Jianfeng Li

Jianfeng is an Research Associate of Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, and Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine. He is the junior editorial board member of iMeta journal and founder of Openbiox open source community for bioinformatics. As co-author, he published several works in Cancer Cell, Blood, PNAS, Advanced Science, Brifling in bioinformatics, Frontiers of Medicine, EBioMedicine, and Bioinformatics. The representative studies identified a series of new molecular subtypes in acute leukemia, i.e., NUTM1 fusion, PAX5 P80R, IKZF1 N159Y, etc., which have been applied in the adult leukemia registry system of China and real clinical diagnosis/treatment. In addition, as the core developer of the online visualization tool (Hiplot), he has contributed nearly 100 one-click data visualization tools to the scientific community. He has received millions of visits and tens of thousands of registrations. His personal blog has been read more than a million times on Zhihu, WeChat public websites, and other platforms.

Contact Information

Email: lee_jianfeng@sjtu.edu.cn

Research Interests

Biomedical data mining, identification of disease subtypes, pathogenesis of acute leukemia, clinical molecular diagnosis, development of visualization methods

Education Background

  • 2018.09 ~ 2022.07 Shanghai Jiaotong University School, Phd.
  • 2015.09 ~ 2018.07 Shanghai Jiaotong University School of Medicine, M.S.
  • 2011.09 ~ 2015.07 Harbin Institute of Technology, B.E.

Employment

  • 2022.07 ~ National Research Center for Translational Medicine (Shanghai), Associate Researcher

Computer Skill

Good at genomics-related data analysis (DNA-seq and RNA-seq-based)

  • Programming language: R, HTML, CSS, JavaScript, PHP, Database language SQL, Scripting tools Awk and Bash scripts, Python
  • Application: Adobe Photoshop / Illustrator / Premiere / After Effects / Dreamweaver; Office [Undergraduate Faculty of Propaganda Department, Graduate First Year Postgraduate Association Propaganda Department]; new media;
  • Operating system: Daily use of Windows, Centos, Ubuntu

Open source package

Publication

In English

Journal

First/Co-first/Corresponding Author

  • #Li J, #Miao B, #Wang S, #Dong W, #Xu H, #Si C, Wang W, Duan S, Lou J, Bao Z, Zeng H, Yang Z, Cheng W, Zhao F, Zeng J, Liu X-S, Wu R, Shen Y, Chen Z, Chen S, Wang M and Consortium H. Hiplot: a comprehensive and easy-to-use web service for boosting the publication-ready biomedical data visualisation. Brifling in bioinformatics. 2022 (In press)
  • #Jianfeng Li, Yuting Dai, Liang Wu, Ming Zhang, Wen Ouyang, Jinyan Huang, Saijuan Chen. Emerging Molecular Subtypes and Therapeutic Targets in Bcell Precursor Acute Lymphoblastic Leukemia. Frontiers of Medicine. 2021 Jan 5. doi: 10.1007/s11684-020-0821-6. Epub ahead of print. PMID: 33400146
  • #Mingjie Wang, #Jianfeng Li, Xiaonan Zhang, Yue Han, Demin Yu, Donghua Zhang, Zhenghong Yuan, Zhitao Yang, Jinyan Huang, Xin-Xin Zhang. An integrated software for virus community sequencing data analysis. BMC Genomics. 2020 May 15;21(1):363. doi: 10.1186/s12864-020-6744-4. PubMed PMID: 32414327
  • #Jian-Feng Li, #Yu-Ting Dai, #Henrik Lilljebjörn, Shu-Hong Shen, Bo-Wen Cui, Ling Bai, Yuan-Fang Liu, Mao-Xiang Qian, Yasuo Kubota, Hitoshi Kiyoi, Itaru Matsumura, Yasushi Miyazaki, Linda Olsson, Ah Moy Tan, Hany Ariffin, Jing Chen, Junko Takita, Takahiko Yasuda, Hiroyuki Mano, Bertil Johansson, Jun J. Yang, Allen Eng-Juh Yeoh, Fumihiko Hayakawa, Zhu Chen, Ching-Hon Pui, Thoas Fioretos, Sai-Juan Chen, Jin-Yan Huang. Transcriptional landscape of B cell precursor acute lymphoblastic leukemia based on an international study of 1,223 cases. Proc Natl Acad Sci U S A. 2018 Dec 11;115(50):E11711-E11720. doi:10.1073/pnas.1814397115. PubMed PMID: 30487223
  • #Bing Chen, #Lu Jiang, #Meng-Ling Zhong, #Jian-Feng Li, #Ben-Shang Li, Li-Jun Peng, Yu-Ting Dai, Bo-Wen Cui, Tian-Qi Yan, Wei-Na Zhang, Xiang-Qin Weng, Yin-Yin Xie, Jing Lu, Rui-Bao Ren, Su-Ning Chen, Jian-Da Hu, De-Pei Wu, Zhu Chen, Jing-Yan Tang, Jin-Yan Huang, Jian-Qing Mi, and Sai-Juan Chen. Identification of fusion genes and characterization of transcriptome features in T-cell acute lymphoblastic leukemia. Proc Natl Acad Sci U S A.. 2018 Jan 9;115(2):373-378. doi:10.1073/pnas.1717125115. PubMed PMID: 29279377
  • #Jianfeng Li, #Bowen Cui, Yuting Dai, Ling Bai, Jinyan Huang. BioInstaller: a comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform. Peerj. 2018 Oct;6:e5853. doi: 10.7717/peerj.5853. PubMed PMID: 30402350

