Jianfeng Li

Contact Information

Email: lee_jianfeng@sjtu.edu.cn; Homepage: http://www.life2cloud.com

Research Interests

Genomics, Bioinformatics, Data visualization, Data mining

Education Background

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

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

Software package

R package

As lead author:

  • configr: Implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file.
  • BioInstaller: A comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform. It also can be used to install and download massive bioinformatics analysis softwares and databases, such as NGS reads mapping tools with its required databases.
  • ngstk: Can be used to facilitate the analysis of NGS data, such as visualization, conversion of data format for WEB service input and other purpose.
  • annovarR:Provides R functions as well as database resources which offer an integrated framework to annotate genetic variants from genome and transcriptome data.

Python package

  • iseq:A integrated analysis toolkits and pipeline for NGS panel sequencing data

Node package

Web service

  • JhuangLab: Laboratory website building by PHP and Bootstrap.
  • life2cloud: Personal blog based on blogdown.
  • qap: Project homepage of a virus quasispecies analysis tool based on Django and Bootstrap.
  • wQAP: A virus quasispecies analysis tool based on Galaxy (Only established and maintain related analysis and WEB platform.


In English


  • #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. Epub 2016 May 13. PubMed PMID: 27428428; PubMed Central PMCID: PMC4919728.
  • #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. Proceedings of the National Academy of Sciences. 2017. 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. PMID: 30402350 PMCID: PMC6215441
  • #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. Proceedings of the National Academy of Sciences. 2018. doi:10.1073/pnas.1814397115
  • QAP: an integrated software for virus community sequencing data analysis. (Co-first 3rd, Submitted, 2018)
  • annovarR: a variant annotation and visualization system based on R and Shiny framework (Co-first 1st, Preparing, 2018)
  • A set of command line tools/workflows and R shiny plugins for exploring next-generation sequencing data. (Preparing, 2019)

In Chinese


  • LI Jian-feng, YAN Tian-qi, CUI Bo-wen, KONG Jie, WANG Shu, CHEN Bing, HUANG Jin-yan. Analysis method based on the gene-panel sequencing data. Journal of Shanghai Jiaotong University(Medical Science). 2017, 37(11): 1575-
  • YAN Tian-qi, CHEN Li-wei, ZHU Yong-mei, LI Jian-feng, DAI Yu-ting, CUI Shu-Ya, JIANG Lu, CHEN Bing, HUANG Jin-yan. Construction of a knowledge database of gene fusion and mutation in acute lymphoblastic leukemia. , 2018, 38(9): 1027-.

Colloquium papers

  • ZHANG Wei-na,LI Jian-feng,et al, Analysis of epigenetic regulatory gene mutations in adult and childhood acute B lymphoblastic leukemia,The 16th National Conference on Experimental Hematology, 2017, Conference Report
  • LI Jian-feng,HUANG Jin-yan, A method of gene mutation detection based on whole transcriptome resequencing of acute lymphoblastic leukemia, The 16th National Conference on Experimental Hematology, 2017, Poster Session
  • LI Jian-feng,HUANG Jin-yan, annovarR:an R package to annotate genetic variants from genomic and transcriptome data, The 16th National Conference on Experimental Hematology, 2017, Poster Session