Dr Jing Li's Group
Department of Bioinformatics and Biostatistics
Shanghai Jiao Tong University
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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.
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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 |
