structural Disruption in Breast Cancers; Biophysical Journal; Vol. 120; No. 3; 196A; 10.1016/j.bpj.2020.11.1347
• Zhu, Meng and Cornwall-Scoones, Jake, et el. (2020) Developmental clock and mechanism of de novo polarization of the mouse embryo; Science; Vol. 370; No. 6522; Art. No. eabd2703; PMCID PMC8210885; 10.1126/science.abd2703
• Dobreva, Tatyana and Brown, David, et el. (2020) Single cell profiling of capillary blood enables out of clinic human immunity studies; Scientific Reports; Vol. 10; Art. No. 20540; PMCID PMC7688970; 10.1038/s41598-020-77073-3
• Chen, Sisi and Rivaud, Paul, et el. (2020) Dissecting heterogeneous cell populations across drug and disease conditions with PopAlign; Proceedings of the National Academy of Sciences of the United States of America; Vol. 117; No. 46; 28784-28794; PMCID PMC7682438; 10.1073/pnas.2005990117
• Gandhi, Shashank and Hutchins, Erica J., et el. (2020) Bimodal function of chromatin remodeler Hmga1 in neural crest induction and Wnt-dependent emigration; eLife; Vol. 2020; No. 9; Art. No. e57779; PMCID PMC7591248; 10.7554/elife.57779
• Dobreva, Tatyana and Brown, David, et el. (2020) Enabling out-of-clinic human immunity studies via single-cell profiling of capillary blood; 10.1101/2020.07.25.210468
• Altermatt, Michael and Brown, David, et el. (2020) In-Depth Parallel Profiling of Tissue and Cell-Type Tropism of AAV Variants by Single-Cell RNA Sequencing; Molecular Therapy; Vol. 28; No. 4; 399-400; 10.1016/j.ymthe.2020.04.019
• Brown, David and Altermatt, Michael, et el. (2020) A Computational and Experimental Platform for Detecting Full Transcriptome Cell Type Tropism of Lowly Expressed Barcoded and Pooled AAV Variants via Single-Cell RNA Sequencing; Molecular Therapy; Vol. 28; No. 4; 80-81; 10.1016/j.ymthe.2020.04.019
• Banks, Rachel and Lee, Heun Jin, et el. (2020) Bridging Kinesin Properties with System-scale Characteristics of Microtubule-Motor Assemblies; Biophysical Journal; Vol. 118; No. 3; 176a-177a; 10.1016/j.bpj.2019.11.1081
• Murrow, Lyndsay M. and Weber, Robert J., et el. (2020) Changes in epithelial proportions and transcriptional state underlie major premenopausal breast cancer risks; 10.1101/430611
• Chen, Sisi and Park, Jong H., et el. (2020) Designing signaling environments to steer transcriptional diversity in neural progenitor cell populations
• Gehring, Jase and Park, Jong Hwee, et el. (2020) Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins; Nature Biotechnology; Vol. 38; No. 1; 35-38; 10.1038/s41587-019-0372-z
• Raghavan, Guruprasad and Thomson, Matt (2019) Neural networks grown and self-organized by noise; 10.48550/arXiv.1906.01039
• Ross, Tyler D. and Lee, Heun Jin, et el. (2019) Controlling Organization and Forces in Active Matter Through Optically-Defined Boundaries; Nature; Vol. 572; No. 7768; 224-229; PMCID PMC6719720; 10.1038/s41586-019-1447-1
• Jiang, Jialong and Sivak, David A., et el. (2019) Active Learning of Spin Network Models; 10.48550/arXiv.1903.10474
• Xu, Alexander M. and Liu, Qianhe, et el. (2018) Integrated measurement of intracellular proteins and transcripts in single cells; Lab on a Chip; Vol. 18; No. 21; 3251-3262; PMCID PMC6752714; 10.1039/c8lc00639c
• Hendel, Nathan L. and Thomson, Matthew, et el. (2018) Diffusion as a Ruler: Modeling Kinesin Diffusion as a Length Sensor for Intraflagellar Transport; Biophysical Journal; Vol. 114; No. 3; 663-674; PMCID PMC5985012; 10.1016/j.bpj.2017.11.3784
• Hendel, Nathan L. and Thomson, Matt, et el. (2018) Diffusion as a Ruler: Modeling Kinesin Diffusion as a Lenth Sensor for Intraflagellar Transport; Biophysical Journal; Vol. 114; No. 3; 335A-336A; 10.1016/j.bpj.2017.11.1877