Co-author

  • Zhang M, Zhang H, Li Z, Bai L, Wang Q, Li J, Jiang M, Xue Q, Cheng N, Zhang W, Mao D, Chen Z, Huang J, Meng G, Chen Z, Chen SJ. Functional, structural and molecular characterizations of leukemogenic driver MEF2D-HNRNPUL1 fusion. Blood. 2022 May 11:blood.2022016241. doi: 10.1182/blood.2022016241. Epub ahead of print. PMID: 35544603
  • Dai YT, Zhang F, Fang H, Li JF, Lu G, Jiang L, Chen B, Mao DD, Liu YF, Wang J, Peng LJ, Feng C, Chen HF, Mu JX, Zhang QL, Wang H, Ariffin H, Moy TA, Wang JH, Lou YJ, Chen SN, Wang Q, Liu H, Shan Z, Matsumura I, Miyazaki Y, Yasuda T, Dou LP, Yan XJ, Yan JS, Yeoh AE, Wu DP, Kiyoi H, Hayakawa F, Jin J, Wang SY, Sun XJ, Mi JQ, Chen Z, Huang JY, Chen SJ. Transcriptome-wide subtyping of pediatric and adult T cell acute lymphoblastic leukemia in an international study of 707 cases. Proc Natl Acad Sci U S A. 2022 Apr 12;119(15):e2120787119. doi: 10.1073/pnas.2120787119. Epub 2022 Apr 6. PMID: 35385357
  • Wang S, Xiong Y, Zhao L, Gu K, Li Y, Zhao F, Li J, Wang M, Wang H, Tao Z, Wu T, Zheng Y, Li X, Liu XS. UCSCXenaShiny: An R/CRAN Package for Interactive Analysis of UCSC Xena Data. Bioinformatics. 2021 Jul 29;38(2):527–9. doi: 10.1093/bioinformatics/btab561. Epub ahead of print. PMID: 34323947; PMCID: PMC8723150
  • Tang H, Cheng Y, Huang J, Li J, Zhang B, Wu ZB. Case Report: Temozolomide Treatment of Refractory Prolactinoma Resistant to Dopamine Agonists. Front Endocrinol (Lausanne). 2021 Mar 12;12:616339. doi: 10.3389/fendo.2021.616339. PMID: 33776913; PMCID: PMC7996095
  • Yuting Dai, Aining Xu, Jianfeng Li, Liang Wu, Shanhe Yu, Jun Chen, Weili Zhao, Xiao-Jian Sun & Jinyan Huang. CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data. BMC Bioinformatics. 2021; 22(1): 138. doi: 10.1186/s12859-021-04054-2. PMID: 33752602 Wu L, Jiang M, Yu P, Li J, Ouyang W, Feng C, Zhao WL, Dai Y, Huang J. Single-Cell Transcriptome Analysis Identifies Ligand-Receptor Pairs Associated With BCP-ALL Prognosis. Front Oncol. 2021 Mar 10;11:639013. doi: 10.3389/fonc.2021.639013. PMID: 33777800; PMCID: PMC7987943
  • Dawei Wang, Guowei Zhang, Junjie Gu, Xiaohu Shao, Yuting Dai, Jianfeng Li, Xiaohong Pan, Shuxian Yao, Aining Xu, Ying Jin, Jinyan Huang, Qizhen Shi, Jiang Zhu, Xiaodong Xi, Zhu Chen, and Saijuan Chen. In vivo generated hematopoietic stem cells from genome edited induced pluripotent stem cells are functional in platelet-targeted gene therapy of murine hemophilia A. Haematologica. 2020 Apr;105(4):e175-e179. doi: 10.3324/haematol.2019.219089. PubMed PMID: 31296582
  • Xiong Jie, Cui Bo-Wen, Wang Nan, Dai Yu-Ting, Zhang Hao, Wang Chao-Fu, Zhong Hui-Juan, Cheng Shu, Ou-Yang Bin-Shen, Hu Yu, Zhang Xi, Xu Bin, Qian Wen-Bin, Tao Rong, Yan Feng, Hu Jian-Da, Hou Ming, Ma Xue-Jun, Wang Xin, Liu Yuan-Hua, Zhu Zun-Min, Huang Xiao-Bin, Liu Li, Wu Chong-Yang, Huang Li, Shen Yun-Feng, Huang Rui-Bin, Xu Jing-Yan, Wang Chun, Wu De-Pei, Yu Li, Li Jian-Feng, Xu Peng-Peng, Wang Li, Huang Jin-Yan, Chen Sai-Juan, Zhao Wei-Li. Genomic and Transcriptomic Characterization of Natural Killer T Cell Lymphoma. Cancer Cell . 2019 Mar 16;37(3):403-419.e6. doi: 10.1016/j.ccell.2020.02.005. PubMed PMID: 32183952
  • Yi Zhou, Xingli Zhu, Yuting Dai, Shumin Xiong, Chuijin Wei, Pei Yu, Yuewen Tang, Liang Wu, Jianfeng Li, Dan Liu, Yanlin Wang, Zhu Chen, Sai-Juan Chen,Jinyan Huang, and Lin Cheng. Chemical Cocktail Induces Hematopoietic Reprogramming and Expands Hematopoietic Stem/Progenitor Cells. Advanced Science. 2019 Nov 11;7(1):1901785. doi: 10.1002/advs.201901785. PubMed PMID: 31921559
  • #Liu YF, #Wang BY, #Zhang WN, #Huang JY, #Li BS, Zhang M, Jiang L, Li JF, Wang MJ, Dai YJ, Zhang ZG, Wang Q, Kong J, Chen B, Zhu YM, Weng XQ, Shen ZX, Li JM, Wang J, Yan XJ, Li Y, Liang YM, Liu L, Chen XQ, Zhang WG, Yan JS, Hu JD, Shen SH, Chen J, Gu LJ, Pei D, Li Y, Wu G, Zhou X, Ren RB, Cheng C, Yang JJ, Wang KK, Wang SY, Zhang J, Mi JQ, Pui CH, Tang JY, Chen Z, Chen SJ. Genomic Profiling of Adult and Pediatric B-cell Acute Lymphoblastic Leukemia. EBioMedicine. 2016 Jun;8:173-83. doi: 10.1016/j.ebiom.2016.04.038. PubMed PMID: 27428428

