Research Menu
Je H. Lee

Je H. Lee

Assistant Professor

M.D., Ph.D., Tufts School of Medicine, 2002

jlee@cshl.edu | (516) 367-5421

Cells are amazingly complex, with the ability to sense, and remember timing, location and history. I am exploring how cells store this information, and how their surroundings influence their communication with other cells. I am also developing various imaging and molecular sequencing methods for tracking genes, molecules, and cells to understand how cancer cells arise and evolve.

The Lee Lab studies how cells interact with their microenvironment to regulate gene expression during development. Single cell heterogeneity in gene expression can result from spatial differences in cell-cell and cell-extracellular matrix interactions. Such differences contribute to stochastic evolution of tumor cells as well as morphogenesis during normal development. However, the spatial control of gene expression in complex tissues, embryos, or tumors remains poorly understood, because most genome-wide studies sample bulk tissues or dissociated single cells.

We have recently developed a method to sequence RNA molecules directly within single cells and tissues using sub-cellular resolution imaging, and we demonstrated subtle differences in cell-cell/ECM signaling and gene expression genome-wide in situ. By clustering transcripts into functionally or morphological discrete regions, we find many unique spatial markers and signaling pathways. My lab focuses on the role of non-coding RNA in chromatin remodeling and tumor progression using mouse and organoid models of human cancer. We use in situ sequencing, cell lineage tracing, and single-cell profiling to understand how non-coding RNA affects tumor cell evolution in their native context. Our long-term goal is to develop better tumor classification tools and anti-cancer therapeutics using our understanding of the tumor microenvironment.

    CSHL scientists Bo Li and Je Lee win HFSP Research Grant awards

    CSHL scientists Bo Li and Je Lee win HFSP Research Grant awards

    April 12, 2016

    Cold Spring Harbor, NY – Two scientists, both leaders of research labs at Cold Spring Harbor Laboratory (CSHL), are among 25 teams that have won Human Frontier Science Program (HFSP) Research Program Grants for 2016. The awards were announced by the International Human Frontier Science Program Organization (HFSPO), based in Strasbourg, France. The two CSHL...


    New junior faculty join CSHL

    New junior faculty join CSHL

    November 12, 2014

    LabDish blog This fall, the Lab welcomes six new faculty members. They’re a diverse group—a mix of junior and senior investigators, with research spanning across Biology. Want to know a little more? We are featuring brief profiles all week. So check back for more! Assistant Professor Je Lee, Genomics Where are you from? George Church’s...


Lee, Je H. (2017) De Novo Gene Expression Reconstruction in Space. Trends in Molecular Medicine, 23(7) pp. 583-593.

Lee, J. H. (2017) Quantitative approaches for investigating the spatial context of gene expression. Wiley Interdiscip Rev Syst Biol Med, 9(2)

Lee, J. H. and Daugharthy, E. R. and Scheiman, J. and Kalhor, R. and Ferrante, T. C. and Terry, R. and Turczyk, B. M. and Yang, J. L. and Lee, H. S. and Aach, J. and Zhang, K. and Church, G. M. (2015) Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat Protoc, 10(3) pp. 442-58.

Lee, J. H. and Daugharthy, E. R. and Scheiman, J. and Kalhor, R. and Yang, J. L. and Ferrante, T. C. and Terry, R. and Jeanty, S. S. and Li, C. and Amamoto, R. and Peters, D. T. and Turczyk, B. M. and Marblestone, A. H. and Inverso, S. A. and Bernard, A. and Mali, P. and Rios, X. and Aach, J. and Church, G. M. (2014) Highly multiplexed subcellular RNA sequencing in situ. Science, 343(6177) pp. 1360-3.

Lee, J. H. and Park, I. H. and Gao, Y. and Li, J. B. and Li, Z. and Daley, G. Q. and Zhang, K. and Church, G. M. (2009) A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells. PLoS Genet, 5(11) pp. e1000718.

Additional materials of the author at
CSHL Institutional Repository