Publications by authors named "Shangwei Ning"

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A cell-specific computational framework reveals a pan-cancer hypoxia signature predicting overall survival and ICI response.
Caiyu Zhang, Yitong Jin, Yifangfei Yu, Yuling Chen, Jiayi Yang, Shangwei Ning

J Biol Chem· December 2025

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So3D: a comprehensive three-dimensional spatial omics resource for decoding tissue architecture in physiology and disease.
Hongying Zhao, Xiangzhe Yin, Siyao Wang, Zhichao Geng, Wentong Yu, Shangwei Ning

Nucleic Acids Res· October 2025

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LnCeVar 2.0: an updated resource and web tools for genomic variations disrupting ceRNA networks from single-cell/spatial transcriptomics data.
Qiuyan Guo, Qian Liu, Mengyu Xin, Houxing Li, Jiatong Li, Shangwei Ning

Nucleic Acids Res· October 2025

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A core driver gene set identified based on geMER reveals its potential driver mechanism in pan-cancer.
Jing Gan, Yuncong Wang, Zhuoran Shi, Haoyu Hu, Manyi Xu, Shangwei Ning

NPJ Precis Oncol· August 2025

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ISENICS: a model for identifying senescent immune cells and samples and characterization of their roles in tumor microenvironment.
Miaomiao Tian, Hao Cui, Xinyu Wang, Huading Hu, Longlong Dong, Shangwei Ning

Brief Bioinform· August 2025

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A comprehensive database for identifying and interpreting ctDNA driver genes and variants in cancer.
Yuncong Wang, Jing Gan, Haoyu Hu, Manyi Xu, Yongle Xu, Shangwei Ning

Sci Data· July 2025

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ImmuProgML: machine learning-based dissection of cancer-immune dynamics during tumor progression to improve immunotherapy.
Hanxiao Zhou, Lan Mei, Qianyi Lu, Yakun Zhang, Yue Sun, Shangwei Ning

J Transl Med· July 2025

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Dynamic changes of synergy relationship between lncRNA and immune checkpoint in cancer progression.
Chenyu Liu, Qianyi Lu, Jian Li, Di Wang, Zhuoru Wang, Shangwei Ning

Brief Bioinform· July 2025

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PD-1 regulates the anti-tumor immune function of macrophages through JAK2-STAT3 signaling pathway in colorectal cancer tumor microenvironment.
Han Jiang, Jingjing Pang, Tengyue Li, Atitso Akofala, Xiaoxi Zhou, Shangwei Ning

J Transl Med· May 2025

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NetLnc: A Network-Based Computational Framework to Identify Immune Checkpoint-Related lncRNAs for Immunotherapy Response in Melanoma.
Qianyi Lu, Jian Li, Wenli Chen, Zhuoru Wang, Di Wang, Shangwei Ning

Int J Mol Sci· May 2025

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Identification and validation of lncRNA mutation hotspot SNPs associated with myasthenia gravis susceptibility.
Ni He, Liting Tian, Jingnan Jin, Yue Liu, Lifang Li, Shangwei Ning

Noncoding RNA Res· April 2025

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Comprehensive characterization of respiratory genes based on a computational framework in pan-cancer to develop stratified treatment strategies.
Caiyu Zhang, Chenyu Liu, Zhuoru Wang, Di Wang, Wenli Chen, Shangwei Ning

PLoS Comput Biol· April 2025

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CNV-mediated dysregulation of the ceRNA network mechanism revealed heterogeneity in diffuse and intestinal gastric cancers.
Rongji Xu, Danni He, Rui Sun, Jiaqi Zhou, Mengyu Xin, Shangwei Ning

J Transl Med· March 2025

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RPL22L1 fosters malignant features of cervical cancer via the modulation of DUSP6-ERK axis.
Dongmei Zhang, Meiqi Zhao, Ping Jiang, Yunzhen Zhou, Xu Yan, Shangwei Ning

J Transl Med· February 2025

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LnCeCell 2.0: an updated resource for lncRNA-associated ceRNA networks and web tools based on single-cell and spatial transcriptomics sequencing data.
Qiuyan Guo, Qian Liu, Danni He, Mengyu Xin, Yifan Dai, Shangwei Ning

Nucleic Acids Res· January 2025

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Common biomarkers of idiopathic pulmonary fibrosis and systemic sclerosis based on WGCNA and machine learning.
Ning Shan, Yu Shang, Yaowu He, Zhe Wen, Shangwei Ning

Sci Rep· January 2025

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A Novel Competing Endogenous RNA Network Reveals Potential Mechanisms and Biomarkers of Chemoresistance in Lung Adenocarcinoma.
Weisha Liu, Hanxiao Zhou, Yue Qi, Peng Wang, Shangwei Ning

J Cancer· January 2025

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MRdb: a comprehensive database of univariate and multivariate Mendelian randomization with large-scale GWAS summary data.
Qian Liu, Yujie Zhang, Houxing Li, Jiatong Li, Mengyu Xin, Shangwei Ning

Database (Oxford)· January 2025

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DNA methylation heterogeneity attributable to a complex tumor immune microenvironment prompts prognostic risk in glioma.
Shuangyue Ma, Xu Pan, Jing Gan, Xiaxin Guo, Jiaheng He, Shangwei Ning

Epigenetics· December 2024

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Single-Cell and Bulk Transcriptomics Reveal the Immunosenescence Signature for Prognosis and Immunotherapy in Lung Cancer.
Yakun Zhang, Jiajun Zhou, Yitong Jin, Chenyu Liu, Hanxiao Zhou, Shangwei Ning

Cancers (Basel)· December 2024

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AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs.
Lan Mei, Yaopan Hou, Jiajun Zhou, Yetong Chang, Yuwei Liu, Shangwei Ning

Genomics Proteomics Bioinformatics· September 2024

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Comprehensive quantitative radiogenomic evaluation reveals novel radiomic subtypes with distinct immune pattern in glioma.
Yue Sun, Yakun Zhang, Jing Gan, Hanxiao Zhou, Shuang Guo, Shangwei Ning

Comput Biol Med· July 2024

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MSGD: a manually curated database of genomic, transcriptomic, proteomic and drug information for multiple sclerosis.
Tao Wu, Yaopan Hou, Guanghao Xin, Jingyan Niu, Shanshan Peng, Shangwei Ning

Database (Oxford)· May 2024

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Role of ferroptosis in neuroimmunity and neurodegeneration in multiple sclerosis revealed by multi-omics data.
Tao Wu, Shangwei Ning, Huixue Zhang, Yuze Cao, Xia Li

J Cell Mol Med· May 2024

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The landscape of immune checkpoint-related long non-coding RNAs core regulatory circuitry reveals implications for immunoregulation and immunotherapy responses.
Changfan Qu, Hao Cui, Song Xiao, Longlong Dong, Qianyi Lu, Shangwei Ning

Commun Biol· March 2024

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