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Yanxiang Deng, PhD
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Assistant Professor of Pathology and Laboratory Medicine
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Core member, Penn Epigenetics Institute
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Member, Penn Institute on Aging
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Full Member , Penn Abramson Cancer Center
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Department: Pathology and Laboratory Medicine
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Graduate Group Affiliations
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Contact information
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422 Curie Boulevard, Stellar-Chance Laboratories 713A
Philadelphia, PA 19104
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Philadelphia, PA 19104
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Publications
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Education:
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39 Rensselaer Polytechnic Institute, 2018.
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Permanent link21 8 PhD c
39 Rensselaer Polytechnic Institute, 2018.
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fd 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.
133 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.
125 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.
1ca 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.
dc Guo, P., Deng, Y.: Spatial Omics: Navigating Neuroscience Research into the New Era. Advances in Neurobiology 41(no issue): 133-149, November 2024.
124 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.
12c 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.
db Deng, Y.#*, Bai, Z.#*, Fan R.*: Microtechnologies for single-cell and spatial multi-omics. Nature Reviews Bioengineering 1(10): 769-784, Jun 2023.
1ba Zhang, D.#, Deng, Y.#*, Kukanja P, Agirre E, Bartosovic M, Dong M, Ma C, Ma S, Su G, Bao S, Liu Y, Xiao Y, Rosoklija GB, Dwork AJ, Mann JJ, Leong KW, Boldrini M, Wang L, Haeussler M, Raphael BJ, Kluger Y, Castelo-Branco G*, Fan R.*: Spatially resolved epigenome-transcriptome co-profiling of mammalian tissues at the cellular level. Nature 616(7955): 113-122, Mar 2023.
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Selected Publications
106 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.fd 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.
133 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.
125 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.
1ca 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.
dc Guo, P., Deng, Y.: Spatial Omics: Navigating Neuroscience Research into the New Era. Advances in Neurobiology 41(no issue): 133-149, November 2024.
124 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.
12c 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.
db Deng, Y.#*, Bai, Z.#*, Fan R.*: Microtechnologies for single-cell and spatial multi-omics. Nature Reviews Bioengineering 1(10): 769-784, Jun 2023.
1ba Zhang, D.#, Deng, Y.#*, Kukanja P, Agirre E, Bartosovic M, Dong M, Ma C, Ma S, Su G, Bao S, Liu Y, Xiao Y, Rosoklija GB, Dwork AJ, Mann JJ, Leong KW, Boldrini M, Wang L, Haeussler M, Raphael BJ, Kluger Y, Castelo-Branco G*, Fan R.*: Spatially resolved epigenome-transcriptome co-profiling of mammalian tissues at the cellular level. Nature 616(7955): 113-122, Mar 2023.
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