Rong Fan

Rong Fan


Fan Lab
Harold Hodgkinson Professor of Biomedical Engineering
Room / Office: Malone 213
Office Address:
55 Prospect Street
New Haven, CT 06511
Mailing Address:
P.O. Box 208260
New Haven, CT 06520
Phone: (203) 432-9905
  • Ph.D., University of California, Berkeley
  • B.S., University of Science and Technology of China


Dr. Fan's research is focused on the development and deployment of single-cell and spatial multi-omics profiling technologies, often based on microfabricated devices, to investigate pathogenesis and therapeutic response of complex human diseases including cancer, autoimmunity, and cardiovascular disease. In particular, his laboratory is interested in hematologic malignancies, brain tumors, and systemic lupus erythematosus. He is also interested in cellular immune function characterization and the application to cancer immunotherapies. A microchip technology his laboratory developed for simultaneous measurement of 42 immune effector proteins in single cells, which remains the highest multiplexing to date for a single-cell protein secretion assay, has been commercialized as IsoCode and IsoLight, and currently used by >100 pharmaceutical companies and medical centers in the U.S. and around the world. Recently, his laboratory developed a novel NGS-based approach called DBiT-seq for spatial transcriptome mapping, spatial high-plex protein mapping, and spatial epigenome mapping, which may find wide-spread applications in developmental biology, cancer research, neuroscience, and immunobiology.

Selected Awards & Honors:

  • Fellow, the National Academy of Inventors (NAI) (2021)
  • Yale Cancer Center Class of 1961 Cancer Research Award (2021)
  • Member, Connecticut Academy of Science and Engineering (2021)
  • Senior Member, the National Academy of Inventors (NAI) (2019)
  • Fellow, the American Institute for Medical and Biological Engineering (AIMBE) (2019)
  • Stand Up to Cancer (SU2C), the Functional CART Cell Convergence Team Award (team lead) (2018)
  • The Rising Star Award, Cellular and Molecular Bioengineering (CMBE) SIG, BMES (2016)
  • Kavli Fellow - Invited to attend 2014 US Kavli Frontier in Science Symposium, National Academy of Sciences (2014)
  • Emerging Investigator – Lab on a Chip Special Issue (2014)
  • National Science Foundation, the Faculty Early Career Development (CAREER) Award (2014)
  • Packard Fellowship for Science and Engineering (2012)
  • Alzheimer’s Association, New Investigator Research Award (2010)
  • Bill & Melinda Gates Foundation, Grand Challenges Exploration Award (2010)
  • National Cancer Institute, Howard Temin Pathway to Independence (K99/R00) Award (2009-2013)

Selected Publications:

