Tim Stuart

Senior Research Scientist,
Laboratory of Genome Function





Every cell within an organism carries essentially the same genetic information. In multicellular organisms, this common genetic sequence is decoded differently by different cell types to produce a multitude of cell states, each performing specialized and essential functions. How these different cell states are encoded in the genome is a major question yet to be fully understood. However, we do know that chromatin states are highly dynamic and instrumental in guiding the proper development of these cellular phenotypic states. Our lab aims to develop novel approaches to study how chromatin states guide cell fates, how these healthy developmental processes are impacted by natural human genetic variation, and how pathogenic somatic mutations perturb healthy cell development.

For more information please visit our lab website at https://stuartlab.org

Selected Publications

  • Stuart, Tim, Stephanie Hao, Bingjie Zhang, Levan Mekerishvili, Dan A. Landau, Silas Maniatis, Rahul Satija, and Ivan Raimondi. 2022. "Nanobody-Tethered Transposition Enables Multifactorial Chromatin Profiling at Single-Cell Resolution." Nature Biotechnology, December. doi:10.1038/s41587-022-01588-5.
  • Zhang, Bingjie, Avi Srivastava, Eleni Mimitou, Tim Stuart, Ivan Raimondi, Yuhan Hao, Peter Smibert, and Rahul Satija. 2022. "Characterizing Cellular Heterogeneity in Chromatin State with scCUT&Tag-Pro." Nature Biotechnology, March. doi:10.1038/s41587-022-01250-0.
  • Stuart, Tim, Avi Srivastava, Shaista Madad, Caleb A. Lareau, and Rahul Satija. 2021. "Single-Cell Chromatin State Analysis with Signac." Nature Methods 18 (11). Nature Publishing Group: 1333–41. doi:10.1038/s41592-021-01282-5.
  • Hao, Yuhan, Stephanie Hao, Erica Andersen-Nissen, William M. Mauck 3rd, Shiwei Zheng, Andrew Butler, Maddie J. Lee, Aaron J. Wilk, Charlotte Darby, Michael Zager, Paul Hoffman, Marlon Stoeckius, Efthymia Papalexi, Eleni P. Mimitou, Jaison Jain, Avi Srivastava, Tim Stuart, Lamar M. Fleming, Bertrand Yeung, Angela J. Rogers, Juliana M. McElrath, Catherine A. Blish, Raphael Gottardo, Peter Smibert, and Rahul Satija. 2021. "Integrated Analysis of Multimodal Single-Cell Data." Cell 184 (13): 3573–87.e29. doi:10.1016/j.cell.2021.04.048.
  • Rood, Jennifer E., Tim Stuart, Shila Ghazanfar, Tommaso Biancalani, Eyal Fisher, Andrew Butler, Anna Hupalowska, Leslie Gaffney, William Mauck, Gökçen Eraslan, John C. Marioni, Aviv Regev, and Rahul Satija. 2019. "Toward a Common Coordinate Framework for the Human Body." Cell 179 (7). Elsevier: 1455–67. doi:10.1016/j.cell.2019.11.019.
  • Stuart, Tim, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M. Mauck 3rd, Yuhan Hao, Marlon Stoeckius, Peter Smibert, and Rahul Satija. 2019. "Comprehensive Integration of Single-Cell Data." Cell 177 (7). Elsevier: 1888–1902.e21. doi:10.1016/j.cell.2019.05.031.
  • Stuart, Tim, and Rahul Satija. 2019. "Integrative Single-Cell Analysis." Nature Reviews. Genetics 20 (5): 257–72. doi:10.1038/s41576-019-0093-7.
  • Stuart, Tim, Steven R. Eichten, Jonathan Cahn, Yuliya V. Karpievitch, Justin O. Borevitz, and Ryan Lister. 2016. "Population Scale Mapping of Transposable Element Diversity Reveals Links to Gene Regulation and Epigenomic Variation." eLife 5 (December). eLife Sciences Publications Limited: e60. doi:10.7554/eLife.20777.
  • Kawakatsu, Taiji, Tim Stuart, Manuel Valdes, Natalie Breakfield, Robert J. Schmitz, Joseph R. Nery, Mark A. Urich, Xinwei Han, Ryan Lister, Philip N. Benfey, and Joseph R. Ecker. 2016. "Unique Cell-Type-Specific Patterns of DNA Methylation in the Root Meristem." Nature Plants 2 (5). Nature Publishing Group: 16058. doi:10.1038/nplants.2016.58.