Andrew Yates, PhD

  • Professor of Pathology & Cell Biology
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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


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

Asterisk (*) denotes joint senior and corresponding author, or joint first author

  • 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
  • Hogan T, Gossel G, Yates AJ*, Seddon B* (2015). Temporal fate mapping reveals age-structured heterogeneity in naive CD4 and CD8 T lymphocyte populations in mice. Proc. Nat. Acad. Sci. USA 10.1073/pnas.1517246112
  • Palma P, Foster C, Rojo P, Zangari P, Yates A et al. (2015) The EPIICAL project: an emerging global collaboration to investigate immunotherapeutic strategies in HIV-infected children. Journal of Virus Eradication 1:134-139
  • Kadolsky U, Yates AJ (2015). How is the effectiveness of immune surveillance impacted by the spatial distribution of spreading infections? Philosophical Transactions of the Royal Society B: Biological Sciences 370:1675
  • Yates AJ (2014). Theories and quantification of thymic selection. Frontiers in Immunology 5(13)
  • Hogan T, Kadolsky U, Tung S, Seddon B, Yates A. (2014). Spatial heterogeneity and peptide availability determine CTL killing efficiency in vivo. PLoS Computational Biology 10(9) e1003805
  • Sinclair C, Bains I , Yates AJ, Seddon B (2013). Asymmetric thymocyte death underlies the CD4:CD8 T cell ratio in the adaptive immune system. Proc. Nat. Acad. Sci. USA 110(31), E2905-E2914
  • Bains I. van Santen H, Seddon B, Yates AJ (2013). Models of self-peptide sampling by developing T cells identify candidate mechanisms of thymic selection. PLoS Computational Biology 9(7): e1003102
  • Cameron A, Reece S, Drew D, Haydon DT, Yates AJ (2013), Plasticity in transmission strategies of the malaria parasite, Plasmodium chabaudi: environmental and genetic effects. Evolutionary Applications 6(2): 365-376
  • Johnson P, Yates A, Goronzy J, Antia R (2012). Peripheral selection rather than thymic involution explains sudden contraction in naive CD4 T-cell diversity with age. Proc Natl Acad Sci U S A, 109:21432-7
  • Lee M, Mandl J, Germain N, Yates AJ (2012) The race for the prize - T cell trafficking strategies for optimal surveillance. Blood 20(7):1432-8
  • Yates A, van Baalen M, Antia R (2011). Virus replication strategies and the critical CTL numbers required for the control of infection. PLoS Computational Biology, 7(11) e1002274
  • Margolis E, Yates A, Levin B (2010). The ecology of nasal colonization of Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus: the roles of competition and interactions with host's immune response. BMC Microbiology 10(59)
  • Bains I, Antia R, Callard R, Yates A (2009). Quantifying the development of the peripheral naive CD4+ T-cell pool in humans. Blood 113(22):5480-5487
  • Bains I, Thiebaut R, Yates A, Callard R (2009). Quantifying thymic export: combining models of naive T cell proliferation and TREC dynamics gives an explicit measure of thymic output. Journal of Immunology 183(7):4329-36
  • Vezys V*, Yates A*, Casey KA, et al. (2009). Memory CD8 T-cell compartment grows in size with immunological experience. Nature 457(7226):196-9.
  • Yates A, Saini M, Mathiot A, Seddon B (2008). Mathematical modeling reveals the biological program regulating lymphopenia-induced proliferation. Journal of Immunology 180(3):1414-1422
  • de Roode JC, Yates A, Altizer S (2008). Virulence-transmission trade-offs and population divergence in virulence in a naturally occurring butterfly parasite. Proc. Nat. Acad. Sci. USA 105(21):7489-94
  • Yates A, Chan C, Strid S, Moon S, Callard R, George AJT, Stark S (2007). Reconstruction of cell population dynamics using CFSE. BMC Bioinformatics 8:196
  • Yates A, Stark J, Klein N, Antia R, Callard R (2007). Understanding the slow depletion of memory CD4+ T cells in HIV infection. PLoS Medicine 4(5):e177.
  • Yates A, Callard R, Stark J (2004). Combining cytokine signalling with T-bet and GATA-3 regulation in Th1 and Th2 differentiation: a model for cellular decision-making. Journal of Theoretical Biology 231(2):181-196
  • Yates A, Bergmann C, van Hemmen L, Stark J, Callard R (2000). Cytokine-modulated regulation of helper T cell populations. Journal of Theoretical Biology 206:539-560