蒋庆华｜哈尔滨医科大学｜学者主页

2026

From the Dark Genome to Immunotherapy Targets: Artificial Intelligence Enables the Identification of Noncanonical Neoantigens

Juan Xu, Yangyang Cai, J Q Guo, Dezhong Lv, Yingying Ma, Wenjun Mao, Qinghua Jiang, Yongsheng Li

Research

2026

AI-driven computational methods and benchmarking for T-cell antigen identification

Yang Deng, Jinhao Que, Guangfu Xue, Yideng Cai, Wenyi Yang, Yilin Wang, Yi Hui, Zuxiang Wang, Yu Lin, Wenyang Zhou, Zhaochun Xu, Qinghua Jiang, Haoxiu Sun

Briefings in Bioinformatics

DOI

2026

Systematic evaluation of computational methods for cell segmentation

Rongrong Yang, Guangfu Xue, Zuxiang Wang, Yideng Cai, Wenyi Yang, Jinhao Que, Renjie Tan, Han Sun, P. Wang, Zhaochun Xu, Qinghua Jiang, Wenyang Zhou

Briefings in Bioinformatics

DOI

2025

Identifying T cell antigen at the atomic level with graph convolutional network

Jinhao Que, Guangfu Xue, Tao Wang, Xiyun Jin, Zuxiang Wang, Yideng Cai, Wenyi Yang, Meng Luo, Qian Ding, Jinwei Zhang, Yilin Wang, Yuexin Yang, Fenglan Pang, Yi Hui, Zheng Wei, Jun Xiong, Shouping Xu, Lin Yi, Haoxiu Sun, Pingping Wang, Zhaochun Xu, Qinghua Jiang

Nature Communications

DOI

2025

Multi-omics-guided characterization of neoantigens improves patient stratification and potentiates combinatorial immunotherapy in glioma

Yingying Ma, Yangyang Cai, Jiaxin Yang, Zheng Zhao, Zefeng Chen, Dezhong Lv, Jiaxin Yu, Changbo Yang, Kefan Liu, Mengqian Zeng, Han Guo, Kang Xu, Qinghua Jiang, Hang Yin, Juan Xu, Yongsheng Li

Cell Reports

DOI

2025

Pan-cancer neural regulation pattern with implications for patient stratification and immunotherapy

Yueying Gao, Jiyu Guo, Wenyi Yang, Kefan Liu, Qingyi Yang, Si Li, Dezhong Lv, Yangyang Cai, Kang Xu, Weiwei Zhou, Qinghua Jiang, Juan Xu, Yongsheng Li, Haoxiu Sun

Molecular Therapy — Nucleic Acids

DOI

2025

TriCLFF: a multi-modal feature fusion framework using contrastive learning for spatial domain identification

Fenglan Pang, Guangfu Xue, Wenyi Yang, Yideng Cai, Jinhao Que, Haoxiu Sun, Pingping Wang, Shuaiyu Su, Xiyun Jin, Qian Ding, Zuxiang Wang, Meng Luo, Yuexin Yang, Lin Yi, Renjie Tan, Yusong Liu, Zhaochun Xu, Qinghua Jiang

Briefings in Bioinformatics

DOI

2024

A comparative analysis of TCR immune repertoire in COVID-19 patients.

Xiao Zhu, Enze Ma, Ke Ning, Xiangyan Feng, Wei Quan, Fei Wang, Chaoqun Zhu, Yuanjun Ma, Yucui Dong, Qinghua Jiang

Human Immunology

DOI

2024

Deciphering cell–cell communication at single-cell resolution for spatial transcriptomics with subgraph-based graph attention network

Wenyi Yang, Pingping Wang, Shouping Xu, Tao Wang, Meng Luo, Yideng Cai, Chang Xu, Guangfu Xue, Jinhao Que, Qian Ding, Xiyun Jin, Yuexin Yang, Fenglan Pang, Boran Pang, Yi Lin, Huan Nie, Zhaochun Xu, Yong Hua Ji, Qinghua Jiang

