宁尚伟｜哈尔滨医科大学｜学者主页

2026

EvoNiche: a comprehensive database for dissecting tumor niche dynamics and spatiotemporal evolution within the cancer ecosystem

Hongying Zhao, Xiangzhe Yin, Siya Wang, Wentong Yu, Zhichao Geng, Yanwu Sun, Wanting Jiao, Hongzheng Yu, Yunpeng Zhang, Peng Wang, Shangwei Ning, Li Wang

Nucleic Acids Research

DOI

2026

Tumor Microenvironment Hijacks and Accelerates a Physiological Myeloid Senescence Signature Associated with Pan-Cancer Immunosuppression and Prognostic Stratification

Han Jiang, Yakun Zhang, Caiyu Zhang, Tengyue Li, Qianyi Lu, Jiajun Zhou, Jiayi Yang, Jialu Zhang, Gao Y, Shangwei Ning

International Journal of Molecular Sciences

DOI

2026

Single-cell multi-omics dissection of RevitalAge Markers uncovers age-dependent immunotherapy resistance and druggable targets in melanoma

Hanxiao Zhou, Benliang Wei, 覃温露, J H Shi, Changyuan Ren, J M Zhang, Changlin Yang, Zheng Zhao, Shangwei Ning

Biology Direct

DOI

2026

Machine learning and single-cell approaches identify an NAD metabolism-related signature for predicting immunotherapy outcomes

Hanxiao Zhou, Wenli Chen, D Wang, Zhuoru Wang, J P Li, Yakun Zhang, Yuanhao Sun, Caiyu Zhang, Han Jiang, Lan Mei, Yunpeng Zhang, Shangwei Ning, Xia Li

Genes & Diseases

DOI

2026

Integration of single-cell RNA-sequencing and machine learning identifies GRN and FCER1G as potential peroxisomal targets in influenza pathogenesis

Ning Shan, Shibin Chen, Zhaoyu Liu, Zhe Wen, Junwei Wang, Yao Yu, Xuan Liu, Shangwei Ning, Hong Chen

BMC Infectious Diseases

DOI

2026

Deciphering the glioblastoma microenvironmental landscape with multi-modal radiogenomics to guide prognosis and personalized therapy

Hongyun Zhao, Kailai Liu, Marui Guan, Xun Tang, Yangxinyue Zheng, Hongzheng Yu, Shangwei Ning, L Wang

Journal of Translational Medicine

DOI

2026

Identification of lncRNAs Indicating Immune Pathway Activity for Predicting Prognosis and Immunotherapy Response in Pan‐Cancer

Mengyu Xin, Danni He, Yifan Dai, Qian Liu, Rui Sun, Houxing Li, Yujie Zhang, Jiatong Li, Shangwei Ning, Qiuyan Guo, Yue Gao, Peng Wang

Cancer Medicine

DOI

2026

Integrated Single-Cell Multi-Omics Analysis Reveals That a CD8+ TPex–Monocyte Interaction Axis Coordinates Immune Infiltration in Alzheimer’s Disease

Yusen Zhao, Xinrong Li, Wenbo Dong, Hongbo Zhu, Shuangshuang Wang, Manyi Xu, Yongle Xu, Mengmeng Liu, Junjie Duan, Yujie Liu, Wei Feng, Shangwei Ning, Hui Zhi

International Journal of Molecular Sciences

DOI

2026

Identification of Immune&Driver Molecular Subtypes Optimizes Immunotherapy Strategies for Gastric Cancer

Jing Gan, Bo Yang, Shuangshuang Wang, Hongbo Zhu, Manyi Xu, Yongle Xu, Xinrong Li, Wenbo Dong, Yusen Zhao, Mengmeng Liu, Wei Feng, Yujie Liu, Junjie Duan, Shangwei Ning, Hui Zhi

International Journal of Molecular Sciences

DOI

2026

Dysregulation of ceRNA mechanisms across pan-cancer drives cancer progression towards acquiring metastatic potential

Danni He, Rui Sun, Xi-ya Shan, Borui Xu, Mengyu Xin, Qian Liu, Jiatong Li, Houxing Li, Yujie Zhang, Yifan Dai, Yuting He, Yue Gao, Hui Zhi, Shangwei Ning, Peng Wang, Qiuyan Guo

Genes & Diseases

DOI

2025

Metabolic and aging related gene risk score for therapeutic stratification and precision oncology in gastric cancer

Yue Zhang, Tian Yang, Shaobo Zheng, Liying Wang, Lu Bai, Tianlai Liu, Xing Li, Weiqi Shan, Meiqi Song, Shangwei Ning, Yu Han

Medicine

DOI

2025

A cell-specific computational framework reveals a pan-cancer hypoxia signature predicting overall survival and ICI response

Caiyu Zhang, Ying Jin, Yifangfei Yu, Yu‐Ling Chen, Jiayi Yang, jialu Zhang, Qianyi Lu, Han Jiang, Yue Sun, Yakun Zhang, Hui Zhi, Yue Gao, Peng Wang, Shangwei Ning

Journal of Biological Chemistry

DOI

2025

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, Yifan Dai, Rui Sun, Yujie Zhang, Yuting He, Borui Xu, Xinxin Shan, Yue Gao, Shangwei Ning, Hui Zhi, Peng Wang

Nucleic Acids Research

DOI

2025

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, Hongzheng Yu, Shangwei Ning, Li Wang

Nucleic Acids Research

DOI

2025

DNA methylation heterogeneity in complex tumor microenvironment: Quantitative methods, influencing factors, and clinical implications

Yongle Xu, Shuangyue Ma, Manyi Xu, Hongbo Zhu, Yuncong Wang, Wenbo Dong, Jing Gan, Zhao Yusen, Xinrong Li, Shuangshuang Wang, Haoyu Hu, Jia He, Shangwei Ning, Hui Zhi

Genes & Diseases

DOI

2025

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, Song Xiao, Changfan Qu, Peng Wang, Hui Zhi, Shangwei Ning, Yue Gao

Briefings in Bioinformatics

DOI

2025

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, Xinrong Li, Wenbo Dong, Jia He, Yusen Zhao, Yakun Zhang, Yue Sun, Caiyu Zhang, Qianyi Lu, Shangwei Ning, Yan Jin, Hui Zhi

npj Precision Oncology

DOI

2025

ImmuProgML: machine learning-based dissection of cancer-immune dynamics during tumor progression to improve immunotherapy

Hanxiao Zhou, Mei Lan, Qianyi Lu, Yakun Zhang, Yakun Zhang, Yue Sun, Caiyu Zhang, Han Jiang, Jiajun Zhou, Xia Li, Yunpeng Zhang, Yunpeng Zhang, Shangwei Ning

Journal of Translational Medicine

DOI

2025

A comprehensive database for identifying and interpreting ctDNA driver genes and variants in cancer

Yuncong Wang, Jing Gan, Haoyu Hu, Manyi Xu, Yongle Xu, Yusen Zhao, Wenbo Dong, Xinrong Li, Hongbo Zhu, Shuangshuang Wang, Jia He, Shangwei Ning, Peng Wang, Hui Zhi

Scientific Data

DOI

2025

Dynamic changes of synergy relationship between lncRNA and immune checkpoint in cancer progression

Chenyu Liu, Qianyi Lu, Jian Li, Di Wang, Zhuoru Wang, Wenli Chen, Yakun Zhang, Caiyu Zhang, Yue Gao, Shangwei Ning

