Google scholar

---

Selected Publications

• Li, H., Dixon, E.E., Wu, H. and Humphreys, B.D., 2022. Comprehensive single-cell transcriptional profiling defines shared and unique epithelial injury responses during kidney fibrosis. Cell Metabolism, 34(12), pp.1977-1998. (DOI)
  → Research featured by NIH NIDDK annual report (PDF)
  → Research Highlights by Nature Reviews Nephrology (DOI)
  → Research Highlights by Kidney International (DOI)
  → 中华人民共和国科学技术部报道《科学家构建肾脏纤维化全景图谱》(网页PDF)
  → 中文媒体报道 (BioArt; 麻省理工科技评论)
  

• Li, H., Li, D., Ledru, N., Xuanyuan, Q., Wu, H., Asthana, A., Byers, L.N., Tullius, S.G., Orlando, G., Waikar, S.S. and Humphreys, B.D., 2024. Transcriptomic, epigenomic, and spatial metabolomic cell profiling redefines regional human kidney anatomy. Cell Metabolism, 36(5), pp.1105-1125. (DOI)
  → Research Highlights by Nature Reviews Nephrology 2024 Year in Review (DOI)
  → Featured Content of the Cell Metabolism journal website
  → 中文媒体报道 (BioArt; 公众号)
  

• Li, H.#, Li, D.# and Humphreys, B.D., 2024. Chromatin conformation and histone modification profiling across human kidney anatomic regions. Scientific Data, 11(1), p.797. (DOI)
  → Highlighted in the collection of Data for epigenetics research
  

• Li, H., Bao, S., Farzad, N., Qin, X., Fung, A.A., Zhang, D., Bai, Z., Tao, B. and Fan, R., 2025. Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq. Nature Protocols, pp.1-35. (DOI)
  → Highlighted in News & Views of Nature Protocols
  → 中文媒体报道 (Link)
  → Selected as the cover paper (Volume 20 Issue 9, September 2025)
  
  

---

All Publications

(21) Malone, A.F., Paul, R., Li, H., Leckie-Harre, A., Wu, H., Ledru, N., McPherson, G., Davies, H.B., Doty, T., Farney, A.C. and Jay, C.C., 2025. Mosaic Loss of Y Chromosome Defines a Proximal Tubular Cell State Associated with Recovery from DGF and of Allograft Quality and Functional Reserve Post DCD Kidney Transplantation. Annals of Surgery, pp.10-1097. (DOI)

(20) Li, H., Bao, S., Farzad, N., Qin, X., Fung, A.A., Zhang, D., Bai, Z., Tao, B. and Fan, R., 2025. Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq. Nature Protocols, pp.1-35. (DOI)
→ Highlighted in News & Views of Nature Protocols
→ 中文媒体报道 (Link)
→ Selected as the cover paper (Volume 20 Issue 9, September 2025)

(19) Baysoy, A.#, Tian, X.#, Zhang, F.#, Renauer, P.#, Bai, Z., Shi, H., Li, H., Tao, B., Yang, M., Enninful, A. and Gao, F., 2024. Spatially Resolved in vivo CRISPR Screen Sequencing via Perturb-DBiT. BioRxiv, pp.2024-11.

(18) Bai, Z.#, Zhang, D.#, Gao, Y.#, Tao, B.#, Zhang, D.#, Bao, S.#, Enninful, A., Wang, Y., Li, H., Su, G. and Tian, X., Zhang, N., Xiao, Y., Liu, Y., Gerstein, M., Li, M., Xing, Y., Lu, J., Xu, ML. and Fan, R. 2024. Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues. Cell, 187(23), pp.6760-6779. (DOI)

(17) Zhao, C.#, Rong, K.#, Liu, P.#, Kong, K., Li, H., Zhang, P., Chen, X., Fu, Q. and Wang, X., 2024. Preventing periprosthetic osteolysis in aging populations through lymphatic activation and stem cell-associated secretory phenotype inhibition. Communications Biology, 7(1), p.962. (DOI)

(16) Li, H. and Humphreys, B.D., 2024. Protocol for multimodal profiling of human kidneys with simultaneous high-throughput ATAC and RNA expression with sequencing. STAR Protocols, 5(3), p.103049. (DOI)