Nature Communications

DOI

2024

stSNV: a comprehensive resource of SNVs in spatial transcriptome

Changbo Yang, Yujie Liu, Xiaohua Wang, Qing Jia, Yuqi Fan, Zhenglin Lu, Jingyi Shi, Zhaoxin Liu, Gengdong Chen, Jianing Li, Weijian Lu, Weiwei Zhou, Dezhong Lv, Haozhe Zou, Juan Xu, Yongsheng Li, Qinghua Jiang, Tao Wang, Tingting Shao

Nucleic Acids Research

DOI

2024

Supplementary Figures S1-S8 from The Deep Learning Framework iCanTCR Enables Early Cancer Detection Using the T-cell Receptor Repertoire in Peripheral Blood

Yideng Cai, Meng Luo, Wenyi Yang, Chang Xu, Pingping Wang, Guangfu Xue, Xiyun Jin, Rui Cheng, Jinhao Que, Wenyang Zhou, Boran Pang, Shouping Xu, Yu Li, Qinghua Jiang, Zhaochun Xu

DOI

2024

The Deep Learning Framework iCanTCR Enables Early Cancer Detection Using the T-cell Receptor Repertoire in Peripheral Blood

Yideng Cai, Meng Luo, Wenyi Yang, Chang Xu, Pingping Wang, Guangfu Xue, Xiyun Jin, Rui Cheng, Jinhao Que, Wenyang Zhou, Boran Pang, Shouping Xu, Yu Li, Qinghua Jiang, Zhaochun Xu

Cancer Research

DOI

2024

Functional requirement of alternative splicing in epithelial-mesenchymal transition of pancreatic circulating tumor

Lixing Xiao, Haoxiu Sun, Rui Cheng, Rongrong Yang, Xiyun Jin, Zhaochun Xu, Yideng Cai, Yuexin Yang, Fenglan Pang, Guangfu Xue, Pingping Wang, Qinghua Jiang, Huan Nie

Molecular Therapy — Nucleic Acids

DOI

2024

Dimension reduction, cell clustering, and cell–cell communication inference for single-cell transcriptomics with DcjComm

Qian Ding, Wenyi Yang, Guangfu Xue, Hongxin Liu, Yideng Cai, Jinhao Que, Xiyun Jin, Meng Luo, Fenglan Pang, Yuexin Yang, Yi Lin, Yusong Liu, Haoxiu Sun, Renjie Tan, Pingping Wang, Zhaochun Xu, Qinghua Jiang

Genome biology

DOI

2023

An interpretable single-cell RNA sequencing data clustering method based on latent Dirichlet allocation

Qi Yang, Zhao-Chun Xu, Wen-Yang Zhou, Pingping Wang, Qinghua Jiang, Liran Juan

Briefings Bioinform.

DOI

2023

Identification of shared characteristics in tumor-infiltrating T cells across 15 cancers

Xiyun Jin, Yideng Cai, Guangfu Xue, Jinhao Que, Rui Cheng, Yuexin Yang, Lixing Xiao, Xiaoyu Lin, Chang Xu, Pingping Wang, Zhaochun Xu, Huan Nie, Qinghua Jiang

Molecular Therapy — Nucleic Acids

DOI

2022

Global Characterization of Peripheral B Cells in Parkinson’s Disease by Single-Cell RNA and BCR Sequencing

Pingping Wang, Meng Luo, Wen-Yang Zhou, Xi-Yun Jin, Zhao-Chun Xu, Shi Yan, Yiqun Li, Chang Xu, Rui Cheng, Yan Huang, Xiaoyu Lin, Li-Fen Yao, Huan Nie, Qinghua Jiang

Frontiers in Immunology

DOI

2022

MutCov: A pipeline for evaluating the effect of mutations in spike protein on infectivity and antigenicity of SARS-CoV-2

Wen-Yang Zhou, Chang Xu, Meng Luo, Pingping Wang, Zhao-Chun Xu, Guang-Fu Xue, Xi-Yun Jin, Yan Huang, Yiqun Li, Huan Nie, Qinghua Jiang, A. Anashkina

