Research Areas
1. Systems Biology
2. Cancer Genomics

Research Interests
Cancer pharmacogenomics: develop computational approaches that can be used to optimize the selection of drugs and their doses for individual patients.
Cancer evolution: molecular basis of cancer development, especially the computational analysis of cancer genome evolution.
Discover new signatures by data integration and mining: understands the complexity of biological systems via networks; identification and characterization of enhancer-target and lncRNA-target interaction in cancer.

Brief Biography
Dr. LI Hong is a principal investigator in the Shanghai Institute of Nutrition and Health of Chinese Academy of Sciences. She received the bachelor degree in Mathematics Science and Computer Technology from Central South University, and PhD degree in Bioinformatics from Shanghai Institutes for Biology Science, CAS (SIBS-CAS). She worked as a Postdoctoral fellow at the Institute for Systems Biology, Seattle in 2010. She worked at SIBS-CAS since 2013, and became the principal investigator in 2020.
Dr. Li’s research focuses on the development of bioinformatics approaches and application in human disease. She has made contribution to proteomics bioinformatics, family genomics and cancer systems biology. She has published >50 research papers that were cited >2600 time, and her work was recognized by several research awards, including The First Prize of Shanghai Natural Science Award (2014) and Sanofi-SIBS 2019 Young Faculty Award (2019).

Selected Publications (*Corresponding Author)

1. Chen X#, Yan X, Shen B, Wang H, Tang Z, Zang Y, Lin P, Zhang H, Li Y*, Li H*. Decomposing multi-scale dynamic regulation from single-cell multiomics with scMagnify. Nat Commun 2026. https://doi.org/10.1038/s41467-026-78441-9
2. Li J#, Lin P, Wang H, Tang Z, Yan X, Chen X, Yuan J, Chen W, Li H*. Pan-cancer analysis of spatial transcriptomics reveals heterogeneous tumor spatial microenvironment. Cell Rep Med 2026 May 19;7(5):102751.
3. Zhang Z#, Li H#*, Chen L#, Lu T, Shentu X, Liu Y, Tang Z, Ji S, Qiu Z, Zou Y, Wen H, Han J, Jiang Z, Fan J, Gao X, Li D, Mesropian A, Pinyol R, Llovet JM, Dong H, Ji Y*, Hui L*. Molecular insights into early malignant transition of hepatocellular carcinoma. Cancer Cell 2026 May 11;44(5):1012-1028.e9.
4. Feng F#, He T#, Lin P#, Hu J#, Shen B, Tang Z, Zhou J, Fan J, Hu B, Li H*. Computational framework for prioritizing candidate compounds overcoming the resistance of pancancer immunotherapy. Cell Rep Med 2025 Aug 19;6(8):102276.
5. Jing SY#, Wang HQ, Lin P, Yuan J, Tang ZX, Li H*. Quantifying and interpreting biologically meaningful spatial signatures within tumor microenvironments. NPJ Precis Oncol 2025 Mar 11;9(1):68.
6. Wang H#, Li J#, Jing S, Lin P, Qiu Y, Yan X, Yuan J, Tang Z, Li Y, Zhang H, Chen Y, Wang Z, Li H*. SOAPy: a Python package to dissect spatial architecture, dynamics, and communication. Genome Biol 2025 Mar 29;26(1):80.
7. Lin P#, Yan X, Jing S, Wu Y, Shan Y, Guo W, Gu J, Li Y, Zhang H, Li H*. Single-cell and spatially resolved transcriptomics for liver biology. Hepatology 2024 Sep 1;80(3):698-720. doi: 10.1097/HEP.0000000000000387.
8. Li L#, Cui L#, Lin P#, Liu Z, Bao S, Ma X, Nan H, Zhu W, Cen J, Mao Y, Ma X, Jiang L, Nie Y, Ginhoux F, Li Y*, Li H*, Hui L*. Kupffer-cell-derived IL-6 is repurposed for hepatocyte dedifferentiation via activating progenitor genes from injury-specific enhancers. Cell Stem Cell 2023, S1934-5909(23)00009-7.
9. Shen B#, Feng F#, Li K, Lin P, Ma L, Li H*. A systematic assessment of deep learning methods for drug response prediction: from in vitro to clinical applications. Brief Bioinform 2023, 24(1):bbac605.
10. Yang J#, Lin P#, Yang M#, Liu W, Fu X, Liu D, Tao L, Huo Y, Zhang J, Hua R, Zhang Z*, Li Y*, Wang L*, Xue J*, Li H*, Sun Y*. Integrated genomic and transcriptomic analysis reveals unique characteristics of hepatic metastases and pro-metastatic role of complement C1q in pancreatic ductal adenocarcinoma. Genome biology 2021, 22(1): 4.
11. Qiu Z#, Li H#, Zhang Z#, Zhu Z, He S, Wang X, Wang P, Qin J, Zhuang L, Wang W, Xie F, Gu Y, Zou K, Li C, Li C, Wang C, Cen J, Chen X, Shu Y, Zhang Z, Sun L, Min L, Fu Y, Huang X, Lv H, Zhou H, Ji Y, Zhang Z, Meng Z, Shi X, Zhang H*, Li Y*, Hui L*. A Pharmacogenomic Landscape in Human Liver Cancers. Cancer Cell 2019 Aug 12;36(2):179-193.e11.
12. Li W#, Yang L#, He Q, Hu C, Zhu L, Ma X, Ma X, Bao S, Li L, Chen Y, Deng X, Zhang X, Cen J, Zhang L, Wang Z, Xie WF, Li H*, Li Y*, Hui L*. A Homeostatic Arid1a-Dependent Permissive Chromatin State Licenses Hepatocyte Responsiveness to Liver-Injury-Associated YAP Signaling. Cell stem cell 2019 Jul 3;25(1):54-68.e5.