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LI Hong

Ph.D.

Professor, Principal Investigator

Laboratory of Systems Biology

Email: lihong01@sinh.ac.cn, lihong01@sibs.ac.cn

Tel: 86-21-54920348

Research Areas:

1. Systems Biology

2. Cancer Genomics

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 (including Education & Academic Background):

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. 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 2023 Apr 3. doi: 10.1097/HEP.0000000000000387.

2. 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.

3. 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.

4. 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.

5. Feng F, Shen B, Mou X, Li Y, Li H*. Large-scale pharmacogenomic studies and drug response prediction for personalized cancer medicine. J Genet Genomics. 2021;48(7):540-551.

6. Hu B#, Li H#, Guo W, Sun YF, Zhang X, Tang WG, Yang LX, Xu Y, Tang XY, Ding GH, Qiu SJ, Zhou J, Li YX, Fan J, Yang XR. Establishment of a hepatocellular carcinoma patient-derived xenograft platform and its application in biomarker identification. Int J Cancer 2020 Mar 15;146(6):1606-1617.

7. 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.

8. 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.

9. Cheng J#, Wei D, Ji Y, Chen L, Yang L, Li G, Wu L, Hou T, Xie L, Ding G, Li H*, Li Y*. Integrative analysis of DNA methylation and gene expression reveals hepatocellular carcinoma-specific diagnostic biomarkers. Genome Med 2018 May 30;10(1):42.

10. Hu H#, Li H#, Jiao F, Han T, Zhuo M, Cui J, Li Y*, Wang L*. Association of a novel point mutation in MSH2 gene with familial multiple primary cancers. J Hematol Oncol 2017 Oct 3;10(1):158.

11. Li H#, Glusman G, Hu H, Caballero J, Hubley R, Witherspoon D, Guthery SL, Mauldin DE, Jorde LB, Hood L, Roach JC*, Huff CD*. Relationship Estimation from Whole-Genome Sequence Data. PLoS Genet 2014 Jan 30;10(1):e1004144.