Comput. Biol. Medicine

DOI

2022

DeepCCI: a deep learning framework for identifying cell–cell interactions from single-cell RNA sequencing data

Wenyi Yang, Zhao-Chun Xu, Meng Luo, Yi-Deng Cai, Chang Xu, Pingping Wang, Songren Wei, Guang-Fu Xue, Xi-Yun Jin, Rui Cheng, Jin-Hao Que, Wen-Yang Zhou, Feng-Lan Pang, Huan Nie, Qinghua Jiang

bioRxiv

DOI

2022

DeepST: identifying spatial domains in spatial transcriptomics by deep learning

Chang Xu, Xi-Yun Jin, Songren Wei, Pingping Wang, Meng Luo, Zhao-Chun Xu, Wenyi Yang, Yi-Deng Cai, Li-Xing Xiao, Xiaoyu Lin, Hongxin Liu, Rui Cheng, Feng-Lan Pang, Rui Chen, Xi Su, Ying Hu, Guohua Wang, Qinghua Jiang

Nucleic Acids Research

DOI

2022

Regional transcriptional vulnerability to basal forebrain functional dysconnectivity in mild cognitive impairment patients.

Peng Ren, Wen-Yu Ding, Siyang Li, Guiyou Liu, Meng Luo, Wen-Yang Zhou, Rui Cheng, Yiqun Li, Pingping Wang, Zhi-Peng Li, Li-Fen Yao, Qinghua Jiang, Xia Liang

Neurobiology of Disease

DOI

2022

Identification of alternative splicing-derived cancer neoantigens for mRNA vaccine development

Rui Cheng, Zhao-Chun Xu, Meng Luo, Pingping Wang, Huimin Cao, Xi-Yun Jin, Wen-Yang Zhou, Li-Xing Xiao, Qinghua Jiang

Briefings Bioinform.

DOI

2022

Network analysis between neuron dysfunction and neuroimmune response based on neural single-cell transcriptome of COVID-19 patients

Xiaoyu Lin, Huan Nie, Ran Tang, Pingping Wang, Xi-Yun Jin, Qinghua Jiang, Fang Han, N. Chen, Yu Li

Comput. Biol. Medicine

DOI

2022

CBLRR: a cauchy-based bounded constraint low-rank representation method to cluster single-cell RNA-seq data

Qian Ding, Wenyi Yang, Meng Luo, Chang Xu, Zhao-Chun Xu, Feng-Lan Pang, Yi-Deng Cai, A. S. Anashkina, Xi Su, Na Chen, Qinghua Jiang

Briefings Bioinform.

DOI

2021

COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas

Xian-Wen Ren, W. Wen, Xiao-Ying Fan, W. Hou, B. Su, Pengfei Cai, Jiesheng Li, Yang Liu, F. Tang, Fan Zhang, Yu Yang, Jiangping He, Wenji Ma, Jingjing He, Pingping Wang, Qi-Qi Cao, Fangjin Chen, Yuqing Chen, Xuelian Cheng, Guohong Deng, Xi-Long Deng, Wenyu Ding, Yingmei Feng, R. Gan, Chuang Guo, Weiqiang Guo, Shuai He, Chen Jiang, Juanran Liang, Yiming Li, Jun Lin, Y. Ling, Haofei Liu, Jianwei Liu, Nianping Liu, Shu-Qiang Liu, Meng Luo, Qiang Ma, Q. Song, Wujianan Sun, Gao-Xiang Wang, Feng Wang, Ying Wang, Xiao-Feng Wen, Qian Wu, Gang Xu, Xiaowei Xie, Xin-Xin Xiong, Xudong Xing, Hao Xu, C. Yin, Dong-Dong Yu, Kezhuo Yu, Jin Yuan, Biao Zhang, Peipei Zhang, Tong Zhang, Jin-Cun Zhao, Pei-Ran Zhao, Jian-Feng Zhou, Wei Zhou, Su-Juan Zhong, Xiaosong Zhong, Shu-Ye Zhang, Lin Zhu, P. Zhu, Bin Zou, J. Zou, Z. Zuo, F. Bai, Xi Huang, P. Zhou, Qinghua Jiang, Zhiwei Huang, Jin-Xin Bei, Lai Wei, X. Bian, Xin-Dong Liu, T. Cheng, Xiang-Pan Li, Ping-Sen Zhao, Fu-Sheng Wang, Hong-Yang Wang, Bing Su, Zheng Zhang, K. Qu, Xiao-Qun Wang, Jie-Kai Chen, R. Jin, Ze-Min Zhang

