靳文菲----中国科学院上海营养与健康研究所

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靳文菲

博士

多组学与肿瘤研究组组长

邮箱: jinwf@sinh.ac.cn

电话: +86-21-54920532

研究组主页: https://sinh-jinlab.github.io/

所属部门: 中国科学院计算生物学重点实验室

个人简历

2023–至今：中国科学院上海营养与健康研究所，研究员
2017-2023年：南方科技大学，副教授，研究员
2013-2017年：美国国立卫生研究院(NIH)，博士后
2012-2012年：中国科学院-马普学会计算生物学伙伴研究所，助理研究员
2006-2012年：中国科学院-马普学会计算生物学伙伴研究所，计算生物学，博士
2001-2006年：郑州大学，生物技术，学士

研究方向

组学，生物信息，肿瘤免疫

研究内容

　　研究组致力于开发和整合组学技术和生物信息手段提升精准医学。即基于多种组学技术刻画人的衰老和癌症样本，通过建立新的人工智能算法和模型解析生物学过程，鉴定关键信号和分子靶点。主要研究方向：
　　（1）开发组学技术和组学计算方法，尤其是单细胞多组学技术及其分析方法；
　　（2）多组学数据整合，构建全息细胞图谱解析细胞解析细胞对外界刺激的应答；
　　（3）利用单细胞技术解析肿瘤微环境和肿瘤微进化，发展精准免疫治疗。

代表论著（#第一作者，*通讯作者）

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)
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)
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.