  • Yang Liu, Marcello DiStasio, Graham Su, Hiromitsu Asashima, Archibald Enninful, Xiaoyu Qin, Yanxiang Deng, Jungmin Nam, Fu Gao, Pino Bordignon, Marco Cassano, Mary Tomayko, Mina Xu, Stephanie Halene, Joseph E Craft, David Hafler, Rong Fan*, High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq. Nature Biotechnology, in press (2023). [LINK]
  • Yanxiang Deng, Marek Bartosovic, Sai Ma, Di Zhang, Petra Kukanja, Yang Xiao, Graham Su, Yang Liu, Xiaoyu Qin, Gorazd B Rosoklija, Andrew J Dwork, J John Mann, Mina L Xu, Stephanie Halene, Joseph E Craft, Kam W Leong, Maura Boldrini, Gonçalo Castelo-Branco*, Rong Fan*. Spatial profiling of chromatin accessibility in mouse and human tissues. Nature, 609, 375–383 (2022). [LINK]
  • Yanxiang Deng, Marek Bartosovic, Petra Kukanja, Di Zhang, Yang Liu, Graham Su, Archibald Enninful, Zhiliang Bai, Gonçalo Castelo-Branco, Rong Fan*. Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level. Science, 375(6581):681-686 (2022). [LINK]
  • Yang Liu, Mingyu Yang, Yanxiang Deng, Graham Su, Archibald Enninful, Cindy C. Guo, Toma Tebaldi, Di Zhang, Dongjoo Kim, Zhiliang Bai, Eileen Norris, Alisia Pan, Jiatong Li, Yang Xiao, Stephanie Halene, and Rong Fan*, High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue, Cell, 183, 1665-1681 (2020). [LINK]
  • Wang N, Zheng J, Chen Z, Liu Y, Dura B, Kwak M, Xavier-Ferrucio J, Lu Y-C,Zhang MM, Roden C, Cheng JJ, Krause D, Ding Y, Fan R* & Lu J*. Single-cell microRNA/mRNA co-profiling reveals non-(epigenetic) heterogeneity and regulatory programs. Nature Communications, 10: 95 (2019). [LINK]
  • Xhangolli I, Dura B, Lee GH, Kim DJ, Xiao Y, and Fan R*. Single-cell integrative analysis of CAR-T cell activation reveals a predominantly TH1/TH2 mixed response independent of differentiation, Genomics, Proteomics & Bioinformatics (GPB), 17(2), 129-139 (2019). (Cover Highlight) [LINK]
  • Xiao Y, Kim DJ, Dura B, Zhang K, Yan RC, Li HM, Han E, Ip J, Zou P, Liu J, Chen AT, Vortmeyer AO, Zhou JB, and Fan R*, Ex vivo dynamics of human glioblastoma cells in a microvasculature-on-a-chip system correlates with tumor heterogeneity and subtypes, Advanced Science, 6, 1801531 (2019). (Cover Highlight) [LINK]
  • Deng YX, Finck A, and Fan R*. Single-cell omics analyses enabled by microchip technologies. Annual Review of Biomedical Engineering, 21, 365-393 (2019). [LINK]
  • Chen Z, Chen JJ, and Fan R*. Single-cell protein secretion detection and profiling. Annual Review of Analytical Chemistry, 12:21.1-21.19, (2019). [LINK]
  • Dura B, Choi JY, Zhang K, Damsky W, Thakral D, Bosenberg M, Craft J, Fan R*, scFTD-seq: freeze-thaw lysis based, portable approach toward highly distributed single-cell 3’ mRNA profiling, Nucleic Acids Research, 47(3), e16 (2019). [LINK]
  • Jayatilaka H, Tyle P, Chen JJ, Kwak M, Ju JA, Kim HJ, Lee J.S.H., WuPH, Gilkes DM, Fan R*, and Wirtz D*, Novel synergistic IL6/8 paracrine signaling pathway infers new strategy to inhibit tumor cell migration, Nature Communications, 8:15584, (2017). [LINK]
  • Kleppe M, Kwak M, Koppikar P, Riester M, Keller M, Bastian L, Hricik T, Bhagwat N, Abdel-Wahab OI, Marubayashi S, Chen JJ, Romanet V, Fridman JS, Bromberg J, Murakami M, Radimerski T, Michor F, Fan R* & Levine RL*.  JAK-STAT Pathway Activation in Malignant and Non-Malignant Cells Contributes to MPN Pathogenesis and Therapeutic Response, Cancer Discovery, 5(3), 316–31 (2015). [LINK]
  • Xue Q, Lu Y, Eisele MR, Sulistijo E, Fan R* & Miller-Jensen K*, Analysis of single-cell secretion reveals a role for paracrine signaling in coordinating macrophage response to TLR4 stimulation, Science Signaling, 8, 381 (2015). [LINK]
  • Lu Y, Xue Q, Eisele MR, Sulistijo E, Brower K, Han L, Amir ED, Pe’er D, Miller-Jensen K *, and Fan R*,  Highly multiplexed profiling of immune effector functions reveals deep functional heterogeneity in response to pathogenic ligands, Proc. Natl. Acad. Sci., U.S.A., 112(7), 607-615 (2015). [LINK]