Dr Jing Li's Group

  Department of Bioinformatics and Biostatistics

  Shanghai Jiao Tong University

PTMint Database of Experimentally Verified PTM Regulation on Protein-Protein Interaction.
X Hong, N Li, J Lv, Y Zhang, J Li*, J Zhang*, HF Chen*.
Bioinformatics 2023.  PMID: 36548389

Three-dimensional genome structure shapes the recombination landscape of chromatin features during female germline stem cell development.
GG Tian, C Hou, … , J Li*, J Wu*.
Clinical and Translational Medicine 2022.  PMID: 35730671

Comparison analysis of multiple-omics data between female germline stem cells and spermatogonial stem cells.
GG Tian , J Li*, J Wu*.
Gene & Disease 2022.  PMID: NA

Drug repurposing for cancer treatment through global propagation with a greedy algorithm in a multilayer network.
X Cheng†, W Zhao†, … , M Tan*, J Li*.
Cancer Biology & Medicine 2022.  PMID: 33893730

Integrative analysis of the 3D genome structure reveals that CTCF maintains the properties of mouse female germline stem cells.
GG Tian†, X Zhao†, C Hou†, … , J Li*, J Wu*.
Cellular and Molecular life sciences 2022.  PMID: 34981210

Pangenomic analysis of Chinese gastric cancer.
Y Yu†, Z Zhang†, X Dong†, R Yang†, Z Duan†, ... , J Li, … , C Wei, H Chen, Z Zhu.
Nature Communications 2022.  PMID: 36109518

mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis.
Y Zeng, J Li, C Wei, H Zhao, W Tao.
Genome Biology 2022.  PMID: 35422001

Microbial community structure and metabolic potential at the initial stage 1 of soil development of the glacial forefields in Svalbard.
Tian C, … , J Li, Y Zhang.
Microbial Ecology 2022.  PMID: 36239777

UBR5 promotes tumor immune evasion through enhancing IFN-γ-induced PDL1 transcription in triple negative breast cancer.
B Wu, M Song, Q Dong, G Xiang, J Li, X Ma, F Wei.
Theranostics 2022.  PMID: 35836797

Treatment outcomes of HIV patients with hepatitis B and C virus co‑infections in Southwest China: an observational cohort study.
J Jia, … , J Li, … , J Zhu, HZ Qian.
Infectious Diseases Poverty 2022.  PMID: 34986877

A proteomic and phosphoproteomic landscape of KRAS mutant cancers identifies combination therapies.
Z Liu, … , J Li, … , F He, M Huang, M Tan.
Molecular Cell 2021.  PMID: 34375582

DRAK2 aggravates nonalcoholic fatty liver disease progression through SRSF6-associated RNA alternative splicing.
Y Li, … , J Li, X Gao, M Xia, M Tan, J Li.
Cell Metabolism 2021.  PMID: 34614409

A community-supported metaproteomic pipeline for improving peptide identifications in hydrothermal vent microbiota.
Y Chang, Q Fan, J Hou, Y Zhang*, J Li*.
Briefings in Bioinformatics 2021.  PMID: 33834201

DeepNetBim: deep learning model for predicting HLA‑epitope interactions based on network analysis by harnessing binding and immunogenicity information.
X Yang, L Zhao, F Wei, J Li*.
BMC Bioinformatics 2021.  PMID: 33952199

SPA: A Quantitation Strategy for MS Data in Patient-derived Xenograft Models .
X Cheng†, L Qian†, B Wang, J Li*, M Tan*.
Genomics Proteomics Bioinformatics 2021.  PMID: 33631430

Integrative Proteomic Characterization of Human Lung Adenocarcinoma.
J Xu†,C Zhang†, X Wang†, L Zhai†, Y Ma†,Y Mao, ...,X Qian, Y Wang*, J Li*, F He*, M Tan*
Cell 182(1):245-261, 2020.  PMID: 32649877

Endothelial microparticles induced by cyclic stretch activate Src and modulate cell apoptosis.
F Zhuang,H Bao,Q Shi, J Li, ..., Z Jiang, Y Qi
The FASEB Journal , 2020.  PMID: 32856783

Alternative splicing signatures in preimplantation embryo development.
G. Tian, J.Li*, J.Wu*
Cell& Bioscience 10,33, ID 3907195, 2020.  PMID: 32175076

