Dr Jing Li's Group


  Department of Bioinformatics and Biostatistics

  Shanghai Jiao Tong University





Recently published: "Integrative Proteomic Characterization of Human Lung Adenocarcinoma". Cell (2020, July).      READ MORE >


Recently published: "Alternative splicing signatures in preimplantation embryo development". Cell& Bioscience (2020, March).      READ MORE >


Recently published: "Molecular characteristics of early-stage female germ cells revealed by RNA sequencing of low-input cells and analysis of genome-wide DNA methylation". DNA Research (2019, April).      READ MORE >


Recently published: "Proteome-wide analysis of USP14 substrates revealed its role in hepatosteatosis via stabilization of FASN". Nature Communications (2018, Nov).      READ MORE >


Recently published: "Quality control of single amino acid variations detected by tandem mass spectrometry". Journal of Proteomics (2018, Sep).      READ MORE >


Recently published: "NIPS, a 3D network-integrated predictor of deleterious protein SAPs, and its application in cancer prognosis". Scientific Reports (2018, May).      READ MORE >


Recently published: "Metagenomic Taxonomy-Guided Database-Searching Strategy for Improving Metaproteomic Analysis". Journal of Proteome Research. (2018, April).      READ MORE >









We develop and apply computational methods of mass spectrometry (MS)-based proteomics for formulating the processes of complex phenotype/diseases by integrating genome/transcriptome data and biological network. Our ambitious is to prioritize key proteins or protein variations/modifications in disease, as well as identify clinical biomarker, predict functional sub-network/pathways, interpret mechanisms underneath specific molecular processes or states by means of developing statistic models and bioinformatic approaches.

  1. Integrative Proteomic Characterization of Human Lung Adenocarcinoma. Cell, 2020.
  2. Quality control of single amino acid variations detected by tandem mass spectrometry. Journal of Proteomics, 2018.
  3. NIPS, a 3D network-integrated predictor of deleterious protein SAPs, and its application in cancer prognosis. Scientific Reports ,2018.
  4. Network Module-Based Model in the Differential Expression Analysis for RNA-seq. Bioinformatics ,2017.
  5. CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation. Journal of Proteome Research , 2017.
  6. Biological Network Module-Based Model for the Analysis of Differential Expression in Shotgun Proteomics. Journal of Proteome Research , 2014.
  7. Evaluation and integration of existing methods for computational prediction of allergens. BMC Bioinformatics, 2013.
  8. A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics. Molecular Cellular Proteomics, 2011.
  9. CanProVar: A Human Cancer Proteome Variation Database. Human mutation, 2010.
  10. Network-assisted Protein Identification and Data Interpretation in Shotgun Proteomics. Molecular Systems Biology, 2009.
  11. Multi-Site Assessment of The Precision and Reproducibility of MRM–based Measurements of Proteins in Plasma. Nature Biotechnology, 2009.
  12. Regulatory Module Network of bHLH Transcription Factors in Mouse Brain. Genome Biology, 2007.


Contact

Jing Li

Dr. Jing Li, PI

Phone: 86 21 34204071
Email: jing.li@sjtu.edu.cn


NEWS:

--- 2021 --------   


[Feb]   Yafei Chang's meta-proteomics paper was accepted by Briefings in Bioinformatics. Congs~.

[Jan]  Prof. Jing Li was selected as a “Rising Stars in Proteomics and Metabolomics” by Journal of Proteome Research.

--- 2020 --------   

[Dec]   Xi Cheng's drug repurposing paper was accepted by Cancer Biology& Medicine , which's a collabrating work with Prof.Minjia Tan, Shanghai Institute of Materia Medica. Chinese Academy of Sciences.

[Sept]   Christopher Reyes (Chris) began his new journey as a PhD student in our group. Congs!

[Sept]   Miss.Qun Dong joined the group as a PhD student. Qun received her master degree in Bioinformatics from Harbin Medical University. Welcome, Qun!

[Sept]   Mr.Syrous Irani (Cheng-de Liu) joined the group as a master student. Cheng-de received his B.S. degree in Pharmacy from Shanghai Jiao Tong University. Welcome, Cheng-de!

[Sept]   Mr.Xinyi Mou joined the group as a master student. Xinyi received his B.S. degree in Bioinformatics from University of Electronic Science and Technology of China. Welcome, Xinyi!

[Sept]   Miss.Siqi Luo joined the group as a master student. She received his B.S. degree in Life Science from Xiamen University. Welcome, Siqi!

[July]   Our LUAD proteome paper was published at Cell, which's a collabrating work with multiple groups in CNHPP.

[March]   Geng Tian (Garen)'s paper was published at Cell & Bioscience, which's a collabrating work with Prof.Ji Wu.

--- 2019 --------   


[Sept]   Miss.Liyuan Zhao joined the group as a master student. Liyuan received her B.S. degree in Bioinformatics from Tongji University. Welcome, Liyuan!

[Sept]   Mr.Guanghua Qiao joined the group as a master student. Quanghua received his B.S. degree in Statistics from Shanghai University of International Business and Economics. Welcome, Guanghua!

[Sept]   Mr.Yiming Ma joined the group as a PhD student. Yiming received his B.S. degree in Bioinformatics from Shanghai Jiao Tong University. Welcome, Yiming!

[July]   Miss. Yimin Zhang joined the group as a Research Intern. Yimin received her B.S. degree in Biological Science from Fudan University. Welcome, Yimin!

[July]   Yafei Chang's paper was accepted by Genomics, Proteomics & Bioinformatics, which's a collabrating work with Prof.Zhiheng Xu, Institute of Genetics and Developmental Biology Chinese Academy of Sciences.

[April]   Jing Li (Junior)'s paper was published at DNA Research, which's a collabrating work with Dr.Binbin Ma and Prof.Ji Wu.

[Jan]   Jing Li was awarded Chenxing Distinguished Young Scholarship of Shanghai Jiao Tong University ( Class A).

[Jan]   Jie Ren's paper was published at BioMed Research International.






Biology Complex,
800 Dongchuan Road, Minhang
Shanghai, China, 200240



©2012-2018 Jing Li