Publications

  • Journal Papers

Publications (#equal contribution; * corresponding author)

40. Preprint: Wenhong Hou#, Li Duan#, Changyuan Huang#, Xingfu Li, Xiao Xu, Pengfei Qin, Ni Hong, Daping Wang*, Wenfei Jin*. Mesenchymal stem cell subpopulations and their heterogeneity of response to inductions revealed by single-cell RNA-seq. doi: https://doi.org/10.1101/2021.05.07.443197

39. Preprint: Xuefei Wang#,Xiangru Shen#, Shan Chen, Hongyi Liu, Ni Hong, Xi Chen, Wenfei Jin*. Re-investigation of classic T cell subsets and identification of novel cell subpopulations by single-cell RNA sequencing. doi: https://www.biorxiv.org/content/10.1101/2021.02.11.430754v1

38. Ruiqing Fu, Pengfei Qin, Xianghui Zou, Zhangli Hu, Ni Hong*, Yun Wang*, Wenfei Jin*. 2021. A comprehensive characterization of monoallelic expression during hematopoiesis and leukemogenesis via single cell RNA-seq.  Front Cell Dev Biol. 9:702897. doi: 10.3389/fcell.2021.702897

37.  Wei Xu , Yi Wen, Yingying Liang, Qiushi Xu, Xuefei Wang, Wenfei Jin and Xi Chen*. 2021. A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin.  Nat protoc. 16:4084-4107. doi: 10.1038/s41596-021-00583-5

36. Zixiang Luo#, Chenyu Xu#, Zhen Zhang*, Wenfei Jin*. 2021. A topology‐preserving dimensionality reduction method for single‐cell RNA‐seq data using graph autoencoder. Sci Rep. 11: 20028. doi: 10.1038/s41598-021-99003-7 

35. Nonthaphat Kent Wong, Shumeng Luo, Eudora Y. D. Chow, Fei Meng, Adenike Adesanya, Jiahong Sun, Herman M. H. Ma, Wenfei Jin, Wan-Chun Shea Ping Yip* and Chien-Ling Huang*. 2021. The Tyrosine Kinase-Driven Networks of Novel Long Non-coding RNAs and Their Molecular Targets in Myeloproliferative Neoplasms. Front Cell Dev Biol. 9:643043. doi: 10.3389/fcell.2021.643043

34. Huiguang Yi, Yanling Lin, Chengqi Lin, Wenfei Jin*. 2021. Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis. Genome Biol. 22:84. doi: 10.1186/s13059-021-02303-4

33. Pengfei Qin#, Yakun Pang#, Wenhong Hou#, Ruiqing Fu#, Yingzhi Zhang#, Xuefei Wang#, Guofeng Meng, Qifa Liu, Xiaofan Zhu, Ni Hong*, Tao Cheng* and Wenfei Jin*. 2021. Integrated decoding hematopoiesis and leukemogenesis using single cell sequencing and its medical implication. Cell Discov. 7:2. doi: 10.1038/s41421-020-00223-4 

32. Xuekun Fu, Bo Zhou, Qinnan Yan, Chu Tao, Lei Qin, Xiaohao Wu, Sixiong Lin, Sheng Chen, Yumei Lai, Xuenong Zou, Zengwu Shao, Meiqing Wang, Di Chen, Wenfei Jin, Youqiang Song, Huiling Cao, Ge Zhang, Guozhi Xiao. 2020. Kindlin-2 regulates skeletal homeostasis by modulating PTH1R in mice. Signal Transduct Target Ther. 5(1):297. doi: 10.1038/s41392-020-00328-y.

31. Jiji T Kurup, Zhijun Han, Wenfei Jin, and Benjamin L Kidder. 2020. H4K20me3 methyltransferase SUV420H2 shapes the chromatin landscape of pluripotent embryonic stem cells. Development. 2020. 147(23):dev188516. doi: 10.1242/dev.188516.

30. Zhijun Han, Cui Kairong, Katarzyna Placek, Ni Hong, Chengqi Lin, Wei Chen, Keji Zhao*, Wenfei Jin*. 2020. Diploid genome architecture revealed by multi-omic data of hybrid mice. Genome Res. 30:1097-1106. doi: 10.1101/gr.257568.119.

29. Wei Chen, Xuefei Wang, Gang Wei, Yin Huang, Yufang Shi, Dan Li, Shengnu Qiu, Bin Zhou, Junhong Cao, Meng Chen*, Pengfei Qin*, Wenfei Jin* and Ting Ni*. 2020 Single-Cell Transcriptome Analysis Reveals Six Subpopulations Reflecting Distinct Cellular Fates in Senescent Mouse Embryonic Fibroblasts. Front Genet. 11:867. doi: 10.3389/fgene.2020.00867.

