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PhosCancer: A comprehensive database for investigating protein phosphorylation in human cancer.
Q Dong, D Shen, J Ye, J Chen, J Li*.
iScience 2024. PMID: 39493875
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Integrative proteogenomic profiling of high-risk prostate cancer samples from Chinese patients indicates metabolic vulnerabilities and diagnostic biomarkers.
B Dong, JY Xu, Y Huang, J Guo, Q Dong, ... , J Li*, W Xue*, M Tan*, J Qin*.
Nature Cancer 2024. PMID: 39242942
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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
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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
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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: 37396531
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Alternative splicing signatures in preimplantation embryo development.
G. Tian, J.Li*, J.Wu*
Cell& Bioscience 10,33, ID 3907195, 2020. PMID: 32175076
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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CanProVar: A Human Cancer Proteome Variation Database
J. Li, D. Dexter, B. Zhang.
Human Mutation. 31(3):219-228，2010. PMID: 20052754
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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
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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
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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
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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
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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
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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
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