Jean Fan

Jean Fan, PhD is an Assistant Professor of Biomedical Engineering at Johns Hopkins University, affiliated with the Center for Computational Biology and Institute for Computational Medicine. Her research focuses on developing machine learning methods to analyze spatially resolved and single-cell omics data. Her team, the JEFworks Lab, creates open-source tools for analyzing high-dimensional biological data to understand cellular identity, tissue organization, and disease progression. Dr. Fan's work bridges computational biology with clinical applications, particularly in leukemia and pediatric brain cancers.

Education: BS in Biomedical Engineering & Applied Math from Johns Hopkins (2013); PhD in Bioinformatics from Harvard Medical School (2018); Postdoc in Chemical Biology/Physics at Harvard (2018–2020) under Xiaowei Zhuang, focusing on spatial transcriptomics.

Research emphasizes spatial genomics and computational tool development, with key contributions to spatial alignment algorithms (STalign), normalization techniques, and cell-type deconvolution methods. Her lab's work has advanced understanding of kidney ischemic injury, glioblastoma spatial dynamics, and CLL pathogenesis.

Awards include Forbes 30 Under 30, NSF CAREER Award, and 2025 PECASE. She founded CuSTEMized, a nonprofit providing STEM storybooks for girls. Recent collaborative projects include HuBMAP 3D reference atlas construction and Discovery Award-funded interdisciplinary initiatives.

Labs/Teams: JEFworks Lab (primary); active collaborations with Dana-Farber Cancer Institute and Harvard Medical School. Current efforts focus on spatially resolved multi-omic integration and clinical translation of computational tools.