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JIN Wenfei


Professor, Principal Investigator

Laboratory of Multi Omics Precision Medicine

Email: jinwf@sinh.ac.cn

Tel: 86-21-

Research Areas:
Dr. Jin has worked on genomics, particular developed singe cell technologies, including scDNase-seq (Nature 2015), ISSAAC-seq (Nature Methods 2022), scPolyA-seq (PNAS 2022), CCI (Cell Discov 2021) and kssd (Genome Biol 2021), to study tumor. He has published >50 articles, including first author and corresponding author articles on Nature, Nature Cancer, Nature Methods, PNAS, Genome Res, AJHG and Genome Biol.
Dr. Jin is interested in: 1) single cell sequencing and its applications in cancer biology; 2) bioinformatics and identifying genetic/epigenetic changes that drive oncogenesis; 3) developing cancer prediction and treatment model for precision medicine.
The long-term goal of the lab is to develop efficient personalized treatment for cancers based on patients’ genetic background. In near future, the lab will focus on investigating genetic/epigenetic heterogeneity and micro-evolution of cancer cells using single cell sequencing related technologies.

Brief Biography:
2023 - present: Principal Investigator, Shanghai Institute of Nutrition and Health, CAS
Mar 2017 - 2023: Associate Professor, Southern University of Science and Technology
Jan 2013 - Mar 2017: Postdoc fellow, National Institutes of Health (NIH) [Mentor: Dr. ZHAO Keji]
Jan 2012 - Dec 2012: Assistant researcher, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology (PICB), SIBS, CAS
Sept 2006 - Dec 2011: Ph.D. in Computational Biology, PICB and University of Chinese Academies of Sciences [Supervisors: Prof. JIN Li (CAS member) and Dr. XU Shuhua]
Feb.2006 - Apr 2006: Intern, Institute of Biochemistry and Cell Biology, SIBS, CAS [Mentors: Prof. LIU Mofang and Prof. WANG Enduo (CAS member)]
Sept 2001 - Jul 2006: B.Sc. in Biotechnology, Zhengzhou University, China

Selected Publications: (from >50 publications, *Co-corresponding author; #Co-first author;)

  1. Huang C#, Wang X#, Wang Y#, Feng Y, Wang X, Chen S, Yan P, Liao J, Zhang Q, Mao C, Li Y, Wang L, Wang X, Yi W, Cai W, Chen S, Hong N*, He W*, Chen J*, Jin W* (2023) Sirpα on tumor-associated myeloid cells restrains anti-tumor immunity in colorectal cancer independent of its interaction with CD47. Nat Cancer (In Press)
  2. Yi H#*, Lin Y#, Chang Q, Jin W* (2023) A fast and globally optimal solution for RNA-seq quantification. Brief Bioinform Aug 18;bbad298. (Advanced online)
  3. Li H#, Liu H#, Liu Y#, Wang X, Yu S, Huang H, Shen X, Zhang Q, Hong N, Jin W* (2023) Exploring the dynamics and influencing factors of CD4 T cell activation using single-cell RNA-seq. iScience Aug 9;26(9):107588.
  4. Zhou J#, Chen G#, Wang J#, Zhou B, Sun X, Wang J, Tang S, Xing X, Hu X, Zhao Y, Peng Y, Shi W, Zhao T, Wu Y, Zhong H, Hong N, Ruan Z*, Zhang Y*, Jin W* (2023) Anti-PD-1 therapy achieves favorable outcomes in HBV-positive non-liver cancer. Oncogenesis Apr 20;12(1):22.
  5. Wang J#, Chen W#, Yue W, Hou W, Rao F, Zhong H, Qi Y*, Hong N*, Ni T*, Jin W* (2022) Comprehensive mapping of alternative polyadenylation site usage and its dynamics at single cell resolution. Proc Natl Acad Sci U S A Dec 6;119(49):e2113504119.
  6. Xu W#,Yang W#, Zhang Y, Chen Y, Hong N, Zhang Q, Wang X, Hu Y, Song K, Jin W*, Chen X* (2022) ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells. Nat Methods Oct;19(10):1243-1249.
  7. Wang X#, Shen X#, Chen S, Liu H, Hong N, Zhong H, Chen X, Jin W* (2022) Reinvestigation of Classic T Cell Subsets and Identification of Novel Cell Subpopulations by Single-Cell RNA Sequencing. J Immunol Jan 15;208(2):396-406.
  8. Yi G, Lin Y, Lin C, Jin W* (2021) Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis. Genome Biol Mar 16;22(1):84.
  9. Qin P#, Pang Y#, Hou W#, Fu R#, Zhang Y#, Wang X#, Meng G, Liu Q, Zhu X, Hong N*, Cheng T*, Jin W* (2021) Integrated decoding hematopoiesis and leukemogenesis using single cell sequencing and its medical implication. Cell Discov Jan 5;7(1):2.
  10. Han Z, Cui K, Placek K, Hong N, Lin C, Chen W, Zhao K*, Jin W* (2020) Diploid genome architecture revealed by multi-omic data of hybrid mice. Genome Res Aug;30(8):1097-1106.
  11. Lai B#, Tang Q#, Jin W#, Hu G#, Wangsa D, Cui K, Stanton BZ, Ren G, Ding Y, Zhao M, Liu S, Song J, Ried T, Zhao K (2018) Trac-looping measures genome structure and chromatin accessibility. Nat Methods Sep;15(9):741-747.
  12. Ren G#, Jin W#, Cui K, Rodrigez J, Hu G, Zhang Z, Larson DR, Zhao K (2017) CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression. Mol Cell Sep 21;67(6):1049-1058.
  13. Jin W#, Tang Q#, Wan M, Cui K, Zhang Y, Ren G, Ni B, Sklar J, Przytycka T, Childs R, Levens D, Zhao K (2015) Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples. Nature Dec 3;528(7580):142-146.
  14. Jin W#, Li R#, Zhou Y, Xu S (2014) Distribution of ancestral chromosomal segments in admixed genomes and its implications for inferring population history and admixture mapping. Euro J Hum Genet Jul;22(7):930-937.
  15. Kraushaar DC#, Jin W#, Maunakea A, Abraham B, Ha M, Zhao K (2013) Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3. Genome Biol 14(10):R121.
  16. Jin W, Wang S, Wang H, Jin L, Xu S (2012) Exploring population admixture dynamics via empirical and simulated genome-wide distribution of ancestral chromosomal segments. Am J Hum Genet Nov 2;91(5):849-862.
  17. Jin W, Qin P, Lou H, Jin L, Xu S (2012) A systematic characterization of genes underlying both complex and Mendelian diseases. Hum Mol Genet Apr 1;21(7):1611-1624.
  18. Jin W, Xu S, Wang H, Yu Y, Shen Y, Wu B, Jin L (2012) Genome-wide detection of natural selection in African Americans pre- and post-admixture. Genome Res Mar;22(3):519-527.