28. Li Wang, Rong Qiu, Zhaoyang Zhang, Zhijun Han, Chao Yao, Guojun Hou, Dai Dai, Wenfei Jin, Yuanjia Tang, Xiang Yu and Nan Shen. 2020. The MicroRNA miR-22 Represses Th17 Cell Pathogenicity by Targeting PTEN-Regulated Pathways. Immunohorizons. 4(6):308-318. doi: 10.4049/immunohorizons.2000008.

27. Rong Qiu, Xiang Yu, Li Wang, Zhijun Han, Chao Yao, Yange Cui, Guojun Hou, Dai Dai, Wenfei Jin, and Nan Shen. 2020. Inhibition of Glycolysis in Pathogenic TH17 Cells through Targeting a miR-21–Peli1–c-Rel Pathway Prevents Autoimmunity. J Immunol. 204(12):3160-3170. doi: 10.4049/jimmunol.2000060.

26. Bo Zhou, Wenfei Jin. Visualization of Single Cell RNA-Seq Data Using t-SNE in R. Methods Mol Biol. 2020;2117:159-167. doi: 10.1007/978-1-0716-0301-7_8.

25. Huiling Cao, Qinnan Yan, Dong Wang, Yumei Lai, Bo Zhou, Qi ZhangWenfei Jin, Simin Lin, Yiming Lei, Liting Ma, Yuxi Guo, Yishu Wang, Yilin Wang, Xiaochun Bai, Chuanju Liu, Jian Q. Feng, Chuanyue Wu, Di Chen, Xu Cao and Guozhi Xiao. 2020. Focal adhesion protein Kindlin-2 regulates bone homeostasis in mice. Bone Res. 8:2. doi: 10.1038/s41413-019-0073-8.

24. Wei Wang, Gang Ren, Ni Hong*, and Wenfei Jin*. 2019 Exploring the Changing Landscape of Cell-to-Cell Variation After CTCF Knockdown via Single Cell RNA-seq. BMC Genomics. 20:1015. doi: 10.1186/s12864-019-6379-5.

23. Binbin Lai, Weiwu Gao, Kairong Cui, Wanli Xie, Qingsong Tang, Wenfei Jin, Gangqing Hu, Bing Ni and Keji Zhao. 2018. Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing. Nature, 562:281-285.

22. Gangqing Hu, Kairong Cui, Difeng Fang, Satoshi Hirose, Xun Wang, Darawalee Wangsa, Wenfei Jin, Thomas Ried, Pentao Liu, Jinfang Zhu, Ellen V. Rothenberg, and Keji Zhao. 2018. Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells. Immunity. 48: 227-242.

21. Binbin Lai#, Qingsong Tang#, Wenfei Jin#, Gangqing Hu#, Darawalee Wangsa, Kairong Cui, Benjamin Z. Stanton, Gang Ren, Yi Ding, Ming Zhao, Shuai Liu, Jiuzhou Song, Thomas Ried, and Keji Zhao. 2018. Trac-looping measures genome structure and chromatin accessibility. Nat Methods. 15:741-747. (# equal contribution)

20. Yi Zhang, Wai Lim Ku, Shuai Liu, Kairong Cui, Wenfei Jin, Qingsong Tang, William Lu, and Bing Ni and Keji Zhao. 2017 Genome-wide identification of histone H2A- and histone variant H2A.Z-interacting proteins by bPPI-seq. Cell Res. 27:1258-1274

19. Gang Ren#, Wenfei Jin#, Kairong Cui#, Joseph Rodrigez, Daniel R. Larson and Keji Zhao. 2017. CTCF-mediated enhancer-promoter interaction is a critical regulator of cell-to-cell variation of gene expression. Mol Cell. 67:1049–1058 (# equal contribution)

18. Wenfei Jin, Qingsong Tang, Mimi Wan, Kairong Cui, Yi Zhang, Gang Ren, Bing Ni, Jeffrey Sklar, Teresa M. Przytycka, Richard Childs, David Levens, and Keji Zhao. 2015 Genome-wide Detection of DNase I Hypersensitive Sites in Single Cells and FFPE Samples. Nature. 528:142-146.

17. Wenfei Jin. 2015. Admixture Dynamics, Natural Selection and Diseases in Admixed Populations. ISBN 978-94-017-7406-2. Springer.

