Dr Jing Li's Group


  Department of Bioinformatics and Biostatistics

  Shanghai Jiao Tong University





Recently published: "Causal Inference and Annotation of Phosphoproteomics Data in Multi-omics Cancer Studies". Molecular & Cellular Proteomics (2025).      READ MORE >


Recently published: "Tumor-associated antigen prediction using a single-sample gene expression state inference algorithm". Cell Reports Methods (2024).      READ MORE >


Recently published: "PhosCancer: A comprehensive database for investigating protein phosphorylation in human cancer". iScience (2024).      READ MORE >


Recently published: "Integrative proteogenomic profiling of high-risk prostate cancer samples from Chinese patients indicates metabolic vulnerabilities and diagnostic biomarkers". Nature Cancer (2024).      READ MORE >


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


Recently 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 >


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


Recently 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 >


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


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


Recently 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 >


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


Recently 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 >


Recently published: "A community-supported metaproteomic pipeline for improving peptide identifications in hydrothermal vent microbiota".Briefings in Bioinformatics (2021, Sept).      READ MORE >


Recently published: "DeepNetBim: deep learning model for predicting HLA-epitope interactions based on network analysis by harnessing binding and immunogenicity information". BMC Bioinformatics (2021, May).      READ MORE >


Recently published: "Drug repurposing for cancer treatment through global propagation with a greedy algorithm in a multilayer network". Cancer Biology & Medicine (2021, Apr).      READ MORE >


Recently published: "SPA: A Quantitation Strategy for MS Data in Patient-derived Xenograft Models". Genomics, Proteomics & Bioinformatics (2021, Feb).      READ MORE >


Recently published: "Different Gene Networks Are Disturbed by Zika Virus Infection in A Mouse Microcephaly Model". Genomics, Proteomics & Bioinformatics (2021, Jan).      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. Causal Inference and Annotation of Phosphoproteomics Data in Multi-omics Cancer Studies. Molecular & Cellular Proteomics, 2025.
  2. Tumor-associated antigen prediction using a single-sample gene expression state inference algorithm. Cell Reports Methods, 2024.
  3. PhosCancer: A comprehensive database for investigating protein phosphorylation in human cancer. iScience, 2024.
  4. Integrative proteogenomic profiling of high-risk prostate cancer samples from Chinese patients indicates metabolic vulnerabilities and diagnostic biomarkers. Nature Cancer, 2024.
  5. Drug repurposing for cancer treatment through global propagation with a greedy algorithm in a multilayer network. Cancer Biology & Medicine, 2022.
  6. 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.
  7. A community-supported metaproteomic pipeline for improving peptide identifications in hydrothermal vent microbiota. Briefings in Bioinformatics, 2021.
  8. SPA: A Quantitation Strategy for MS Data in Patient-derived Xenograft Models . Genomics Proteomics Bioinformatics, 2021.
  9. Different Gene Networks Are Disturbed by Zika Virus Infection in A Mouse Microcephaly Model . Genomics Proteomics Bioinformatics, 2021.
  10. Integrative Proteomic Characterization of Human Lung Adenocarcinoma. Cell, 2020.
  11. Network Module-Based Model in the Differential Expression Analysis for RNA-seq. Bioinformatics , 2017.
  12. CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation. Journal of Proteome Research , 2017.
  13. A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics. Molecular Cellular Proteomics, 2011.
  14. Network-assisted Protein Identification and Data Interpretation in Shotgun Proteomics. Molecular Systems Biology, 2009.
  15. 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:

--- 2025 --------   

[Mar]   Xinyi Mou's paper was accepted by Briefings in Bioinformatics. Congs~.

[Feb]   Qun Dong was awarded SJTU excellent graduate in 2025(上海交通大学优秀毕业生).

[Jan]   Qun Dong's Phoslink model paper was accepted by Molecular & Cellular Proteomics. Congs~.

--- 2024 --------   

[Nov]   Jingsi Xu won the National Scholarship for graduate student in 2024 (国家奖学金).

[Oct]   Qun Dong won the Best Oral Presentation Award (最佳口头报告奖) at the 2024 Annual Conference of the Shanghai Society for Bioinformatics.

[Oct]   Qun Dong was awarded PhD Excellence Scholarship in 2024 (卓越博士奖学金).

[Sept]   Xinpei Yi's single-sample antigen sequencing paper was accepted by Cell Reports Methods. Congs~.

[Sept]   Qun Dong's PhosCancer database paper was accepted by iScience. Congs~.

[Sept]   Miss.Xi Shan joined the group as a master student. Xi received her B.S. degree in Biochemistry from Nanjing University. Welcome, Xi!

[May]   Xingyu Chen won Award of Excellent Graduate of Shanghai in 2024 (上海市优秀毕业生).

--- 2023 --------   

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

[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.







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



©2012-2025 Jing Li