Colloquium papers

  • #Bing Chen, #Lu Jiang, #Meng-Ling Zhong, #Jian-Feng Li, #Ben-Shang Li, Li-Jun Peng, Yu-Ting Dai, Bo-Wen Cui, Tian-Qi Yan, Wei-Na Zhang, Xiang-Qin Weng, Yin-Yin Xie, Jing Lu, Rui-Bao Ren, Su-Ning Chen, Jian-Da Hu, De-Pei Wu, Zhu Chen, Jing-Yan Tang, Jin-Yan Huang, Jian-Qing Mi, and Sai-Juan Chen. Identification of fusion genes and characterization of transcriptome features in T-cell acute lymphoblastic leukemia. (The American Society of Hematology(ASH) Meeting, 2017, poster]
  • #Jian-Feng Li, #Yu-Ting Dai, #Henrik Lilljebjörn, Shu-Hong Shen, Bo-Wen Cui, Ling Bai, Yuan-Fang Liu, Mao-Xiang Qian, Yasuo Kubota, Hitoshi Kiyoi, Itaru Matsumura, Yasushi Miyazaki, Linda Olsson, Ah Moy Tan, Hany Ariffin, Jing Chen, Junko Takita, Takahiko Yasuda, Hiroyuki Mano, Bertil Johansson, Jun J. Yang, Allen Eng-Juh Yeoh, Fumihiko Hayakawa, Zhu Chen, Ching-Hon Pui, Thoas Fioretos, Sai-Juan Chen, Jin-Yan Huang. Transcriptional landscape of B cell precursor acute lymphoblastic leukemia based on an international study of 1,223 cases. [The American Society of Hematology(ASH) Meeting, 2018, poster]