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Rong Fan, PhD

Harold Hodgkinson Professor of Biomedical Engineering; Professor, Pathology

Contact Information

Rong Fan, PhD

Mailing Address

  • Biomedical Engineering

    55 Prospect St, MEC 213

    New Haven, CT 06520

    United States



Dr. Rong Fan is the Harold Hodgkinson Professor of Biomedical Engineering and of Pathology. His research interest has been centered on the development and deployment of single-cell and spatial omics technologies to investigate normal development, aging, and disease. He received a B.S. in Applied Chemistry from University of Science and Technology of China, a Ph.D. in Chemistry from the University of California at Berkeley, and then completed his postdoctoral training at California Institute of Technology, prior to joining the faculty of Department of Biomedical Engineering at Yale University in 2010. He developed a microchip that allows for simultaneous measurement of 42 immune effector proteins in single cells at high throughput, which remains the highest multiplexing to date for a single-cell protein secretion assay. In collaboration with Novartis and Kite Pharma, it was applied to profiling antigen-specific activation states of chimeric antigen receptor (CAR)-engineered T cells, resulting in the discovery of novel single-cell biomarkers including polyfunctional strength index to characterize the quality of CAR-T infusion products and predict the clinical responses and immune-related adverse effects(irAEs) prior to treatment. This microchip, called IsoCode, and the automation system, called IsoLight, have been commercialized by IsoPlexis, a company co-founded by Dr. Fan. Now, this system has been used by >100 major pharmaceutical companies and cancer centers around the world for monitoring CAR-T or checkpoint inhibitor immunotherapies. Dr. Fan is also a pioneer in developing NGS-based spatial omics sequencing technologies. He conceived the concept of spatial multi-omics and developed the first spatially resolved multi-omics sequencing technology called DBiT-seq (Liu et al., Cell 183, 1665–1681, 2020) which allows for spatial co-profiling of whole transcriptome and hundreds of proteins (spatial-CITE-seq) at cellular level in complex tissues. He further developed a first-of-its-kind technology to enable spatial epigenome sequencing including spatial-ATAC-seq (Deng et al., Nature 609 (7926), 375-383, 2022) and spatial-CUT&Tag (Deng et al., Science 375 (6581), 681-686, 2022). These technologies may unlock a whole new field in spatial biology with applications in a wide range of biological and biomedical research. Dr. Fan co-founded IsoPlexis, Singleron Biotechnologies, and AtlasXomics. He is the recipient of multiple awards including the NCI Howard Temin Career Transition Award, the NSF CAREER Award, and the Packard Fellowship for Science and Engineering. He has been elected to American Institute for Medical and Biological Engineering (AIMBE), Connecticut Academy of Science and Engineering (CASE), and the National Academy of Inventors (NAI).

Education & Training

  • PhD
    University of California, Berkeley (2006)
  • BS
    University of Science and Technology of China (1999)

Departments & Organizations