Ranking Cancer Proteins by Integrating PPI Network and Protein Expression Profiles.
J.Ren, L.Shang, Q.Wang, J.Li*
BioMed Research International Vol 2019, ID 3907195, 2019.  PMID: 6339728

Leukocyte Proteomic Profiling in First-Episode Schizophrenia Patients: Does Oxidative Stress Play Central Roles in the Pathophysiology Network of Schizophrenia?
J Jiang,C Peng, L Sun, J Li,..., Q.Wang, W Wan
Antioxid & Redox Signaling3:8, 2019.  PMID: 31126188

Molecular characteristics of early-stage female germ cells revealed by RNA sequencing of low-input cells and analysis of genome-wide DNA methylation.
B. Ma†, T.Lee†, B. Hu†, J. Li†,...,X.Chen*,J.Li*,J Wu*
DNA Research 26(2),105-117, 2019.  PMID: 30590473

Proteome-wide analysis of USP14 substrates revealed its role in hepatosteatosis via stabilization of FASN.
B.Liu, S.Jiang, M.Li, X.Xiong, M.Zhu, D.Li, L.Zhao, L.Qian, L.Zhai, J.Li, H.Lu, S.Shan, J.Lin, Y.Lu, X.Li, M.Tan.
Nature Communications 9(1),4770, 2018.  PMID: 30425250

Integrating proteomic and phosphoproteomic data for pathway analysis in breast cancer.
J Ren, B.Wang, J.Li*
BMC Systems Biology 12(Suppl 8):130, 2018.  PMID: 30577793

Quality control of single amino acid variations detected by tandem mass spectrometry.
X.Yi,B.Wang, Z.An, F.Gong, J.Li*, Y. Fu*.
Journal of Proteomics 187,144-151, 2018.  PMID: 30012419

Genomic variation in 3,010 diverse accessions of Asian cultivated rice.
W.Wang, R. Mauleon,Z.Hu,D.Chebotarov, S.Tai,Z.Wu, M.Li,T.Zheng,R.R.Fuentes,F.Zhang, L.Mansueto, D.Copetti, ..., J.Li, et al.
Nature 557(7703),43-49, 2018.  PMID: 29695866

NIPS, a 3D network-integrated predictor of deleterious protein SAPs, and its application in cancer prognosis.
B.Wang, J.Li, X.Cheng, Q.Zhou, J.Yang, M.Zhang, H.Chen, J.Li*.
Scientific Reports 8:6021, 2018.  PMID: 29662108

Metagenomic Taxonomy-Guided Database-Searching Strategy for Improving Metaproteomic Analysis.
J.Xiao,A.Tanca, B.Jia, R.Yang, B.Wang,Y.Zhang J.Li*.
Journal of Proteome Research 6;17(4):1596-1605, 2018.  PMID: 29436230

Network module-based model in the differential expression analysis for RNA-seq.
M.Lei, J.Xu, LC.Huang, L.Wang, J.Li*.
Bioinformatics 33(17):2699-2705, 2017.  PMID: 28407034

CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation.
M.Zhang, B.Wang, J.Xu, X.Wang, L.Xie, B.Zhang*, Y.Li*, J.Li*.
Journal of Proteome Research 16(2):421-432, 2017.  PMID: 27977206

Improving Allergen Prediction in Main Crops Using a Weighted Integrative Method.
J.Li, J.Wang,J.Li*.
Interdiscip Sci Comput Life Sci 9:545–549, 2017.  PMID: 27734271

Construction and Deciphering of Human Phosphorylation-Mediated Signaling Transduction Networks.
M.Zhang, H.Li, Y.He, H.Sun, L.Xia, L.Wang, B.Sun,L.Ma, G.Zhang, J.Li*, Y.Li*, L.Xie*.
Journal of Proteome Research 14(7):2745-57, 2015.  PMID: 26006110

Network-Based Association Study of Obesity and Type 2 Diabetes with Gene Expression Profiles
S.Zhang, B.Wang, J.Shi, J. Li*
Biomed Res Int.2015:619730,2015.  PMID: 26273637

Biological network module-based model for the analysis of differential expression in shotgun proteomics
J. Xu, L. Wang, J. Li*
Journal of Proteome Research 13 (12): 5743-50, 2014.  PMID: 25327611

