Dr Jing Li's Group


  Department of Bioinformatics and Biostatistics

  Shanghai Jiao Tong University





Rcently published: "PTMint Database of Experimentally Verified PTM Regulation on Protein-Protein Interaction".Bioinformatics (2023).      READ MORE >

Rcently published: "Three-dimensional genome structure shapes the recombination landscape of chromatin features during female germline stem cell development".Clinical and Translational Medicine (2022).      READ MORE >

Rcently published: "Comparison analysis of multiple-omics data between female germline stem cells and spermatogonial stem cells".Gene & Disease (2022).      READ MORE >

Rcently published: "Drug repurposing for cancer treatment through global propagation with a greedy algorithm in a multilayer network".Cancer Biology & Medicine (2022).      READ MORE >

Rcently published: "Integrative analysis of the 3D genome structure reveals that CTCF maintains the properties of mouse female germline stem cells".Cellular and Molecular life sciences (2022).      READ MORE >

Rcently published: "Pangenomic analysis of Chinese gastric cancer".Nature Communications (2022).      READ MORE >

Rcently published: "mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis".Genome Biology (2022).      READ MORE >

Rcently published: "Microbial community structure and metabolic potential at the initial stage 1 of soil development of the glacial forefields in Svalbard".Microbial Ecology (2022).      READ MORE >

Rcently published: "UBR5 promotes tumor immune evasion through enhancing IFN-γ-induced PDL1 transcription in triple negative breast cancer".Theranostics (2022).      READ MORE >

Rcently published: "Treatment outcomes of HIV patients with hepatitis B and C virus co‑infections in Southwest China: an observational cohort study".Infectious Diseases Poverty (2022).      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 with differential expression, variations or 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. Drug repurposing for cancer treatment through global propagation with a greedy algorithm in a multilayer network. Cancer Biology & Medicine, 2022.
  2. Integrative analysis of the 3D genome structure reveals that CTCF maintains the properties of mouse female germline stem cells. Cellular and Molecular life sciences, 2022.
  3. A community-supported metaproteomic pipeline for improving peptide identifications in hydrothermal vent microbiota. Briefings in Bioinformatics, 2021.
  4. SPA: A Quantitation Strategy for MS Data in Patient-derived Xenograft Models . Genomics Proteomics Bioinformatics, 2021.
  5. Integrative Proteomic Characterization of Human Lung Adenocarcinoma. Cell, 2020.
  6. Network Module-Based Model in the Differential Expression Analysis for RNA-seq. Bioinformatics , 2017.
  7. CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation. Journal of Proteome Research , 2017.
  8. A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics. Molecular Cellular Proteomics, 2011.
  9. Network-assisted Protein Identification and Data Interpretation in Shotgun Proteomics. Molecular Systems Biology, 2009.
  10. Regulatory Module Network of bHLH Transcription Factors in Mouse Brain. Genome Biology, 2007.
Contact

Jing Li

Dr. Jing Li, PI (李婧)

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

NEWS:

--- 2023 --------   


[May]   Jingya Jia won Award of Excellent Graduate of Shanghai in 2023 (上海市优秀毕业生).

--- 2022 --------   


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

[Sept]   Miss.Danqing Shen joined the group as a PhD student. Danqing received her B.S. degree from Shanghai Jiao Tong University School of Medicine. Welcome, Danqing!

[Sept]   Miss.Zhuoxuan Song joined the group as a master student. Zhuoxuan received her B.S. degree in Bioengineering from Tianjin University. Welcome, Zhuoxuan!

--- 2021 --------   


[Sept]   Miss.Weiyi Li joined the group as a PhD student. Weiyi received her B.S. degree in Bioinformatics from Shanghai Jiao Tong University. Welcome, Weiyi!

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

[May]   Yafei Chang was awarded SJTU excellent graduate in 2021 （上海交通大学优秀毕业生）.

[May]   Xiaoyun Yang won Award of Excellent Graduate of Shanghai in 2021 (上海市优秀毕业生).

[May]    Xiaoyun Yang's DEepNetBim paper was published at BMC Bioinformatics.Congs~.

[April]   Xi Cheng's paper was published at Cancer Biology & Medicine, which's a collabrating work with Prof.Minjia Tan, Shanghai Institute of Materia Medica Chinese Academy of Sciences.

[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 --------   

[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.

[April]   Xi Cheng was awarded SJTU excellent graduate in 2020 （上海交通大学优秀毕业生）.

[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


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