Briefings in Bioinformatics

DOI

2025

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, Chenyu Liu, Yue Sun, Han Jiang, Caiyu Zhang, Yetong Chang, Jiajun Zhou, Xiaohong Wu, Yue Gao, Shangwei Ning

International Journal of Molecular Sciences

DOI

2025

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, Changhua Yi, Shangwei Ning, Xu Gao, Yu Qiao, Jiayuan Kou

Journal of Translational Medicine

DOI

2025

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, Jian Li, Qianyi Lu, Jiajun Zhou, Yetong Chang, Peng Wang, Yue Gao, Junwei Wang, Hui Zhi, Shangwei Ning

PLoS Computational Biology

DOI

2025

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, Qian Liu, Yifan Dai, Houxing Li, Yujie Zhang, Jiatong Li, Xi-ya Shan, Yuting He, Borui Xu, Qiuyan Guo, Shangwei Ning, Yue Gao, Peng Wang

Journal of Translational Medicine

DOI

2025

RPL22L1 fosters malignant features of cervical cancer via the modulation of DUSP6-ERK axis

Dongmei Zhang, Meiqi Zhao, Ping Jiang, Yunzhen Zhou, Yan Xu, Chong Zhou, Yu Mu, Shan Xiao, Guohua Ji, Nan Wu, Donglin Sun, Xiaobo Cui, Shangwei Ning, Hongxue Meng, Sheng Xiao, Yan Jin

Journal of Translational Medicine

DOI

2025

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, Hong Chen

Scientific Reports

DOI

2025

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, Rui Sun, Yifan Dai, Xinxin Shan, Yuting He, Borui Xu, Shangwei Ning, Peng Wang, Qiuyan Guo

Database

DOI

2024

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, Yue Huang, Liuying Wang, Lei Cao, Kang Li

Journal of Cancer

DOI

2024

Identification and validation of lncRNA mutation hotspot SNPs associated with myasthenia gravis susceptibility

Ni He, Liting Tian, Jingnan Jin, Yue Liu, Lifang Li, Xiaokun Wang, Danyang Li, Xia Wang, Xiaoju Li, Zihong Chen, Lanxin Zhang, Lukuan Qiao, Shangwei Ning, Lihua Wang, Jianjian Wang

Non-coding RNA Research

DOI

2024

Single-Cell and Bulk Transcriptomics Reveal the Immunosenescence Signature for Prognosis and Immunotherapy in Lung Cancer

Yakun Zhang, Jiajun Zhou, Ying Jin, Chenyu Liu, Hanxiao Zhou, Yue Sun, Han Jiang, Jing Gan, Caiyu Zhang, Qianyi Lu, Yetong Chang, Yunpeng Zhang, Xia Li, Shangwei Ning

Cancers

DOI

2024

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, Rui Sun, Houxing Li, Yujie Zhang, Jiatong Li, Congcong Kong, Yue Gao, Hui Zhi, Feng Li, Shangwei Ning, Peng Wang

Nucleic Acids Research

DOI

2024

AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs

Lan Mei, Yaopan Hou, Jiajun Zhou, Yetong Chang, Yuwei Liu, Di Wang, Yunpeng Zhang, Shangwei Ning, Xia Li

Genomics Proteomics & Bioinformatics

DOI

2024

Comprehensive quantitative radiogenomic evaluation reveals novel radiomic subtypes with distinct immune pattern in glioma

Yue Sun, Yakun Zhang, Jing Gan, Hanxiao Zhou, Shuang Guo, Xinyue Wang, Caiyu Zhang, Wen Zheng, Xiaoxi Zhao, Xia Li, Li Wang, Shangwei Ning

Computers in Biology and Medicine

DOI

2024

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, Junwei Hao, Lihua Wang

Journal of Cellular and Molecular Medicine

DOI

2024

The landscape of immune checkpoint-related long non-coding RNAs core regulatory circuitry reveals implications for immunoregulation and immunotherapy responses

Changfan Qu, Hao Cui, Xiao Mei Song, Longlong Dong, Qianyi Lu, Lei Zhang, Peng Wang, Mengyu Xin, Hui Zhi, Chenyu Liu, Shangwei Ning, Yue Gao

Communications Biology

DOI

2024

DNA methylation heterogeneity attributable to a complex tumor immune microenvironment prompts prognostic risk in glioma

Shuangyue Ma, Pan Xu, Jing Gan, Xiaxin Guo, Jiaheng He, Haoyu Hu, Yuncong Wang, Shangwei Ning, Hui Zhi

Epigenetics

DOI

2024

A comprehensive database of exosome molecular biomarkers and disease-gene associations

Yue Qi, Rongji Xu, Chengxin Song, Ming Hao, Yue Gao, Mengyu Xin, Qian Liu, Hongyan Chen, Xiaoting Wu, Rui Sun, Yuanfu Zhang, Danni He, Yifan Dai, Congcong Kong, Shangwei Ning, Qiuyan Guo, Guangmei Zhang, Peng Wang

Scientific Data

DOI

2024

Metabolic-Related Gene Prognostic Index for Predicting Prognosis, Immunotherapy Response, and Candidate Drugs in Ovarian Cancer

Shuang Guo, Yuwei Liu, Yue Sun, Hanxiao Zhou, Yue Gao, Peng Wang, Hui Zhi, Yakun Zhang, Jing Gan, Shangwei Ning

Journal of Chemical Information and Modeling

DOI

2024

Identification of cuproptosis-related diagnostic biomarkers in idiopathic pulmonary fibrosis

Qi Wang, Yu Shang, Yupeng Li, Xincheng Li, Xue Wang, Yaowu He, Jing Ma, Shangwei Ning, Hong Chen

Medicine

DOI

2024

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, Fanfan Xu, Ying Li, Yuling Chen, Yifangfei Yu, Huixue Zhang, Xiaotong Kong, Yuze Cao, Shangwei Ning, Lihua Wang, Junwei Hao

Database

DOI

2023

Proteomic characterization of epithelial ovarian cancer delineates molecular signatures and therapeutic targets in distinct histological subtypes

Ting‐Ting Gong, Shuang Guo, Fang-Hua Liu, Yun-Long Huo, Meng Zhang, Yan Shi, Hanxiao Zhou, Pan Xu, Xinyue Wang, He-Li Xu, Ye Kang, Yi-Zi Li, Xue Qin, Qian Xiao, Donghui Huang, Xiao-Ying Li, Yueyang Zhao, Xinxin Zhao, Yali Wang, Xiaoxin Ma, Song Gao, Yuhong Zhao, Shangwei Ning, Qi‐Jun Wu

Nature Communications

DOI

2023

Tumor biology, immune infiltration and liver function define seven hepatocellular carcinoma subtypes linked to distinct drivers, survival and drug response

Ruihong Wu, Yue Gao, Xiaoxi Zhao, Shuang Guo, Hanxiao Zhou, Yakun Zhang, Yakun Zhang, Yaopan Hou, Mei Lan, Hui Zhi, Peng Wang, Xia Li, Shangwei Ning, Yunpeng Zhang, Yunpeng Zhang

Computers in Biology and Medicine

DOI

2023

Identifying immune checkpoint-related lncRNA biomarkers for immunotherapy response and prognosis in cancers

Yue Gao, Xinyue Wang, Longlong Dong, Changfan Qu, Qianyi Lu, Peng Wang, Mengyu Xin, Wen Zheng, Chenyu Liu, Shangwei Ning

Scientific Data

DOI

2023

Reconstructing the immunosenescence core pathway reveals global characteristics in pan-cancer

