Rong Fan, PhD
Harold Hodgkinson Professor of Biomedical Engineering and Professor of PathologyCards
Education
University of California, Berkeley (2006)
University of Science and Technology of China (1999)
Contact Info
Biomedical Engineering
55 Prospect St, MEC 213
New Haven, CT 06520
United States
Fan Lab
Education
University of California, Berkeley (2006)
University of Science and Technology of China (1999)
Contact Info
Biomedical Engineering
55 Prospect St, MEC 213
New Haven, CT 06520
United States
Fan Lab
Education
University of California, Berkeley (2006)
University of Science and Technology of China (1999)
Contact Info
Biomedical Engineering
55 Prospect St, MEC 213
New Haven, CT 06520
United States
Fan Lab
About
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Titles
Harold Hodgkinson Professor of Biomedical Engineering and Professor of Pathology
Biography
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).
Appointments
Pathology
ProfessorSecondary
Other Departments & Organizations
- Cancer Signaling Networks
- Center for RNA Science and Medicine
- Computational Biology and Biomedical Informatics
- Dean's Workshops
- Global Health Studies
- Human and Translational Immunology Program
- Lu Lab
- Molecular Medicine, Pharmacology, and Physiology
- Pathology
- Yale Biomedical Imaging Institute
- Yale Cancer Center
- Yale Center for Research on Aging (Y-Age)
- Yale Combined Program in the Biological and Biomedical Sciences (BBS)
- Yale Stem Cell Center
- Yale Ventures
Education & Training
- PhD
- University of California, Berkeley (2006)
- BS
- University of Science and Technology of China (1999)
Research
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Overview
BioMEMS; Single-Cell Omics: Spatial Omics; Hematology Oncology; Immunology
Medical Research Interests
ORCIDs
Fan Lab
Single-cell & Spatial Omics for Systems Biomedicine
View Lab Website
Research at a Glance
Yale Co-Authors
Publications Timeline
Research Interests
Bo Tao
Former YSMMina Xu, MD
Stephanie Halene, MD, Dr Med
Yang Liu, PhD
David A. Hafler, MD, FANA, MSc
Sidi Chen, PhD
Publications
2026
3D multi-omics tumour atlases: from technology to biology and clinical translation
Liu M, Villazon J, Forjaz A, Tian X, Fan R, Wang S, Shi L, Wirtz D, Kiemen A. 3D multi-omics tumour atlases: from technology to biology and clinical translation. Nature Reviews Cancer 2026, 1-28. PMID: 42298141, DOI: 10.1038/s41568-026-00940-0.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsThis study investigates 3D tumour atlases, showing how spatial multi-omics technologies uncover tumour evolution, aiding early cancer detection, risk stratification, and innovative treatment strategies.Large-scale, spatially resolved panoramic CRISPR screening in native tissue environments using Perturb-DBiT
Baysoy A, Tian X, Renauer P, Zhang F, Bai Z, Shi H, Yang M, Zhang D, Liu M, Li H, Tao B, Enninful A, Lu Y, Gao F, Wang G, Zhang W, Tran T, Patterson N, Sheng J, Bao S, Dong C, Xin S, Chen B, Zhong M, Rankin S, Guy C, Wang Y, Connelly J, Pruett-Miller S, Wang D, Xu M, Gerstein M, Chi H, Chen S, Fan R. Large-scale, spatially resolved panoramic CRISPR screening in native tissue environments using Perturb-DBiT. Nature Biotechnology 2026, 1-14. PMID: 42277225, DOI: 10.1038/s41587-026-03127-y.Peer-Reviewed Original ResearchThis study introduces Perturb-DBiT, a method enabling spatially resolved CRISPR screens and transcriptomics in tissues, uncovering genetic and RNA-level mechanisms driving cancer and immune interactions.Clinical translation of spatial omics
Wang Z, Guo F, Sun H, Kong Y, Wang Z, Tao J, Xu M, Yeong J, Fan R, Shi P. Clinical translation of spatial omics. Nature Reviews Bioengineering 2026, 1-3. DOI: 10.1038/s44222-026-00458-y.Peer-Reviewed Original ResearchAltmetricSpatially resolved m6A profiling using m6A-ARTR-DBiT