• Obernier, Kirsten and Cebrian-Silla, Arantxa, et el. (2018) Adult Neurogenesis Is Sustained by Symmetric Self-Renewal and Differentiation; Cell Stem Cell; Vol. 22; No. 2; 221-234; PMCID PMC5802882; 10.1016/j.stem.2018.01.003
• Hendel, N. L. and Thomson, M., et el. (2017) Diffusion as a ruler: Modeling kinesin diffusion as a length sensor for intraflagellar transport; Molecular Biology of the Cell; Vol. 28; No. 26; Art. No. M196; 10.1091/mbc.E17-10-0618
• Aull, Katherine H. and Tanner, Elizabeth J., et el. (2017) Transient Thresholding: A Mechanism Enabling Noncooperative Transcriptional Circuitry to Form a Switch; Biophysical Journal; Vol. 112; No. 11; 2428-2438; PMCID PMC5474885; 10.1016/j.bpj.2017.05.002
• Thomson, Matthew (2016) Signaling Boundary Conditions Drive Self-Organization of Human "Gastruloids"; Developmental Cell; Vol. 39; No. 3; 279-280; 10.1016/j.devcel.2016.10.016
• Heimberg, Graham and Bhatnagar, Rajat, et el. (2016) Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing; Cell Systems; Vol. 2; No. 4; 239-250; PMCID PMC4856162; 10.1016/j.cels.2016.04.001
• Myers, Samuel A. and Peddada, Sailaja, et el. (2016) SOX2O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells; eLife; Vol. 5; Art. No. e10647; PMCID PMC4841768; 10.7554/eLife.10647
• Morsut, Leonardo and Roybal, Kole T., et el. (2016) Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors; Cell; Vol. 164; No. 4; 780-791; PMCID PMC4752866; 10.1016/j.cell.2016.01.012
• Sokolik, Cameron and Liu, Yanxia, et el. (2015) Transcription Factor Competition Allows Embryonic Stem Cells to Distinguish Authentic Signals from Noise; Cell Systems; Vol. 1; No. 2; 117-129; PMCID PMC4576702; 10.1016/j.cels.2015.08.001
• Finkbeiner, Stacy R. and Hill, David R., et el. (2015) Transcriptome-wide Analysis Reveals Hallmarks of Human Intestine Development and Maturation In Vitro and In Vivo; Stem Cell Reports; Vol. 4; No. 6; 1140-1155; PMCID PMC4471827; 10.1016/j.stemcr.2015.04.010
• Cerchiari, Alec E. and Garbe, James C., et el. (2015) A strategy for tissue self-organization that is robust to cellular heterogeneity and plasticity; Proceedings of the National Academy of Sciences of the United States of America; Vol. 112; No. 7; 2287-2292; PMCID PMC4343104; 10.1073/pnas.1410776112
• Sivak, David A. and Thomson, Matt (2015) Environmental Statistics and Optimal Regulation; Biophysical Journal; Vol. 108; No. 2, Supp. 1; 364a-365a; 10.1016/j.bpj.2014.11.1999
• Sivak, David A. and Thomson, Matt (2014) Environmental Statistics and Optimal Regulation; PLOS Computational Biology; Vol. 10; No. 9; Art. No. e1003826; PMCID PMC4177669; 10.1371/journal.pcbi.1003826
• Thomson, Matt and Liu, Siyuan John, et el. (2011) Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers; Cell; Vol. 145; No. 6; 875-889; 10.1016/j.cell.2011.05.017
• Thomson, Matthew and Gunawardena, Jeremy (2009) The rational parameterisation theorem for multisite post-translational modification systems; Journal of Theoretical Biology; Vol. 261; No. 4; 626-636; PMCID PMC2800989; 10.1016/j.jtbi.2009.09.003
• Thomson, Matthew and Gunawardena, Jeremy (2009) Unlimited multistability in multisite phosphorylation systems; Nature; Vol. 460; No. 7252; 274-277; PMCID PMC2859978; 10.1038/nature08102
• Mallavarapu, Aneil and Thomson, Matthew, et el. (2009) Programming with models: modularity and abstraction provide powerful capabilities for systems biology; Journal of the Royal Society Interface; Vol. 6; No. 32; 257-270; PMCID PMC2659579; 10.1098/rsif.2008.0205
• Ben-Porath, Ittai and Thomson, Matthew W., et el. (2008) An embryonic stem cell–like gene expression signature in poorly differentiated aggressive human tumors; Nature Genetics; Vol. 40; No. 5; 499-507; PMCID PMC2912221; 10.1038/ng.127