Yakun Zhang, Yakun Zhang, Yue Sun, Jing Gan, Hanxiao Zhou, Shuang Guo, Xinyue Wang, Wen Zheng, Wen Zheng, Xiaoxi Zhao, Yunpeng Zhang, Yunpeng Zhang, Shangwei Ning, Xia Li

Cancer Immunology Immunotherapy

DOI

2023

CRS: a circadian rhythm score model for predicting prognosis and treatment response in cancer patients

Yuwei Liu, Shuang Guo, Yue Sun, Caiyu Zhang, Jing Gan, Shangwei Ning, Junwei Wang

Journal of Translational Medicine

DOI

2023

Pan-cancer transcriptomic analysis identified six classes of immunosenescence genes revealed molecular links between aging, immune system and cancer

Xinyue Wang, Shuang Guo, Hanxiao Zhou, Yue Sun, Jing Gan, Yakun Zhang, Wen Zheng, Caiyu Zhang, Peng Wang, Hui Zhi, Yue Gao, Xiaofeng Chen, Shangwei Ning

Genes and Immunity

DOI

2023

Radiogenomic analysis of prediction HER2 status in breast cancer by linking ultrasound radiomic feature module with biological functions

Hao Cui, Yue Sun, Dantong Zhao, Xudong Zhang, Hanqing Kong, Nana Hu, Panting Wang, Xiaoxuan Zuo, Wei Fan, Yuan Yao, Baiyang Fu, Jiawei Tian, Meixin Wu, Yue Gao, Shangwei Ning, Lei Zhang

Journal of Translational Medicine

DOI

2023

Immune Pathways with Aging Characteristics Improve Immunotherapy Benefits and Drug Prediction in Human Cancer

Xinyue Wang, Shuang Guo, Hanxiao Zhou, Yue Sun, Jing Gan, Yakun Zhang, Wen Zheng, Caiyu Zhang, Xiaoxi Zhao, Jiebin Xiao, Li Wang, Yue Gao, Shangwei Ning

Cancers

DOI

2023

LncPCD: a manually curated database of experimentally supported associations between lncRNA-mediated programmed cell death and diseases

Ni He, Danyang Li, Fanfan Xu, Jingnan Jin, Lifang Li, Liting Tian, Biying Chen, Xiaoju Li, Shangwei Ning, Lihua Wang, Jianjian Wang

Database

DOI

2022

基于GEO数据库分析支气管肺发育不良发生的关键基因及通路

颉相君，张博，吕莹，宁尚伟，曲书强

《江苏大学学报(医学版)》

2022

Construction of a ferroptosis-related signature based on seven lncRNAs for prognosis and immune landscape in clear cell renal cell carcinoma

Shi-Yao Wei, Bei Feng, Min Bi, Haiying Guo, Shangwei Ning, Rui Cui

BMC Medical Genomics

DOI

2022

The dynamic dysregulated network identifies stage-specific markers during lung adenocarcinoma malignant progression and metastasis

Li Wang, Li Wang, Kailai Liu, Kailai Liu, Lixia Wang, Lixia Wang, Xiangzhe Yin, Shihua Lin, Haotian Xu, Shihua Lin, Ke Feng, Xinyu Zhou, Lin Lin, Meiting Fei, Caiyu Zhang, Shangwei Ning, Hongying Zhao

Molecular Therapy — Nucleic Acids

DOI

2022

LncTarD 2.0: an updated comprehensive database for experimentally-supported functional lncRNA–target regulations in human diseases

Hongying Zhao, Xiangzhe Yin, Haotian Xu, Kailai Liu, Wangyang Liu, Lixia Wang, Lixia Wang, Caiyu Zhang, Lin Bo, Xicheng Lan, Shihua Lin, Ke Feng, Shangwei Ning, Yunpeng Zhang, Li Wang, Li Wang

Nucleic Acids Research

DOI

2022

CellTracer: a comprehensive database to dissect the causative multilevel interplay contributing to cell development trajectories

Qiuyan Guo, Peng Wang, Qian Liu, Yangyang Hao, Yue Gao, Yue Qi, Rongji Xu, Hongyan Chen, Mengyu Xin, Xiaoting Wu, Rui Sun, Hui Zhi, Yunpeng Zhang, Shangwei Ning, Xia Li

Nucleic Acids Research

DOI

2022

AgingBank: a manually curated knowledgebase and high-throughput analysis platform that provides experimentally supported multi-omics data relevant to aging in multiple species

Yue Gao, Shipeng Shang, Shuang Guo, Xinyue Wang, Hanxiao Zhou, Yue Sun, Jing Gan, Yakun Zhang, Yakun Zhang, Xia Li, Shangwei Ning, Yunpeng Zhang, Yunpeng Zhang

Briefings in Bioinformatics

DOI

2022

Identifying enhancer-driven subtype-specific prognostic markers in breast cancer based on multi-omics data

Hongying Zhao, Siwen Zhang, Xiangzhe Yin, Caiyu Zhang, Lixia Wang, Lixia Wang, Kailai Liu, Haotian Xu, Wangyang Liu, Lin Bo, Shihua Lin, Ke Feng, Lin Lin, Meiting Fei, Shangwei Ning, Lı Wang, Lı Wang

Frontiers in Immunology

DOI

2022

Human RNA Modifications Disease Database (HRMDD): A web resource for the molecular and clinical landscape of RNA modifications in human diseases

Jianjian Wang, Lifang Li, Hanxiao Zhou, Shuang Li, Liting Tian, Xinyue Wang, Danyang Li, Yue Yin, Shangwei Ning, Lihua Wang

Genes & Diseases

DOI

2022

PD-L1-Mediated Immunosuppression in Hepatocellular Carcinoma: Relationship with Macrophages Infiltration and Inflammatory Response Activity

Shuang Guo, Xinyue Wang, Hanxiao Zhou, Yue Gao, Peng Wang, Hui Zhen Zhi, Yue Sun, Yakun Zhang, Jing Gan, Yun Xiao, Shangwei Ning

Biomolecules

DOI

2022

Comprehensive characterization of clonality of driver genes revealing their clinical relevance in colorectal cancer

Jian Shi, Li Wang, Li Wang, Xiangzhe Yin, Lixia Wang, Lixia Wang, Lin Bo, Shihua Lin, Ke Feng, Shihua Lin, Yanjun Xu, Shangwei Ning, Hongying Zhao

Journal of Translational Medicine

DOI

2022

Functional regulations between genetic alteration-driven genes and drug target genes acting as prognostic biomarkers in breast cancer

Li Wang, Lei Yu, Jian Shi, Feng Li, Caiyu Zhang, Haotian Xu, Xiangzhe Yin, Lixia Wang, Shihua Lin, Litvinova Anastasiia, Yanyan Ping, Shangwei Ning, Hongying Zhao

Scientific Reports

DOI

2022

Enhancer methylation dynamics drive core transcriptional regulatory circuitry in pan-cancer

Pan Xu, Xin Li, Jie Sun, Zhiying Xiong, Haoyu Hu, Shangwei Ning, Hui Zhi

Oncogene

DOI

2022

RNA2Immune: A Database of Experimentally Supported Data Linking Non-Coding RNA Regulation to the Immune System

Jianjian Wang, Shuang Li, Tianfeng Wang, Si Xu, Xu Wang, Xiaotong Kong, Xiaoyu Lu, Huixue Zhang, Lifang Li, Meng Feng, Shangwei Ning, Lihua Wang

Genomics Proteomics & Bioinformatics

DOI

2022

Prioritizing Cancer lncRNA Modulators via Integrated lncRNA-mRNA Network and Somatic Mutation Data

