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Matt Thomson

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Matt Thomson is an American computational biologist, academic, and entrepreneur. He works in the fields of computational biology, biophysics, and machine learning.[1]

Early life and education

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Matt Thomson's academic journey began at Harvard University, where he pursued his undergraduate education and graduated magna cum laude with an AB in Physics in 2001.[2]

Thomson continued at Harvard University for graduate studies in Biophysics, completing his Ph.D. in 2011. His doctoral research focused on the mathematical modeling and analysis of biochemical networks, aiming to understand the control mechanisms[3] behind cellular decision-making processes.[4][5]

After earning his Ph.D., Thomson received an independent fellowship at the University of California, San Francisco (UCSF), where he worked on developing mathematical methods to model cell fate determination and tissue self-organization.[6][7]

Research and career

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Matt Thomson is a faculty member in the field of computational biology at the California Institute of Technology (Caltech).[8] He is also the principal investigator of SPEC, the Beckman Center for Single Cell Profiling and Engineering at Caltech, and an investigator with the Heritage Medical Research Institute.[9] His research group studies "living algorithms," focusing on the information processing strategies used by cells and organisms to interact with their environment.[10] This interdisciplinary area includes computational biology, physics, machine learning, and neuroscience.[11]

Thomson's research aims to understand and replicate the information processing strategies found in biological systems to develop new technologies and algorithms in fields such as machine learning, physics, and materials science. His work has led to the development of mathematical models for predicting cellular responses to external stimuli, including D-SPIN, Popalign, and ActiveSVM.[12] His research in bio-inspired machine learning algorithms, such as FIP, Herd, and spatial predictive coding, has contributed to advancements in neural network flexibility.[13]

Additionally, Thomson's research includes the creation of optically programmable active materials by engineering light-switchable proteins integrated into cytoskeletal networks.[14]

Awards

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Matt Thomson has received several awards and honors for his work in computational biology, machine learning, and systems biology. In 2019, he received the Packard Fellowship.[15] He also received the NIH Early Independence Award in 2011.[16] Additionally, Thomson received the NIH Transformative R01 in 2023 and the Okawa Research Award in 2020.

Selected publications

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  • Ross, Tyler D.; Lee, Heun Jin; Qu, Zijie; Banks, Rachel A.; Phillips, Rob; Thomson, Matt (August 2019). "Controlling organization and forces in active matter through optically defined boundaries". Nature. 572 (7768): 224–229. arXiv:1812.09418. Bibcode:2019Natur.572..224R. doi:10.1038/s41586-019-1447-1. ISSN 1476-4687. PMC 6719720. PMID 31391558.
  • Thomson, Matthew; Gunawardena, Jeremy (July 2009). "Unlimited multistability in multisite phosphorylation systems". Nature. 460 (7252): 274–277. Bibcode:2009Natur.460..274T. doi:10.1038/nature08102. ISSN 1476-4687. PMC 2859978. PMID 19536158.
  • Thomson, Matt; Liu, Siyuan John; Zou, Ling-Nan; Smith, Zack; Meissner, Alexander; Ramanathan, Sharad (June 2011). "Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers". Cell. 145 (6): 875–889. doi:10.1016/j.cell.2011.05.017. PMC 5603300. PMID 21663792.
  • Zhu, Meng; Cornwall-Scoones, Jake; Wang, Peizhe; Handford, Charlotte E.; Na, Jie; Thomson, Matt; Zernicka-Goetz, Magdalena (2020-12-11). "Developmental clock and mechanism of de novo polarization of the mouse embryo". Science. 370 (6522). doi:10.1126/science.abd2703. ISSN 0036-8075. PMC 8210885. PMID 33303584.
  • Raghavan, Guruprasad; Thomson, Matt (2019). "Neural networks grown and self-organized by noise". arXiv:1906.01039 [cs.NE].
  • Raghavan, Guruprasad; Tharwat, Bahey; Hari, Surya Narayanan; Satani, Dhruvil; Thomson, Matt (2022). "Engineering flexible machine learning systems by traversing functionally-invariant paths". arXiv:2205.00334 [cs.LG].
  • Jiang, Jialong; Chen, Sisi; Tsou, Tiffany; McGinnis, Christopher S.; Khazaei, Tahmineh; Zhu, Qin; Park, Jong H.; Strazhnik, Inna-Marie; Hanna, John; Chow, Eric D.; Sivak, David A.; Gartner, Zev J.; Thomson, Matt (2023-05-20). "D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response". bioRxiv 10.1101/2023.04.19.537364.

References

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  1. ^ "Matt Thomson - Biology and Biological Engineering". www.bbe.caltech.edu. Retrieved 2024-05-20.
  2. ^ "Matthew Thomson". ramanathanbiophysics.seas.harvard.edu. Retrieved 2024-05-20.
  3. ^ Jiang, Jialong; Chen, Sisi; Tsou, Tiffany; McGinnis, Christopher S.; Khazaei, Tahmineh; Zhu, Qin; Park, Jong H.; Strazhnik, Inna-Marie; Hanna, John (2023-04-21). "D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response". bioRxiv 10.1101/2023.04.19.537364.
  4. ^ "Matt Thomson - Biology and Biological Engineering". www.bbe.caltech.edu. Retrieved 2024-05-20.
  5. ^ "MATT THOMSON – SPEC at Caltech". Retrieved 2024-05-20.
  6. ^ "Matt Thomson Named a Packard Fellow". California Institute of Technology. 2019-10-15. Retrieved 2024-05-20.
  7. ^ "Matt Thomson • The David and Lucile Packard Foundation". The David and Lucile Packard Foundation. Retrieved 2024-05-20.
  8. ^ "Matt Thomson - Chen Institute". neuroscience.caltech.edu. Retrieved 2024-05-20.
  9. ^ Technology, California Institute of. "Controlling the shape-shifting skeletons of cells". phys.org. Retrieved 2024-05-20.
  10. ^ "Thomson Lab |". thomsonlab.caltech.edu. Retrieved 2024-05-20.
  11. ^ Raghavan, Guruprasad; Thomson, Matt (2019-06-03). "Neural networks grown and self-organized by noise". arXiv:1906.01039 [cs.NE].
  12. ^ Jiang, Jialong; Chen, Sisi; Tsou, Tiffany; McGinnis, Christopher S.; Khazaei, Tahmineh; Zhu, Qin; Park, Jong H.; Strazhnik, Inna-Marie; Hanna, John; Chow, Eric D.; Sivak, David A.; Gartner, Zev J.; Thomson, Matt (2023-05-20). "D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response". bioRxiv 10.1101/2023.04.19.537364.
  13. ^ Gornet, James A.; Thomson, Matt (2024-04-18). "Automated construction of cognitive maps with visual predictive coding". bioRxiv 10.1101/2023.09.18.558369.
  14. ^ Young, Y.-N.; Shelley, Michael J.; Stein, David B.; Young, Y.-N.; Shelley, Michael J.; Stein, David B. (2021). "The many behaviors of deformable active droplets". Mathematical Biosciences and Engineering. 18 (3): 2849–2881. doi:10.3934/mbe.2021145. ISSN 1551-0018. PMID 33892575.
  15. ^ "Fellowships for Science and Engineering Archives • Page 4 of 14 • The David and Lucile Packard Foundation". The David and Lucile Packard Foundation. 2024-02-16. Retrieved 2024-05-20.
  16. ^ "News". Sandler Fellows Program. Retrieved 2024-05-20.
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