(15) Li, H.#, Li, D.# and Humphreys, B.D., 2024. Chromatin conformation and histone modification profiling across human kidney anatomic regions. Scientific Data, 11(1), p.797. (DOI)
→ Highlighted in the collection of Data for epigenetics research

(14) Li, H. and Humphreys, B.D., 2024. Spatially resolved metabolomic dataset of distinct human kidney anatomic regions. Data in Brief, 54, p.110431. (DOI)

(13) Li, H. and Humphreys, B.D., 2024. Multimodal characterization of sexual dimorphism in the mammalian kidney. Kidney International, 105(4), pp.653-655. (DOI)

(12) Li, H., Li, D., Ledru, N., Xuanyuan, Q., Wu, H., Asthana, A., Byers, L.N., Tullius, S.G., Orlando, G., Waikar, S.S. and Humphreys, B.D., 2024. Transcriptomic, epigenomic, and spatial metabolomic cell profiling redefines regional human kidney anatomy. Cell Metabolism, 36(5), pp.1105-1125. (DOI)
→ Research Highlights by Nature Reviews Nephrology 2024 Year in Review (DOI)
→ Featured Content of the Cell Metabolism journal website
→ 中文媒体报道 (BioArt; 公众号)

(11) Li, H. and Humphreys, B.D., 2024. Targeting de novo lipogenesis to mitigate kidney disease. The Journal of Clinical Investigation, 134(4). (DOI)

(10) Wilson, P.C., Verma, A., Yoshimura, Y., Muto, Y., Li, H., Malvin, N.P., Dixon, E.E. and Humphreys, B.D., 2024. Mosaic loss of Y chromosome is associated with aging and epithelial injury in chronic kidney disease. Genome biology, 25(1), p.36. (DOI)

(9) Wang, J.#, Ku, X.#, Ma, Q.#, Li, H.#, Huang, S.#, Mao, L., Yu, F., Jin, J. and Yan, W., 2024. Hsa_circ_0007099 and PIP4K2A coexpressed in diffuse large B-cell lymphoma with clinical significance. Genes & Diseases, 11(4), p.101056. (DOI)

(8) Ku, X.#, Wang, J.#, Li, H.#, Meng, C., Yu, F., Yu, W., Li, Z., Zhou, Z., Zhang, C., Hua, Y. and Yan, W., 2023. Proteomic portrait of human lymphoma reveals protein molecular fingerprint of disease specific subtypes and progression. Phenomics, 3(2), pp.148-166. (DOI)

(7) Cheng, Z. et al. (special journal issue; author list alphabetically ordered) (2023). RNA-seq: questions and answers. STAR Protocols. (link)

(6) Li, H. and Humphreys, B.D., 2022. Mouse kidney nuclear isolation and library preparation for single-cell combinatorial indexing RNA sequencing. STAR Protocols, 3(4), p.101904. (DOI)

(5) Li, H., Dixon, E.E., Wu, H. and Humphreys, B.D., 2022. Comprehensive single-cell transcriptional profiling defines shared and unique epithelial injury responses during kidney fibrosis. Cell Metabolism, 34(12), pp.1977-1998. (DOI)
→ Research featured by NIH NIDDK annual report (PDF)
→ Research Highlights by Nature Reviews Nephrology (DOI)
→ Research Highlights by Kidney International (DOI)
→ 科技部报道《科学家构建肾脏纤维化全景图谱》(网页PDF)
→ 中文媒体报道 (BioArt; 麻省理工科技评论)

(4) Muto, Y.#, Li, H.# and Humphreys, B.D., 2022. Single Cell Transcriptomics. Innovations in Nephrology: Breakthrough Technologies in Kidney Disease Care (pp. 87-102). Cham: Springer International Publishing. (DOI)
→ Chapter has been translated into German (DOI)

(3) Li, H. and Humphreys, B.D., 2022. New functions for basophils identified in kidney fibrosis. Nature Immunology, 23(6), pp.824-825. (DOI)
→ 中文媒体报道 (公众号)

(2) Li, H. and Humphreys, B.D., 2021. Single cell technologies: Beyond microfluidics. Kidney360, 2(7), pp.1196-1204. (DOI)

(1) Li, H. and Humphreys, B.D., 2020. Surveying the human single-cell landscape. Kidney International, 98(6), pp.1385-1387. (DOI)