Dianshuang Zhou, Xin Li, Shipeng Shang, Hui Zhi, Peng Wang, Yue Gao, Shangwei Ning

Current Bioinformatics

DOI

2022

S100A12 as Biomarker of Disease Severity and Prognosis in Patients With Idiopathic Pulmonary Fibrosis

Yupeng Li, Yaowu He, Shibin Chen, Qi Wang, Yi Yang, Danting Shen, Jing Ma, Zhe Wen, Shangwei Ning, Hong Chen

Frontiers in Immunology

DOI

2022

Identification and Characterization of Immunogene-Related Alternative Splicing Patterns and Tumor Microenvironment Infiltration Patterns in Breast Cancer

Shuang Guo, Xinyue Wang, Hanxiao Zhou, Yue Gao, Peng Wang, Hui Zhi, Yue Sun, Yangyang Hao, Jing Gan, Yakun Zhang, Jie Sun, Wen Zheng, Xiaoxi Zhao, Yun Xiao, Shangwei Ning

Cancers

DOI

2022

An 8-ferroptosis-related genes signature from Bronchoalveolar Lavage Fluid for prognosis in patients with idiopathic pulmonary fibrosis

Yaowu He, Yu Shang, Yupeng Li, Menghan Wang, Dongping Yu, Yi Yang, Shangwei Ning, Hong Chen

BMC Pulmonary Medicine

DOI

2021

Competitive endogenous RNA network and pathway-based analysis of LncRNA single-nucleotide polymorphism in myasthenia gravis

Tianfeng Wang, Si Xu, Huixue Zhang, Xiaoyu Lu, Shuang Li, Li Liu, Xiaotong Kong, Hongyu Gao, Xu Wang, Shangwei Ning, Jianjian Wang, Lihua Wang

Scientific Reports

DOI

2021

Identifying and characterizing lincRNA genomic clusters reveals its cooperative functions in human cancer

Hanxiao Zhou, Yue Gao, Xin Li, Xin Li, Shipeng Shang, Peng Wang, Hui Zhi, Shuang Guo, Dailin Sun, Hongjia Liu, Xia Li, Xia Li, Yunpeng Zhang, Shangwei Ning

Journal of Translational Medicine

DOI

2021

Identification of miRNA-mRNA network and immune-related gene signatures in IgA nephropathy by integrated bioinformatics analysis

Shi-Yao Wei, Shuang Guo, Bei Feng, Shangwei Ning, Xuanyi Du

BMC Nephrology

DOI

2021

CD247, a Potential T Cell–Derived Disease Severity and Prognostic Biomarker in Patients With Idiopathic Pulmonary Fibrosis

Yupeng Li, Shibin Chen, Xincheng Li, Xue Wang, Huiwen Li, Shangwei Ning, Hong Chen

Frontiers in Immunology

DOI

2021

LncACTdb 3.0: an updated database of experimentally supported ceRNA interactions and personalized networks contributing to precision medicine

Peng Wang, Qiuyan Guo, Yue Qi, Yangyang Hao, Yue Gao, Hui Zhi, Yuanfu Zhang, Yuanfu Zhang, Yue Sun, Yakun Zhang, Yakun Zhang, Mengyu Xin, Yunpeng Zhang, Yunpeng Zhang, Shangwei Ning, Xia Li

Nucleic Acids Research

DOI

2021

Identification of the regulatory role of lncRNA HCG18 in myasthenia gravis by integrated bioinformatics and experimental analyses

Shuang Li, Xu Wang, Tianfeng Wang, Huixue Zhang, Xiaoyu Lu, Li Liu, Lifang Li, Chunrui Bo, Xiaotong Kong, Si Xu, Shangwei Ning, Jianjian Wang, Lihua Wang

Journal of Translational Medicine

DOI

2021

Epigenome signature as an immunophenotype indicator prompts durable clinical immunotherapy benefits in lung adenocarcinoma

Pan Xu, Caiyu Zhang, Junwei Wang, Peng Wang, Yue Gao, Shipeng Shang, Shuang Guo, Xin Li, Hui Zhi, Shangwei Ning

Briefings in Bioinformatics

DOI

2021

Inferring SARS-CoV-2 functional genomics from viral transcriptome with identification of potential antiviral drugs and therapeutic targets

Pan Xu, Xin Li, Shangwei Ning, Hui Zhi

Cell & Bioscience

DOI

2021

DNA Methylation Dynamics of Long Noncoding RNA During Human Fetal Development

Xin Li, Yuanyuan Fu, Yue Gao, Shipeng Shang, Shuang Guo, Hanxiao Zhou, Shuqiang Qu, Shangwei Ning

Epigenomics

DOI

2021

Construction of lncRNA-Mediated ceRNA Network for Investigating Immune Pathogenesis of Ischemic Stroke

Shuang Li, Yuze Cao, Huixue Zhang, Xiaoyu Lu, Tianfeng Wang, Si Xu, Tongxiao Kong, Chunrui Bo, Lifang Li, Shangwei Ning, Jianjian Wang, Lihua Wang

Molecular Neurobiology

DOI

2021

MeImmS: Predict Clinical Benefit of Anti-PD-1/PD-L1 Treatments Based on DNA Methylation in Non-small Cell Lung Cancer

Shipeng Shang, Xin Li, Xin Li, Yue Gao, Shuang Guo, Dailin Sun, Hanxiao Zhou, Yue Sun, Peng Wang, Hui Zhi, Jing Bai, Shangwei Ning, Xia Li, Xia Li

Frontiers in Genetics

DOI

2021

Construction of a TF–miRNA–gene feed-forward loop network predicts biomarkers and potential drugs for myasthenia gravis

Chunrui Bo, Huixue Zhang, Yuze Cao, Xiaoyu Lu, Cong Zhang, Shuang Li, Xiaotong Kong, Xiaoming Zhang, Ming Bai, Kuo Tian, Aigul R. Saitgareeva, Gaysina Lyaysan, Jianjian Wang, Shangwei Ning, Lihua Wang

Scientific Reports

DOI

2021

Network and Pathway-Based Integrated Analysis Identified a Novel “rs28457673–miR-15/16/195/424/497 Family–IGF1R–MAPK Signaling Pathway” Axis Associated With Post-stroke Depression

Yan Li, Zhichao Wang, Mingxi Zhu, Gui-bo Fan, Gao-shuo Xu, Tianyang Zhao, A.-yang Zhao, Shangwei Ning, Sihua Qi

Frontiers in Cell and Developmental Biology

DOI

2020

Immune Characterization of Ovarian Cancer Reveals New Cell Subtypes With Different Prognoses, Immune Risks, and Molecular Mechanisms

Shanshan Cong, Qiuyan Guo, Yan Cheng, Yanan He, Xibo Zhao, Congcong Kong, Shangwei Ning, Guangmei Zhang

Frontiers in Cell and Developmental Biology

DOI

2020

Identification of Potential Long Non-coding RNA Expression Quantitative Trait Methylations in Lung Adenocarcinoma and Lung Squamous Carcinoma

Xiaohong Wu, Yue Gao, Jianlong Bu, Linhong Deng, Pinyi Zhang, Meng Chi, Lihua Jiang, Xiaoding Shi, Shangwei Ning, Guonian Wang

Frontiers in Genetics

DOI

2020

ILDGDB: a manually curated database of genomics, transcriptomics, proteomics and drug information for interstitial lung diseases

Yupeng Li, Gangao Wu, Yu Shang, Yue Qi, Xue Wang, Shangwei Ning, Hong Chen

BMC Pulmonary Medicine

DOI

2020

LincSNP 3.0: an updated database for linking functional variants to human long non-coding RNAs, circular RNAs and their regulatory elements