Xiao Y, Bai Z, Zou Z, Ye C, Tao B, Zheng Z, Chen Y, Zou Z, Jiang L, Zhao L, Fan Y, Gao Y, Fan R, He C. Spatially resolved m6A profiling using m6A-ARTR-DBiT. Nature Methods 2026, 1-9. PMID: 42265211, DOI: 10.1038/s41592-026-03123-9.Peer-Reviewed Original ResearchCitationsAltmetricCharting human cellular senescence in aging and disease
Suryadevara V, Farzad N, Yang M, Xu K, Tsankov A, Thompson R, Sloan N, Phatnani H, Olinger B, Mares J, Lund A, Li D, Gorospe M, Ding L, Beckmann N, Basisty N, Anerillas C, consortium T, Robbins P, Fan R. Charting human cellular senescence in aging and disease. Cell 2026, 189: 3501-3505. PMID: 42276030, DOI: 10.1016/j.cell.2026.05.028.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsAltmetricMeSH KeywordsA spatial multi-omics atlas of immunosenescence reveals germinal-center B cell alteration in human lymph nodes
Farzad N, Enninful A, Lu Y, Parisi F, Fung A, Kwon Y, Li Y, Labrosse M, Yang M, Strino F, Chen L, Yang J, Zhong M, Gao F, Tao B, Cunningham J, Bai Z, Li H, Wang F, Stankewich M, Kim D, Dong M, Bramer L, Li K, Bhat M, Loe E, Craft J, Pasa-Tolic L, Halene S, Shi L, Kluger Y, Xu M, Fan R. A spatial multi-omics atlas of immunosenescence reveals germinal-center B cell alteration in human lymph nodes. Mining Technology Transactions Of The Institutions Of Mining And Metallurgy 2026, 100053. DOI: 10.1016/j.cpblue.2026.100053.Peer-Reviewed Original ResearchCitationsAltmetricSpatially decoding genotype-associated epigenetic landscapes in human lymphoma FFPE tissues via epi-Patho-DBiT
Li H, Tao B, Enninful A, Zhang D, Dai Y, Oh F, Farzad N, Li K, Bai Z, Qin X, Yang M, Hwang E, Zhang J, Lu J, Gerstein M, Zhou J, Xu M, Fan R. Spatially decoding genotype-associated epigenetic landscapes in human lymphoma FFPE tissues via epi-Patho-DBiT. Nature Communications 2026 PMID: 42067542, DOI: 10.1038/s41467-026-71576-9.Peer-Reviewed Original ResearchCitationsAltmetricMapping cellular and ECM heterogeneity in pulmonary fibrosis—Insights from recent spatiomics studies
Yazdani M, Wang L, Ding Q, Frazad N, Yang M, Venkatesan S, Stachowiak M, Ikonomou L, Chen Y, Fan R, Liu Y, Zhao R. Mapping cellular and ECM heterogeneity in pulmonary fibrosis—Insights from recent spatiomics studies. Cell Biomaterials 2026, 2: 100315. PMID: 42183153, PMCID: PMC13197085, DOI: 10.1016/j.celbio.2025.100315.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsCitationsRational Design of Immune Gene Therapy Combinations via In Vivo CRISPR Activation Screen of Tumor Microenvironment Modulators.
Zhang F, Dong C, Chow R, Xin S, He E, Feng Y, Zhu L, Mirza D, Tian X, Yang L, Zhou L, Ling X, Han Q, Fan R, Chen S, Wang G. Rational Design of Immune Gene Therapy Combinations via In Vivo CRISPR Activation Screen of Tumor Microenvironment Modulators. Cancer Discovery 2026, 16: 1222-1244. PMID: 41747251, DOI: 10.1158/2159-8290.cd-25-0545.Peer-Reviewed Original ResearchCitationsAltmetricIntegration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus
Enninful A, Zhang Z, Klymyshyn D, Ingalls M, Yang M, Zong H, Bai Z, Farzad N, Su G, Baysoy A, Nam J, Lu Y, Bao S, Deng S, Zhang N, Braubach O, Xu M, Ma Z, Fan R. Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus. Nature Methods 2026, 1-13. PMID: 41540123, DOI: 10.1038/s41592-025-02948-0.Peer-Reviewed Original ResearchCitationsAltmetric
News
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News
- June 11, 2026
Scientists Develop First Comprehensive Atlas of Human Cellular Senescence in Aging
- April 23, 2026
New Research Presented from Yale Cancer Center at the AACR Annual Meeting
- April 06, 2026
Yale Cancer Center Experts to Share Latest Findings at 2026 AACR Conference
- April 01, 2026
Four YSM Researchers Named Biohub Investigators
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Biomedical Engineering
55 Prospect St, MEC 213
New Haven, CT 06520
United States