Faculty

Yanxiang Deng, PhD

Assistant Professor of Pathology and Laboratory Medicine

Department: Pathology and Laboratory Medicine

Graduate Group Affiliations

Contact information

Perelman School of Medicine at the University of Pennsylvania
Stellar-Chance Laboratories, Rm 713A
422 Curie Boulevard
Philadelphia, PA 19104

Email:
Yanxiang.Deng@Pennmedicine.upenn.edu

Publications

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Education
PhD
Rensselaer Polytechnic Institute, 2018.

Links
Search PubMed for articles
Deng Lab Website

Permanent link

> Perelman School of Medicine > Faculty > Details

Description of Research Expertise

Keywords: Spatial omics, Single-cell analysis, Microfluidics

Research Interests:
We are developing new tools at the intersection of microchip, microscopy, genomics, and computational analysis to profile genome, epigenome, transcriptome, and proteome within the spatial context of tissues and cells. These novel technologies will greatly improve our ability to study tissue complexity and reveal the salient features of tissue architecture in physiology and disease.

Selected Publications

Guo, P., Cui, Y., He, J., Waldman, A.J., Zhu, J., Chen, Y., Huang, Z., Zhou, J., Phillips-Cremins, J.E., and Deng, Y.: Integrative spatial profiling of 3D genome organization and gene expression in tissue. Cell August 2026.

Liu, S., Rook, A.H., Huang, A.C., Maity, A., Qin, Z., Chen, Y., Song, D., Deng, Y., Huang, Z., Karakousis, G.C., Mitchell, T.C., Amaravadi, R.K., Schuchter, L.M., Binder, Z.A., O'Rourke, D.M., Herlyn, M., Guo, W., Xu, X.: Topical resiquimod elicits systemic protection and improves anti-PD1 therapy in melanoma via priming of CD8+ T cells. Cancer Immunology Research Jun 2026.

Goldberg, DC., Fu, H., Atkins, D., Moyer, E., Lee, CN., Deng, Y., Zhou, W.: KnowYourCG: Facilitating base-level sparse methylome interpretation. Science Advances 11(43): eadw3027, Oct 2025.

Lee, C., Fu, H., Cardilla, A., Zhou, W., and Deng, Y.: Spatial joint profiling of DNA methylome and transcriptome in mammalian tissues. Nature 646(8087): 1261-1271, September 2025.

Guo, P., Chen, Y., Mao, L., Cardilla, A., Lee, C., Cui, Y., Jin, D., Hua, Y., Xu, X., and Deng, Y.: Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues. Nature Communications 16(1): 5945, Jul 2025.

Coleman K, Schroeder A, Loth M, Zhang D, Park JH, Sung JY, Blank N, Cowan AJ, Qian X, Chen J, Jiang J, Yan H, Samarah LZ, Clemenceau JR, Jang I, Kim M, Barnfather I, Rabinowitz JD, Deng Y, Lee EB, Lazar A, Gao J, Furth EE, Hwang TH, Wang L, Thaiss CA, Hu J, Li M.: Resolving tissue complexity by multimodal spatial omics modeling with MISO. Nature Methods 22(3): 530-538, January 2025.

Guo, P., Mao, L., Chen, Y., Lee, C., Cardilla, A., Li, M., Bartosovic, M., and Deng, Y.: Multiplexed spatial mapping of chromatin features, transcriptome, and proteins in tissues. Nature Methods 22(3): 520-529, Jan 2025.

Guo, P., Deng, Y.: Spatial Omics: Navigating Neuroscience Research into the New Era. Advances in Neurobiology 41(no issue): 133-149, November 2024.

Farzad, N., Enninful, A., Bao, S., Zhang, D., Deng, Y., and Fan, R.: Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue. Nature Protocols 19(11): 3389-3425, Jun 2024.

Malik, S., Pradeep, S.P., Kumar, V., Xiao, Y., Deng, Y., Fan, R., Vasquez, J.C., Singh, V., and Bahal, R: Antitumor efficacy of a sequence-specific DNA-targeted γPNA-based c-Myc inhibitor. Cell Reports Medicine 5(1), Jan 2024.