Yue Gao, Xin Li, Xin Li, Shipeng Shang, Shuang Guo, Peng Wang, Dailin Sun, Jing Gan, Jie Sun, Yakun Zhang, Yakun Zhang, Junwei Wang, Xinyue Wang, Xia Li, Xia Li, Yunpeng Zhang, Yunpeng Zhang, Shangwei Ning

Nucleic Acids Research

DOI

2020

Lnc2Cancer 3.0: an updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data

Yue Gao, Shipeng Shang, Shuang Guo, Xin Li, Xin Li, Hanxiao Zhou, Hongjia Liu, Yue Sun, Peng Wang, Peng Wang, Hui Zhi, Xia Li, Xia Li, Shangwei Ning, Yunpeng Zhang

Nucleic Acids Research

DOI

2020

LnCeCell: a comprehensive database of predicted lncRNA-associated ceRNA networks at single-cell resolution

Peng Wang, Qiuyan Guo, Yangyang Hao, Qian Liu, Yue Gao, Hui Zhi, Xin Li, Xin Li, Shipeng Shang, Shuang Guo, Yunpeng Zhang, Shangwei Ning, Xia Li, Xia Li

Nucleic Acids Research

DOI

2020

GABC : A comprehensive resource and Genome Atlas for Breast Cancer

Yunpeng Zhang, Peng Wang, Xin Li, Xin Li, Shangwei Ning, Xia Li, Xia Li, Yan Wei Cao, Steven Xi Chen

International Journal of Cancer

DOI

2020

Long noncoding RNAs in gastric cancer: From molecular dissection to clinical application

Yue Gao, Wang Jun-wei, Jiayi Ren, Mian Guo, Cheng-Wang Guo, Shangwei Ning, Shan Yu

World Journal of Gastroenterology

DOI

2020

CpG methylation signature defines human temporal lobe epilepsy and predicts drug‐resistant

Wenbiao Xiao, Chaorong Liu, Kuo Zhong, Shangwei Ning, Rui Hou, Na Deng, Yuchen Xu, Zhaohui Luo, Yujiao Fu, Yi Zeng, Bo Xiao, Hongyu Long, Lili Long

CNS Neuroscience & Therapeutics

DOI

2020

Dynamic TF-lncRNA Regulatory Networks Revealed Prognostic Signatures in the Development of Ovarian Cancer

Qiuyan Guo, Junwei Wang, Yue Gao, Xin Li, Yangyang Hao, Shangwei Ning, Peng Wang

Frontiers in Bioengineering and Biotechnology

DOI

2020

CLING: Candidate Cancer-Related lncRNA Prioritization via Integrating Multiple Biological Networks

Jizhou Zhang, Yue Gao, Peng Wang, Hui Zhi, Yan Zhang, Maoni Guo, Ming Yue, Xin Li, Dianshuang Zhou, Yanxia Wang, Weitao Shen, Junwei Wang, Jian Hua Huang, Shangwei Ning

Frontiers in Bioengineering and Biotechnology

DOI

2020

The multifaceted roles of long noncoding RNAs in pancreatic cancer: an update on what we know

Wenjia Zhou, Lu Chen, Chao Li, Rui Huang, Mian Guo, Shangwei Ning, Jingjing Ji, Xiaorong Guo, Ge Lou, Xinqi Jia, Junjie Zhao, Feng Luo, Chunlong Li, Zhao-Wei Qu, Shan Yu, Sheng Tai

Cancer Cell International

DOI

2020

Identification of the Regulatory Role of lncRNA SNHG16 in Myasthenia Gravis by Constructing a Competing Endogenous RNA Network

Jianjian Wang, Yuze Cao, Xiaoyu Lu, Xiaolong Wang, Xiaotong Kong, Chunrui Bo, Shuang Li, Ming Bai, Yang Jiao, Hongyu Gao, Xiuhua Yao, Shangwei Ning, Lihua Wang, Huixue Zhang

Molecular Therapy — Nucleic Acids

DOI

2020

Overexpression of MicroRNA-9a-5p Ameliorates NLRP1 Inflammasome-mediated Ischemic Injury in Rats Following Ischemic Stroke

Yuze Cao, Huixue Zhang, Xiaoyu Lu, Jianjian Wang, Xiaoming Zhang, Shengnan Sun, Zhonglei Bao, Wenqi Tian, Shangwei Ning, Lihua Wang, Liying Cui

Neuroscience

DOI

2020

Construction of asthma related competing endogenous RNA network revealed novel long non-coding RNAs and potential new drugs

Yifang Liao, Ping Li, Yanxia Wang, Hong Chen, Shangwei Ning, Dongju Su

Respiratory Research

DOI

2019

大数据研究给肿瘤诊治带来新启示

衣晓峰，宁尚伟

《健康报》

2019

CancerClock: A DNA Methylation Age Predictor to Identify and Characterize Aging Clock in Pan-Cancer

Tongtong Zhu, Yue Gao, Junwei Wang, Xin Li, Shipeng Shang, Yanxia Wang, Shuang Guo, Hanxiao Zhou, Hongjia Liu, Dailin Sun, Hong Chen, Li Wang, Shangwei Ning

Frontiers in Bioengineering and Biotechnology

DOI

2019

LnCeVar: a comprehensive database of genomic variations that disturb ceRNA network regulation

Peng Wang, Xin Li, Xin Li, Qiuyan Guo, Qiuyan Guo, Shangwei Ning, Shipeng Shang, Shipeng Shang, Yanxia Wang, Yanxia Wang, Hui Zhi, Ying Fang, Weitao Shen, Guangmei Zhang, Steven Xi Chen, Xia Li, Xia Li

Nucleic Acids Research

DOI

2019

Comprehensive Characterization of Somatic Mutations Impacting lncRNA Expression for Pan-Cancer

Yue Gao, Xin Li, Xin Li, Hui Zhi, Yunpeng Zhang, Yanxia Wang, Yanxia Wang, Shipeng Shang, Ying Fang, Weitao Shen, Shangwei Ning, Steven Xi Chen, Xia Li, Xia Li

Molecular Therapy — Nucleic Acids

DOI

2019

Network and Pathway-Based Analysis of Single-Nucleotide Polymorphism of miRNA in Temporal Lobe Epilepsy

Wenbiao Xiao, Yanhao Wu, Jianjian Wang, Zhaohui Luo, Lili Long, Na Deng, Shangwei Ning, Yi Zeng, Hongyu Long, Bo Xiao

Molecular Neurobiology

DOI

2019

Building the drug-GO function network to screen significant candidate drugs for myasthenia gravis

Shuang Li, Yuze Cao, Lei Li, Huixue Zhang, Xiaoyu Lu, Chunrui Bo, Xiaotong Kong, Zhaojun Liu, Lixia Chen, Peifang Liu, Yang Jiao, Jianjian Wang, Shangwei Ning, Lihua Wang

PLoS ONE

DOI

2019

MicroRNAs and nervous system diseases: network insights and computational challenges

Jianjian Wang, Yuze Cao, Xiaoyu Lu, Tianfeng Wang, Shuang Li, Xiaotong Kong, Chunrui Bo, Jie Li, Xiaolong Wang, He‐Ping Ma, Lei Li, Huixue Zhang, Shangwei Ning, Lihua Wang

