Andrew Yates, PhD

  • Professor of Pathology & Cell Biology
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Overview

Affiliations

  • Associate, Irving Institute for Cancer Dynamics
  • Columbia Data Science Institute, Health Analytics
  • Systems Biology, Program for Mathematical Genomics

Academic Appointments

  • Professor of Pathology & Cell Biology

Research

T and B lymphocytes are key components of vertebrate immune systems. They form richly structured and highly interactive communities that provide protection against infection while maintaining tolerance to innocuous antigens. They also encode immunological memory, responding rapidly and potently to previously encountered antigens. Our research integrates theoretical and computational tools with more traditional experimental approaches to study multiple aspects of lymphocyte dynamics. Our aim is to develop a mechanistic understanding of the rules underlying lymphocyte development, homeostasis, and their trajectories in response to infectious agents. Our philosophy is to confront and break models with data to search for robust and quantitative explanations of immunological phenomena. Our current interests relate to the formation and dynamical structure of memory T cell populations,  dynamical modeling of time series of high-dimensional phenotypic data, the spatial ecology of tissue-resident T cells, and identifying early correlates of vaccine efficacy.

Selected Publications

Sectected recent publications. Asterisk (*) denotes joint senior and corresponding author, or joint first author.

  • Christiaan H. van Dorp, Joshua I. Gray, Daniel H. Paik, Donna L. Farber*, Andrew J. Yates*. A variational deep-learning approach to modeling memory T cell dynamics. PLoS Computational Biology, in press (2025)
  • Nora Lam, J. Carlos Angel, Bruce A. Buchholz, Stuart P. Weisberg, Brea H. Brown, Julia Davis-Porada, Daniel P. Caron, Isaac J. Jensen, YoonSeung Lee, Peter A. Szabo, Basak B. Ural, Steven B. Wells, Masaru Kubota, Rei Matsumoto, Maigan Brusko, Todd M. Brusko, Chao Lu, Andrew J. Yates, Donna L. Farber. Continuous turnover and asynchronous aging of human memory T cells across tissues. Immunity, in press (2025)
  • Sanmoy Pathak, Thea Hogan, Sanket Rane, Yundi Huang, Charles Sinclair, Simon Barry, Larissa Carnevalli, Andrew J. Yates*, Benedict Seddon*. A linear ontogeny accounts for the development of naive, memory, and tumor-infiltrating regulatory T cells in mice. Science Immunology, 10(108):eadu7341 (2025)
  • Jodie Chandler, M. Elise Bullock, Arpit. C. Swain, Cayman Williams, Christiaan H. van Dorp, Benedict Seddon*, and Andrew J. Yates*. Tissue resident memory CD4+ T cells are sustained by site-specific levels of self-renewal and replacement from precursors. eLife 14:RP104278 (2025)
  • M. Elise Bullock, Thea Hogan, Cayman Williams, Sinead Morris, Maria Nowicka, Minahil Sharjeel, Christiaan van Dorp, Andrew J. Yates*, Benedict Seddon*. The dynamics and longevity of circulating CD4+ memory T cells depend on cell age and not the chronological age of the host. PLoS Biology, 22(8):e3002380 (2024)
  • Rob J. de Boer and Andrew J. Yates (2023). Modeling T cell fate. Annual Review of Immunology, 41:513-532
  • Eva Lukas, Thea Hogan, Cayman Williams, Benedict Seddon*, Andrew J. Yates* (2023). Quantifying cellular dynamics in mice using a novel fluorescent division reporter system. Frontiers in Immunology, 15 (10.3389/fimmu.2023.1157705)