Cell

DOI

2021

Single-cell transcriptome and TCR profiling reveal activated and expanded T cell populations in Parkinson’s disease

Pingping Wang, Li-Fen Yao, Meng Luo, Wen-Yang Zhou, Xi-Yun Jin, Zhao-Chun Xu, Shi Yan, Yiqun Li, Chang Xu, Rui Cheng, Yan Huang, Xiaoyu Lin, Kexin Ma, Huimin Cao, Hongxin Liu, Guang-Fu Xue, Fangzhu Han, Huan Nie, Qinghua Jiang

Cell Discovery

DOI

2021

Global characterization of B cell receptor repertoire in COVID-19 patients by single-cell V(D)J sequencing

Xi-Yun Jin, Wen-Yang Zhou, Meng Luo, Pingping Wang, Zhao-Chun Xu, Kexin Ma, Huimin Cao, Chang Xu, Yan Huang, Rui Cheng, Li-Xing Xiao, Xiaoyu Lin, Feng-Lan Pang, Yiqun Li, Huan Nie, Qinghua Jiang

Briefings Bioinform.

DOI

2021

Comprehensive analysis of partial methylation domains in colorectal cancer based on single-cell methylation profiles

Yan Huang, Pingping Wang, Wen-Yang Zhou, Meng Luo, Zhao-Chun Xu, Rui Cheng, Chang Xu, Xi-Yun Jin, Yiqun Li, Qinghua Jiang

Briefings Bioinform.

DOI

2021

A pan-cancer analysis of alternative splicing of splicing factors in 6904 patients

Rui Cheng, Li-Xing Xiao, Wen-Yang Zhou, Xi-Yun Jin, Zhao-Chun Xu, Chang Xu, Pingping Wang, Meng Luo, Mengyun Wang, Kexin Ma, Huimin Cao, Yan Huang, Xiaoyu Lin, Feng-Lan Pang, Yiqun Li, Qinghua Jiang

Oncogene

DOI

2021

Alternative splicing associated with cancer stemness in kidney renal clear cell carcinoma

Li-Xing Xiao, Guoying Zou, Rui Cheng, Pingping Wang, Kexin Ma, Huimin Cao, Wen-Yang Zhou, Xi-Yun Jin, Zhao-Chun Xu, Yan Huang, Xiaoyu Lin, Huan Nie, Qinghua Jiang

BMC Cancer

DOI

2021

Identification of potential vaccine targets for COVID‐19 by combining single‐cell and bulk TCR sequencing

Pingping Wang, Zhao-Chun Xu, Wen-Yang Zhou, Xi-Yun Jin, Chang Xu, Meng Luo, Kexin Ma, Huimin Cao, Yan Huang, Xiaoyu Lin, Feng-Lan Pang, Yiqun Li, Qinghua Jiang

Clinical and Translational Medicine

DOI

2021

Impact of mutations in SARS-COV-2 spike on viral infectivity and antigenicity

Wen-Yang Zhou, Chang Xu, Pingping Wang, A. S. Anashkina, Qinghua Jiang

Briefings Bioinform.

DOI

2021

DLpTCR: an ensemble deep learning framework for predicting immunogenic peptide recognized by T cell receptor

Zhao-Chun Xu, Meng Luo, Weizhong Lin, Guang-Fu Xue, Pingping Wang, Xi-Yun Jin, Chang Xu, Wen-Yang Zhou, Yi-Deng Cai, Wenyi Yang, Huan Nie, Qinghua Jiang

Briefings Bioinform.