Briefings in Bioinformatics

DOI

2019

Global pathway view analysis of microRNA clusters in myasthenia gravis

Chunrui Bo, Jianjian Wang, Huixue Zhang, Yuze Cao, Xiaoyu Lu, Tianfeng Wang, Yu Wang, Shuang Li, Xiaotong Kong, Xue-Song Sun, Zhaojun Liu, Shangwei Ning, Lihua Wang

Molecular Medicine Reports

DOI

2018

LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low- and high-throughput experiments

Peng Wang, Xin Li, Xin Li, Qiuyan Guo, Qiuyan Guo, Ying Fang, Ying Fang, Xueyan Ma, Hui Zhi, Dianshuang Zhou, Weitao Shen, Weisha Liu, Lihua Wang, Yunpeng Zhang, Shangwei Ning, Xia Li, Xia Li

Nucleic Acids Research

DOI

2018

Lnc2Cancer v2.0: updated database of experimentally supported long non-coding RNAs in human cancers

Yue Gao, Peng Wang, Yanxia Wang, Xueyan Ma, Hui Zhi, Dianshuang Zhou, Xin Li, Xin Li, Ying Fang, Weitao Shen, Yingqi Xu, Shipeng Shang, Li Wang, Lihua Wang, Xia Li, Li Wang, Shangwei Ning, Xia Li, Xia Li

Nucleic Acids Research

DOI

2018

Inferences of individual drug responses across diverse cancer types using a novel competing endogenous RNA network

Yan Zhang, Xin Li, Xin Li, Dianshuang Zhou, Hui Zhi, Peng Wang, Yue Gao, Maoni Guo, Ming Yue, Yanxia Wang, Weitao Shen, Shangwei Ning, Yixue Li, Xia Li, Xia Li

Molecular Oncology

DOI

2018

Lung Cancer and Pulmonary Embolism: What Is the Relationship? A Review

Yupeng Li, Yu Shang, Wenwen Wang, Shangwei Ning, Hong Chen

Journal of Cancer

DOI

2017

基于基因功能相似性预测小分子药物与lncRNA的相关关系

吕莹丽，王世缘，闫琰，宁尚伟，付强，杨磊

《哈尔滨医科大学学报》

2017

MSDD: a manually curated database of experimentally supported associations among miRNAs, SNPs and human diseases

Ming Yue, Dianshuang Zhou, Hui Zhi, Peng Wang, Yan Zhang, Yan Zhang, Maoni Guo, Maoni Guo, Xin Li, Xin Li, Yanxia Wang, Yunpeng Zhang, Yunpeng Zhang, Shangwei Ning, Xia Li, Xia Li

Nucleic Acids Research

DOI

2017

Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease

Hui Zhi, Xin Li, Xin Li, Peng Wang, Baoqing Gao, Baoqing Gao, Dianshuang Zhou, Yan Zhang, Maoni Guo, Ming Yue, Weitao Shen, Shangwei Ning, 金连弘, Xia Li, Xia Li

Nucleic Acids Research

DOI

2017

Corrigendum to “Detecting Key Genes Regulated by miRNAs in Dysfunctional Crosstalk Pathway of Myasthenia Gravis”

Yuze Cao, Jianjian Wang, Huixue Zhang, Qinghua Tian, Lixia Chen, Shangwei Ning, Peifang Liu, Xue-Song Sun, Xiaoyu Lu, Chang Song, Shuai Zhang, Bo Xiao, Lihua Wang

BioMed Research International

DOI

2017

Autophagy-related gene expression is an independent prognostic indicator of glioma

Huixue Zhang, Xiaoyan Lu, Ning Wang, Jianjian Wang, Yuze Cao, Tianfeng Wang, Xueling Zhou, Yang Jiao, Lei Yang, Xiaokun Wang, Lin Cong, Jianlong Li, Jie Li, He‐Ping Ma, Yonghui Pan, Shangwei Ning, Lihua Wang

Oncotarget

DOI

2017

Construction of an miRNA-regulated drug-pathway network reveals drug repurposing candidates for myasthenia gravis

Yuze Cao, Xiaoyan Lu, Jianjian Wang, Huixue Zhang, Zhaojun Liu, Si Xu, Tianfeng Wang, Shangwei Ning, Bo Xiao, Lihua Wang

International Journal of Molecular Medicine

DOI

2017

Genome-Wide DNA Methylation Patterns Analysis of Noncoding RNAs in Temporal Lobe Epilepsy Patients

Wenbiao Xiao, Yuze Cao, Hongyu Long, Zhaohui Luo, Shuyu Li, Na Deng, Jianjian Wang, Xiaoyan Lu, Tianfeng Wang, Shangwei Ning, Lihua Wang, Bo Xiao

Molecular Neurobiology

DOI

2017

Response to: Comment on “Detecting Key Genes Regulated by miRNAs in Dysfunctional Crosstalk Pathway of Myasthenia Gravis”

Yuze Cao, Jianjian Wang, Huixue Zhang, Qinghua Tian, Lixia Chen, Shangwei Ning, Peifang Liu, Xue-Song Sun, Xiaoyu Lu, Chang Song, Shuai Zhang, Bo Xiao, Lihua Wang

BioMed Research International

DOI

2017

Dihydroartemisinin-regulated mRNAs and lncRNAs in chronic myeloid leukemia

Xiang Li, Yue Gao, Qiang Zhang, Nan Hu, Dong Chul Han, Shangwei Ning, Zhuo Ao

Oncotarget

DOI

2017

LncNetP, a systematical lncRNA prioritization approach based on ceRNA and disease phenotype association assumptions

Chaohan Xu, Yanyan Ping, Hongying Zhao, Shangwei Ning, Peng Xia, Weida Wang, Linyun Wan, Jie Li, Li Zhang, Lei Yu, Yun Xiao

Oncotarget

DOI

2016

浅谈医学院校生物信息学专业青年教师规范培训模式的建立

王乐天，肖云，宁尚伟，杨力明

《中国校外教育》

2016

Improved method for prioritization of disease associated lncRNAs based on ceRNA theory and functional genomics data

Peng Wang, Qiuyan Guo, Yue Gao, Hui Zhi, Yan Zhang, Yue Liu, Jizhou Zhang, Ming Yue, Maoni Guo, Shangwei Ning, Guangmei Zhang, Xia Li

Oncotarget

DOI

2016

Immunoglobulin superfamily genes are novel prognostic biomarkers for breast cancer

Yue Li, Maoni Guo, Zhenkun Fu, Peng Wang, Yan Zhang, Yue Gao, Ming Yue, Shangwei Ning, Dianjun Li

Oncotarget

DOI

2016

NSDNA: a manually curated database of experimentally supported ncRNAs associated with nervous system diseases

Jianjian Wang, Yuze Cao, Huixue Zhang, Tianfeng Wang, Qinghua Tian, Xiaoyu Lu, Xiaoyan Lu, Xiaotong Kong, Zhaojun Liu, Ning Wang, Shuai Zhang, He‐Ping Ma, Shangwei Ning, Lihua Wang

Nucleic Acids Research

DOI

2016

LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs

Shangwei Ning, Ming Yue, Peng Wang, Yue Liu, Hui Zhi, Yan Zhang, Jizhou Zhang, Yue Gao, Maoni Guo, Dianshuang Zhou, Xin Li, Xia Li, Xia Li, Xia Li

Nucleic Acids Research

DOI

2016

Construction of a lncRNA-mediated feed-forward loop network reveals global topological features and prognostic motifs in human cancers

Shangwei Ning, Yue Gao, Peng Wang, Xiang Li, Hui Zhi, Yan Zhang, Yue Liu, Jizhou Zhang, Maoni Guo, Dong Chul Han, Xia Li

