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Jean Fan, PhD

Jean Fan
Research Interests: Single-cell bioinformatics and computational methods development
Lab Website: The JEFworks Lab
Publications: From Google Scholar
Wyman S253
Research Interests

Research Interests

My lab is interested in understanding the spatial-contextual and other regulatory mechanisms that shape cellular identity and heterogeneity. We are particularly interested in characterizing heterogeneity in the context of cancer and understanding how this heterogeneity shapes tumor progression, therapeutic resistance, and ultimately clinical outcomes. While heterogeneity within cellular systems has long been widely recognized, only recently have technological advances enabled measurements to be made on a single cell level. Applying traditional bulk analysis methods on single cells has met with varied degrees of success due to the high levels of technical as well as biological stochasticity and noise inherent in single cell measurements. Therefore, we develop machine learning and other statistical methods to harness the power of these new large-scale multi-omic single cell resolution data in addressing basic science and translational research questions. Our methods are available as open-source computational software and accessible to the broader scientific community.

Titles & Affiliations


  • Assistant Professor, Biomedical Engineering

Affiliated Centers & Institutes



  • Postdoctoral Fellowship, Chemistry & Chemical Biology, Physics, Harvard University, 2018-2020
  • PhD, Bioinformatics and Integrative Genomics, Harvard Medical School, 2018
  • BS, Biomedical Engineering, Applied Math & Statistics, Johns Hopkins University, 2013
Faculty News

Recent Highlights

  • February 14, 2023
    There is a certain class of pediatric brain cancers that is “universally deadly,” with a median survival of 15 months and few, if any, viable treatment options. The key to combating these cancers might be in analyzing how the cells within tumor tissue—cancer cells, immune cells, and others—express genes and organize themselves spatially.
  • June 8, 2021
    Jean Fan, assistant professor in the Department of Biomedical Engineering, is a recipient of the National Science Foundation’s Early CAREER Award, which recognizes early stage scholars with high levels of promise and excellence.
  • February 23, 2021
    In this interview, Fan discusses her research using imaging and sequencing technologies to study genes, the impact she hopes her work will produce, her non-profit organization that works to encourage young girls to become interested in science, and more.

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