  • Thomas J. Connors, Rei Matsumoto, Shivali Verma, Peter A. Szabo, Rebecca Guyer, Joshua Gray, Zicheng Wang, Puspa Thapa, Pranay Dogra, Maya M.L. Poon, Ksenia Rybkina, Marissa C. Bradley, Emma Idzikowski, James McNichols, Masaru Kubota, Kalpana Pethe, Yufeng Shen, Mark A. Atkinson, Maigan Brusko, Todd M. Brusko, Andrew J. Yates, Peter A. Sims, Donna L. Farber (2023). Site-specific development and progressive maturation of human tissue-resident memory T cells over infancy and childhood. Immunity, S1074-7613(23)00265-0
  • Sinead E. Morris, Renate Strehlau, Stephanie Shiau, Elaine J. Abrams, Caroline T. Tiemessen, Louise Kuhn, Andrew J. Yates, on behalf of the EPIICAL Consortium and the LEOPARD study team (2022). Healthy dynamics of CD4 T cells may drive HIV resurgence in perinatally-infected infants on antiretroviral therapy. PLoS Pathogens, 18(8): e1010751
  • Sanket Rane, Thea Hogan, Edward Lee, Benedict Seddon*, Andrew J. Yates* (2022). Towards a unified model of naive T cell dynamics across the lifespan. eLife, 10.7554/eLife.78168
  • Szabo PA, Dogra P, Gray JI, Wells SB, Connors TJ, Weisberg SP, Krupska I, Matsumoto R, Poon MML, Idzikowski E, Morris SE, Pasin C, Yates AJ, Ku A, Chait M, Davis-Porada J, Guo XV, Zhou J, Steinle M, Mackay S, Saqi A, Baldwin MR, Sims PA, Farber DL (2021). Longitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19. Immunity 54(4):797-814.e6
  • Pasin C, Moy RH, Reshef R, Yates AJ. Variable selection methods for predicting clinical outcomes following allogeneic hematopoietic cell transplantation. Sci Rep. 2021 Feb 5;11(1):3230
  • Morris SE, Dziobek-Garrett L, Yates AJ, in collaboration with the EPIICAL consortium. ushr: Understanding suppression of HIV in R. BMC Bioinformatics. 2020 Feb 11;21(1):52
  • Verheijen M, Rane S, Yates AJ*, Seddon B* (2020). Fate mapping quantifies the dynamics of B cell development and activation throughout life. Cell Reports 33 (7), 108376
  • Morris SE, Dziobek-Garrett L, Strehlau R, Schroeter J, Shiau S, Anelone AJN, Paximadis M, de Boer RJ, Abrams EJ, Tiemessen CT, Kuhn L, Yates AJ, EPIICAL Consortium and the LEOPARD study team. Quantifying the dynamics of HIV decline in perinatally-infected neonates on antiretroviral therapy. J Acquir Immune Defic Syndr., 2020 Oct.1;85(2):209-218
  • Hogan T, Nowicka M, Cownden D, Pearson CF, Yates AJ*, Seddon B* (2019). Differential impact of self and environmental antigens on the ontogeny and maintenance of CD4+ T cell memory. eLife 8:e48901
  • Morris SE, Farber DL, Yates AJ (2019). Tissue-Resident Memory T Cells in Mice and Humans: Towards a Quantitative Ecology. Journal of Immunology 203(10):2561-2569
  • Mold JE, Réu P, Olin A, Bernard S, Michaëlsson J, Rane S, Yates AJ, Khosravi A, Salehpour M, Possnert G, Brodin P, Frisén J. Cell generation dynamics underlying naive T-cell homeostasis in adult humans. PLoS Biol. 2019 Oct 29;17(10):e3000383
  • Ferrer IR, West HC, Henderson S, Ushakov DS, Santos E Sousa P, Strid J, Chakraverty R, Yates AJ, Bennett CL (2019). A wave of monocytes is recruited to replenish the long-term Langerhans cell network after immune injury. Science Immunology, 4:38
  • Rane S, Hogan T, Seddon B, Yates AJ (2018). Age is not just a number: Naive T cells increase their ability to persist in the circulation over time. PLoS Biology 16(4):e2003949
  • Seddon B, Yates AJ (2018). The natural history of naive T cells from birth to maturity. Immunological Reviews 285 (1):218-232
  • Gossel G, Hogan T, Cownden D, Seddon B, Yates AJ (2017). Memory CD4 T cell subsets are kinetically heterogeneous and replenished from naive T cells at high levels. eLife 10.7554/eLife.23013
  • Lee E, Thomas PG, Mold J, Yates AJ (2017). Identifying T cell receptors from high-throughput sequencing: dealing with promiscuity in TCRalpha and TCRbeta pairing. PLoS Computational Biology 13(1): e1005313