Oncotarget

DOI

2016

Identification of prognostic biomarkers in glioblastoma using a long non-coding RNA-mediated, competitive endogenous RNA network

Yuze Cao, Peng Wang, Shangwei Ning, Wenbiao Xiao, Bo Xiao, Xia Li

Oncotarget

DOI

2015

Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers

Shangwei Ning, Jizhou Zhang, Peng Wang, Hui Zhi, Jianjian Wang, Yue Liu, Yue Gao, Maoni Guo, Ming Yue, Lihua Wang, Xia Li

Nucleic Acids Research

DOI

2015

Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer

Peng Wang, Shangwei Ning, Yunpeng Zhang, Ronghong Li, Jingrun Ye, Zuxianglan Zhao, Hui Zhi, Tingting Wang, Zheng Guo, Xia Li

Nucleic Acids Research

DOI

2015

miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs

Peng Wang, Hui Zhi, Yunpeng Zhang, Yue Liu, Jizhou Zhang, Yue Gao, Maoni Guo, Shangwei Ning, Xia Li

Database

DOI

2015

Detecting Key Genes Regulated by miRNAs in Dysfunctional Crosstalk Pathway of Myasthenia Gravis

Yuze Cao, Jianjian Wang, Huixue Zhang, Qinghua Tian, Lixia Chen, Shangwei Ning, Peifang Liu, Xue-Song Sun, Xiaoyu Lu, Chang Song, Shuai Zhang, Bo Xiao, Lihua Wang

BioMed Research International

DOI

2014

四阶段教学法在生物信息学实验课教学中的应用

宁尚伟，王君玮

《赤子(上中旬)》

2014

Identifying a Polymorphic ‘Switch’ That Influences miRNAs' Regulation of a Myasthenia Gravis Risk Pathway

Lili Yang, Jianjian Wang, Xuesong Sun, Yuze Cao, Shangwei Ning, Huixue Zhang, Lixia Chen, Ronghong Li, Qinghua Tian, Lihua Wang, Weizhi Wang, Xia Li

PLoS ONE

DOI

2014

SNP@lincTFBS: An Integrated Database of Polymorphisms in Human LincRNA Transcription Factor Binding Sites

Shangwei Ning, Zuxianglan Zhao, Jingrun Ye, Peng Wang, Hui Zhi, Ronghong Li, Tingting Wang, Jianjian Wang, Lihua Wang, Xia Li

PLoS ONE

DOI

2014

A novel reannotation strategy for dissecting DNA methylation patterns of human long intergenic non-coding RNAs in cancers

Hui Zhi, Shangwei Ning, Xiang Li, Yuyun Li, Wei Wu, Xia Li

Nucleic Acids Research

DOI

2014

Identification of a Core miRNA-Pathway Regulatory Network in Glioma by Therapeutically Targeting miR-181d, miR-21, miR-23b, β-Catenin, CBP, and STAT3

Ronghong Li, Xiang Li, Xiang Li, Shangwei Ning, Jingrun Ye, Lei Han, Chunsheng Kang, Xia Li, Xia Li

PLoS ONE

DOI

2014

LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs

Shangwei Ning, Zuxianglan Zhao, Jingrun Ye, Peng Wang, Hui Zhi, Ronghong Li, Tingting Wang, Xia Li

BMC Bioinformatics

DOI

2013

MicroRNA function and molecular mechanism in ovarian cancer

Letian Wang, Shangwei Ning, Yixue Li

Int J Genet

DOI

2013

A global map for dissecting phenotypic variants in human lincRNAs

Shangwei Ning, Peng Wang, Jingrun Ye, Xiang Li, Ronghong Li, Ronghong Li, Zuxianglan Zhao, Xiao Huo, Li Wang, Feng Li, Xia Li, Xia Li

European Journal of Human Genetics

DOI

2013

mirTarPri: Improved Prioritization of MicroRNA Targets through Incorporation of Functional Genomics Data

Peng Wang, Shangwei Ning, Qianghu Wang, Ronghong Li, Jingrun Ye, Zuxianglan Zhao, Yan Li, Teng Huang, Xia Li

PLoS ONE

DOI

2012

Prioritising risk pathways of complex human diseases based on functional profiling

Yan Li, Yan Li, Teng Huang, Yun Xiao, Shangwei Ning, Peng Wang, Qianghu Wang, Xin Chen, Chaohan Xu, Donglin Sun, Xia Li, Yixue Li, Yixue Li

European Journal of Human Genetics

DOI

2012

Community of protein complexes impacts disease association

Qianghu Wang, Weisha Liu, Shangwei Ning, Jingrun Ye, Teng Huang, Yan Li, Peng Wang, Hongbo Shi, Xia Li

European Journal of Human Genetics

DOI

2011

A novel method to quantify gene set functional association based on gene ontology

Sali Lv, Yan Li, Qianghu Wang, Shangwei Ning, Teng Huang, Peng Wang, Jie Sun, Yan Zheng, Weisha Liu, Jing Ai, Xia Li

Journal of The Royal Society Interface

DOI

2011

Prioritizing human cancer microRNAs based on genes’ functional consistency between microRNA and cancer

Xia Li, Qianghu Wang, Yan Zheng, Sali Lv, Shangwei Ning, Jie Sun, Teng Huang, Qi‐Fan Zheng, Huan Ren, Jin Xu, Xishan Wang, Yixue Li

Nucleic Acids Research

DOI

2010

Systematic analysis of human microRNA divergence based on evolutionary emergence

Qianghu Wang, Meng Zhou, Jie Sun, Shangwei Ning, Yan Li, Li Chen, Yan Zheng, Xiang Li, Xiang Li, Sali Lv, Xia Li, Xia Li

FEBS Letters

DOI

2009

In silico detection and characteristics of novel microRNA genes in the Equus caballus genome using an integrated ab initio and comparative genomic approach

Meng Zhou, Qianghu Wang, Jie Sun, Xia Li, Liangde Xu, Haixiu Yang, Hongbo Shi, Shangwei Ning, Li Chen, Yan Li, Taotao He, Yan Zheng

Genomics

DOI

精选作品

期刊论文

EvoNiche: a comprehensive database for dissecting tumor niche dynamics and spatiotemporal evolution within the cancer ecosystem

Tumor Microenvironment Hijacks and Accelerates a Physiological Myeloid Senescence Signature Associated with Pan-Cancer Immunosuppression and Prognostic Stratification

Single-cell multi-omics dissection of RevitalAge Markers uncovers age-dependent immunotherapy resistance and druggable targets in melanoma

Machine learning and single-cell approaches identify an NAD metabolism-related signature for predicting immunotherapy outcomes

Integration of single-cell RNA-sequencing and machine learning identifies GRN and FCER1G as potential peroxisomal targets in influenza pathogenesis

Deciphering the glioblastoma microenvironmental landscape with multi-modal radiogenomics to guide prognosis and personalized therapy

Identification of lncRNAs Indicating Immune Pathway Activity for Predicting Prognosis and Immunotherapy Response in Pan‐Cancer

Integrated Single-Cell Multi-Omics Analysis Reveals That a CD8+ TPex–Monocyte Interaction Axis Coordinates Immune Infiltration in Alzheimer’s Disease

Identification of Immune&Driver Molecular Subtypes Optimizes Immunotherapy Strategies for Gastric Cancer

Dysregulation of ceRNA mechanisms across pan-cancer drives cancer progression towards acquiring metastatic potential

Metabolic and aging related gene risk score for therapeutic stratification and precision oncology in gastric cancer