GroupRank: Rank Candidate Genes in PPI Network by Differentially Expressed Gene Groups
Q. Wang, S. Zhang, S. Pang, M. Zhang, B. Wang, Q. Liu*,J. Li*
PLoS One 9(10): e110406, 2014.  PMC: 4199715

Characterization and Phylogenetic Analysis of Allergenic Tryp_alpha_amyl Protein Family in Plants
J Wang, L. Yang, X. Zhao, J. Li*, D. Zhang*
J Agric Food Chem 62 (1): 270–278, 2014.  PMID: 24328177

PREAL: Prediction of Allergenic Protein By Maximum Relevance Minimum Redundancy (MRMR) Feature Selection
J Wang, D. Zhang, J. Li*
BMC Systems Biology 7(Suppl 5):S9, 2013.  PMID: 24565053

A Quantitative Analysis of the Impact on Chromatin Accessibility by Histone Modifications and Binding of Transcription Factors in DNase I Hypersensitive Sites
P. Cui, J. Li, B. Sun, M. Zhang, B. Lian,Y. Li, L. Xie
BioMed Research International 914971, 2013.  PMID: 24236298

Evaluation and Integration of Existing Methods for Computational Prediction of Allergens
J Wang, Y Yu, Y Zhao, D. Zhang and J. Li*
BMC Bioinformatics. 14(Suppl 4):S1, 2013.  PMID: 23514097

dbDEPC 2.0: database of differentially expressed proteins in human cancers
Y. He, M. Zhang, Y. Ju, ..., H. Li, J. Li, Y.Li, G. Zhang, L. Xie.
Nucleic Acids Research, 40(Database issue):D964-71, 2012.  PMID::22096234

A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics
J. Li
, Z. Su, Z. Ma, R.C.Slebos, P. Halvey, D.L. Tabb, D.C. Liebler, W. Pao, B. Zhang.
Molecular & Cellular Proteomics. 10:M110.006536, 2011.  PMID: 21389108

The discovery of novel protein-coding features in mouse genome based on mass spectrometry data
X. Xing, Q. Li, H. Sun, X. Fu, F. Zhan, X. Huang,J. Li, C. Chen, Y. Shyr, R. Zeng, Y. Li, L. Xie.
Genomics. 5:343-351, 2011.  PMID: 21840390

CanProVar: A Human Cancer Proteome Variation Database
J. Li
, D. Dexter, B. Zhang.
Human Mutation. 31(3):219-228,2010.  PMID: 20052754

Cysteinyl Peptide Capture for Shotgun Proteomics: Global Assessment of Chemoselective Fractionation
D. Lin, J. Li, R.J. Slebos, D.C. Liebler.
J Proteome Res. 9(10):5461-72, 2010.  PMID: 20731415

Network-assisted Protein Identification and Data Interpretation in Shotgun Proteomics
J. Li
, L. L. Zimmerman, B.-H. Park, D.L. Tabb, D.C. Liebler, B. Zhang.
Molecular Systems Biology. 5: 303, 2009.  PMID: 19690572

Multi-Site Assessment of The Precision and Reproducibility of Multiple Reaction Monitoring–based Measurements of Proteins in Plasma
T.A.Addona, … J. Li, …S.A. Carr.
Nature Biotechnology.27, 633-641, 2009.  PMID: 19561596

Shwachman-Bodian Diamond syndrome Is A Multi-functional Protein Implicated in Cellular Stress Responses
H.L Ball, B. Zhang, J. Riches, R. Gandhi, J. Li, J. M. Rommens, J.S. Myers.
Human Molecular Genetics. 18(19): 3684-95, 2009.  PMID: 19602484

Regulatory Module Network of bHLH Transcription Factors in Mouse Brain
J. Li
, Z. Liu, Y. Pan, Q. Liu, X. Fu, N.GF. Cooper, Y. Li, M. Qiu, T. Shi.
Genome Biology. 8: R244, 2007.  PMID: 18021424

Identification and Analysis of The Mouse Basic/Helix-Loop-Helix Transcription Factor Family
J. Li
, Q. Liu, M. Qiu, Y. Pan, Y. Li, T. Shi.
Biochem Biophys Res Commun. 350:648-656, 2006.  PMID: 17027923


©2012-2018 Jing Li