16. Hao Hu, Xiang Liu, Wenfei Jin, H.Hilger Ropers, Thomas Wienker. 2015. Evaluating information content of SNPs for sample tagging in re-sequencing projects. Sci Rep. 5:10247

15. Haiyi Lou, Shilin Li, Wenfei Jin, Ruiqing Fu, Dongsheng Lu, Xinwei Pan, Huaigu Zhou, Yuan Ping, Li Jin, Shuhua Xu. 2015. Copy number variations and genetic admixtures in three Xinjiang ethnic minority groups. Euro J Hum Genet. 23:536-42

14. Wan Isa Hatin, Ali Etemad, Wenfei Jin, Pengfei Qin, Shuhua Xu, Li Jin, Soon-Guan Tan, Pornprot Limprasert, Merican Amir Feisal, Mohammed Rizman-Idid, Bin Alwi Zilfalil, HUGO Pan-Asian SNP Consortium. 2014. A genome wide pattern of population structure and admixture in peninsular Malaysia Malays. HUGO J, 8:1-18

13. Shi Yan, Chuan-Chao Wang, Hong-Xiang Zheng, Wei Wang, Zhen-Dong Qin, Lan-Hai Wei, Yi Wang, Xue-Dong Pan, Wen-Qing Fu, Yun-Gang He, Li-Jun Xiong, Wen-Fei Jin, Shi-Lin Li, Yu An, Hui Li, Li Jin. 2014. Y chromosomes of 40% chinese descend from three neolithic super-grandfathers. PloS one, e105691

12. Wenfei Jin, Ran Li, Ying Zhou, Shuhua Xu. 2014. Distribution of ancestral chromosomal segments in admixed genomes and its implications for inferring population history and admixture mapping. Euro J Hum Genet. 22, 930-937.

11. Pengfei Qin, Zhiqiang Li, Wenfei Jin, Dongsheng Lu, Haiyi Lou, Jiawei Shen, Li Jin, Yongyong Shi and Shuhua Xu. 2014. A panel of ancestry informative markers to estimate and correct potential effects of population stratification in Han Chinese. Euro J Hum Genet. 22: 248-53.

10. Daniel Kraushaar#, Wenfei Jin#, Alika Maunakea, Brian Abraham, Misook Ha, Keji Zhao. 2013. Genome-wide H3.3 incorporation dynamics reveal distinct categories of histone variant H3.3 turnover. Genome Biol. 14: R121. (# equal contribution)

9. Erli Wang#, Wenfei Jin#, Wenyuan Duan#, Bin Qiao, Shuna Sun, Guoying Huang, Kaihu Shi, Li Jin, Hongyan Wang. 2013. Association of Two Variants in SMAD7 with the Risk of Congenital Heart Disease in the Han Chinese Population. PLoS ONE. 8: e72423. (# equal contribution)

8. Wenfei Jin, Shuhua Xu, Haifeng Wang, Yongguo Yu, Yiping Shen, Bailin Wu, Li Jin. 2012. Genome-Wide Detection of Natural Selection in African Americans Pre-and Post-Admixture. Genome Res. 22: 519-527.

7. Wenfei Jin, Pengfei Qin, Haiyi Lou, Li Jin, Shuhua Xu. 2012. A Systematic Characterization of Genes Underlying Both Complex and Mendelian Diseases. Hum Mol Genet. 21: 1611-1624.

6. Wenfei Jin, Sijia Wang, Haifeng Wang, Li Jin, Shuhua Xu. 2012. Exploring Population Admixture Dynamics via Empirical and Simulated Genome-Wide Distribution of Ancestral Chromosomal Segments. Am J Hum Genet. 91: 849-862

5. Shuhua Xu, Wenfei Jin. 2012. Population Genetics in the Genomic Era. Studies in Population Genetics, M. Carmen Fusté (Ed.). ISBN 978-953-51-0588-6. Intech. UK

4. Shuhua Xu, Shilin Li, Yajun Yang, Jingze Tan, Haiyi Lou, Wenfei Jin, Ling Yang, Xuedong Pan, Jiucun Wang, Yiping Shen, Bailin Wu, Hongyan Wang, and Li Jin. 2011. A Genome-Wide Search for Signals of High Altitude Adaptation in Tibetans. Mol Biol Evol. 28: 1003-1011.

3. Haiyi Lou, Shilin Li, Yajun Yang, Xin Zhang, Wenfei Jin, Bailin Wu, Li Jin, Shuhua Xu. 2011. A Map of Copy Number Variations in Chinese Populations. PLoS ONE. 6: e27341.

2. Shuhua Xu, Xianyong Yin, Shilin Li, Wenfei Jin, Haiyi Lou, Ling Yang, Xiaohong Gong, Hongyan Wang, Yiping shen, Xuedong Pan, Yungang He, Yajun Yang, Yi Wang, Wenqing Fu, Yu An, Jiucun Wang, Jingze Tan, Ji Qian, Xiaoli Chen, Xin Zhang, Yangfei Sun, Xuejun Zhang, Bailin Wu, Li Jin. 2009. Genomic Dissection of Population Substructure of Han Chinese and Its Implication in Association Studies. Am J Hum Genet. 85:762-774.

1. Shuhua Xu, Wenfei Jin, Li Jin. 2009. Haplotype Sharing Analysis Showing Uyghurs Are Unlikely Genetic Donors. Mol Biol Evol. 26: 2197-2206.

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