A cell-specific computational framework reveals a pan-cancer hypoxia signature predicting overall survival and ICI response

LnCeVar 2.0: an updated resource and web tools for genomic variations disrupting ceRNA networks from single-cell/spatial transcriptomics data

So3D: a comprehensive three-dimensional spatial omics resource for decoding tissue architecture in physiology and disease

DNA methylation heterogeneity in complex tumor microenvironment: Quantitative methods, influencing factors, and clinical implications

ISENICS: a model for identifying senescent immune cells and samples and characterization of their roles in tumor microenvironment

A core driver gene set identified based on geMER reveals its potential driver mechanism in pan-cancer

ImmuProgML: machine learning-based dissection of cancer-immune dynamics during tumor progression to improve immunotherapy

A comprehensive database for identifying and interpreting ctDNA driver genes and variants in cancer

Dynamic changes of synergy relationship between lncRNA and immune checkpoint in cancer progression

NetLnc: A Network-Based Computational Framework to Identify Immune Checkpoint-Related lncRNAs for Immunotherapy Response in Melanoma

PD-1 regulates the anti-tumor immune function of macrophages through JAK2-STAT3 signaling pathway in colorectal cancer tumor microenvironment

Comprehensive characterization of respiratory genes based on a computational framework in pan-cancer to develop stratified treatment strategies

CNV-mediated dysregulation of the ceRNA network mechanism revealed heterogeneity in diffuse and intestinal gastric cancers

RPL22L1 fosters malignant features of cervical cancer via the modulation of DUSP6-ERK axis

Common biomarkers of idiopathic pulmonary fibrosis and systemic sclerosis based on WGCNA and machine learning

MRdb: a comprehensive database of univariate and multivariate Mendelian randomization with large-scale GWAS summary data

A Novel Competing Endogenous RNA Network Reveals Potential Mechanisms and Biomarkers of Chemoresistance in Lung Adenocarcinoma

Identification and validation of lncRNA mutation hotspot SNPs associated with myasthenia gravis susceptibility

Single-Cell and Bulk Transcriptomics Reveal the Immunosenescence Signature for Prognosis and Immunotherapy in Lung Cancer

LnCeCell 2.0: an updated resource for lncRNA-associated ceRNA networks and web tools based on single-cell and spatial transcriptomics sequencing data

AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs

Comprehensive quantitative radiogenomic evaluation reveals novel radiomic subtypes with distinct immune pattern in glioma

Role of ferroptosis in neuroimmunity and neurodegeneration in multiple sclerosis revealed by multi‐omics data

The landscape of immune checkpoint-related long non-coding RNAs core regulatory circuitry reveals implications for immunoregulation and immunotherapy responses

DNA methylation heterogeneity attributable to a complex tumor immune microenvironment prompts prognostic risk in glioma

A comprehensive database of exosome molecular biomarkers and disease-gene associations

Metabolic-Related Gene Prognostic Index for Predicting Prognosis, Immunotherapy Response, and Candidate Drugs in Ovarian Cancer

Identification of cuproptosis-related diagnostic biomarkers in idiopathic pulmonary fibrosis

MSGD: a manually curated database of genomic, transcriptomic, proteomic and drug information for multiple sclerosis

Proteomic characterization of epithelial ovarian cancer delineates molecular signatures and therapeutic targets in distinct histological subtypes

Tumor biology, immune infiltration and liver function define seven hepatocellular carcinoma subtypes linked to distinct drivers, survival and drug response

Identifying immune checkpoint-related lncRNA biomarkers for immunotherapy response and prognosis in cancers

Reconstructing the immunosenescence core pathway reveals global characteristics in pan-cancer

CRS: a circadian rhythm score model for predicting prognosis and treatment response in cancer patients

Pan-cancer transcriptomic analysis identified six classes of immunosenescence genes revealed molecular links between aging, immune system and cancer

Radiogenomic analysis of prediction HER2 status in breast cancer by linking ultrasound radiomic feature module with biological functions

Immune Pathways with Aging Characteristics Improve Immunotherapy Benefits and Drug Prediction in Human Cancer

LncPCD: a manually curated database of experimentally supported associations between lncRNA-mediated programmed cell death and diseases

基于GEO数据库分析支气管肺发育不良发生的关键基因及通路

Construction of a ferroptosis-related signature based on seven lncRNAs for prognosis and immune landscape in clear cell renal cell carcinoma

The dynamic dysregulated network identifies stage-specific markers during lung adenocarcinoma malignant progression and metastasis

LncTarD 2.0: an updated comprehensive database for experimentally-supported functional lncRNA–target regulations in human diseases

CellTracer: a comprehensive database to dissect the causative multilevel interplay contributing to cell development trajectories

AgingBank: a manually curated knowledgebase and high-throughput analysis platform that provides experimentally supported multi-omics data relevant to aging in multiple species

Identifying enhancer-driven subtype-specific prognostic markers in breast cancer based on multi-omics data

Human RNA Modifications Disease Database (HRMDD): A web resource for the molecular and clinical landscape of RNA modifications in human diseases

PD-L1-Mediated Immunosuppression in Hepatocellular Carcinoma: Relationship with Macrophages Infiltration and Inflammatory Response Activity

Comprehensive characterization of clonality of driver genes revealing their clinical relevance in colorectal cancer

Functional regulations between genetic alteration-driven genes and drug target genes acting as prognostic biomarkers in breast cancer

Enhancer methylation dynamics drive core transcriptional regulatory circuitry in pan-cancer

RNA2Immune: A Database of Experimentally Supported Data Linking Non-Coding RNA Regulation to the Immune System

Prioritizing Cancer lncRNA Modulators via Integrated lncRNA-mRNA Network and Somatic Mutation Data

S100A12 as Biomarker of Disease Severity and Prognosis in Patients With Idiopathic Pulmonary Fibrosis

Identification and Characterization of Immunogene-Related Alternative Splicing Patterns and Tumor Microenvironment Infiltration Patterns in Breast Cancer

An 8-ferroptosis-related genes signature from Bronchoalveolar Lavage Fluid for prognosis in patients with idiopathic pulmonary fibrosis

Competitive endogenous RNA network and pathway-based analysis of LncRNA single-nucleotide polymorphism in myasthenia gravis

Identifying and characterizing lincRNA genomic clusters reveals its cooperative functions in human cancer

Identification of miRNA-mRNA network and immune-related gene signatures in IgA nephropathy by integrated bioinformatics analysis

CD247, a Potential T Cell–Derived Disease Severity and Prognostic Biomarker in Patients With Idiopathic Pulmonary Fibrosis

LncACTdb 3.0: an updated database of experimentally supported ceRNA interactions and personalized networks contributing to precision medicine

Identification of the regulatory role of lncRNA HCG18 in myasthenia gravis by integrated bioinformatics and experimental analyses

Epigenome signature as an immunophenotype indicator prompts durable clinical immunotherapy benefits in lung adenocarcinoma

Inferring SARS-CoV-2 functional genomics from viral transcriptome with identification of potential antiviral drugs and therapeutic targets

DNA Methylation Dynamics of Long Noncoding RNA During Human Fetal Development

Construction of lncRNA-Mediated ceRNA Network for Investigating Immune Pathogenesis of Ischemic Stroke

MeImmS: Predict Clinical Benefit of Anti-PD-1/PD-L1 Treatments Based on DNA Methylation in Non-small Cell Lung Cancer

Construction of a TF–miRNA–gene feed-forward loop network predicts biomarkers and potential drugs for myasthenia gravis