DOI

2021

N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation

Wen-Yang Zhou, Chang Xu, Pingping Wang, Meng Luo, Zhao-Chun Xu, Rui Cheng, Xi-Yun Jin, Yu Guo, Guang-Fu Xue, Liran Juan, A. Anashkina, Huan Nie, Qinghua Jiang

Frontiers in Cell and Developmental Biology

DOI

2020

Comprehensive Analysis of Copy Number Variations in Kidney Cancer by Single-Cell Exome Sequencing

Wen-Yang Zhou, Fan Yang, Zhao-Chun Xu, Meng Luo, Pingping Wang, Yu Guo, Huan Nie, Li-Fen Yao, Qinghua Jiang

Frontiers in Genetics

DOI

2020

Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients

Xiang-Juan Ren, W. Wen, Xiang-Rong Fan, W. Hou, B. Su, Pengfei Cai, Jing Li, Yang Liu, Fu-Chou Tang, Fan Zhang, Ying Yang, J. He, Wei-Rui Ma, Pingping Wang, Q. Cao, F. Chen, Yu-Hong Chen, X. Cheng, Guohong Deng, X. Deng, W. Ding, Y. Feng, R. Gan, Chuang Guo, W. Guo, Su-Hua He, Chen Jiang, Jin-Yi Liang, Ying-Ting Li, Jun Lin, Y. Ling, Hong-Chao Liu, J.-B. Liu, Nianping Liu, Meng Luo, Qiu-Xiang Ma, Q. Song, W. Sun, Gang Wang, F. Wang, Yin-Juan Wang, Xin-Chen Wen, Qian Wu, G. Xu, X. Xie, X. Xiong, X. Xing, H. Xu, C. Yin, D. Yu, Kai-Kai Yu, Ji-Min Yuan, Bin Zhang, Tao Zhang, Jing-Xian Zhao, P. Zhao, Jie-Jun Zhou, W. Zhou, S. Zhong, Xiaosong Zhong, Shu-Tian Zhang, Lian-Bang Zhu, P. Zhu, Bin Zou, J. Zou, Z. Zuo, F. Bai, Xiu-Ting Huang, X. Bian, P. Zhou, Qinghua Jiang, Zhiwei Huang, Jin-Xin Bei, Lai Wei, X. Liu, T. Cheng, Xuedond Li, Hong-Yang Wang, Zhao Zhang, K. Qu, Xiao-Jue Wang, Jie-Kai Chen, R. Jin

bioRxiv

DOI

2020

PGsim: A Comprehensive and Highly Customizable Personal Genome Simulator

Liran Juan, Yongtian Wang, Jingyi Jiang, Qi Yang, Qinghua Jiang, Ya-Dong Wang

Frontiers in Bioengineering and Biotechnology

DOI

2020

An Information Gain-based Method for Evaluating the Classification Power of Features Towards Identifying Enhancers

Tianjiao Zhang, Rongjie Wang, Qinghua Jiang, Ya-Dong Wang

DOI

2020

Identification of sub-Golgi protein localization by use of deep representation learning features

Zhi-Bin Lv, Pingping Wang, Quan Zou, Qinghua Jiang

Bioinform.

DOI

2020

ERDS-Exome: A Hybrid Approach for Copy Number Variant Detection from Whole-Exome Sequencing Data

Renjie Tan, Jixuan Wang, Xiaoliang Wu, Liran Juan, Tianjiao Zhang, Rui Ma, Qing Zhan, Tao Wang, Shuilin Jin, Qinghua Jiang, Ya-Dong Wang

IEEE/ACM Transactions on Computational Biology & Bioinformatics

DOI

2020

Comprehensive analysis of TCR repertoire in COVID-19 using single cell sequencing

Pingping Wang, Xi-Yun Jin, Wen-Yang Zhou, Meng Luo, Zhao-Chun Xu, Chang Xu, Yiqun Li, Kexin Ma, Huimin Cao, Y. Huang, Guang-Fu Xue, Shuilin Jin, Huan Nie, Qinghua Jiang

Genomics

DOI

2020

Single cell RNA and immune repertoire profiling of COVID-19 patients reveal novel neutralizing antibody

Fang Li, Meng Luo, Wen-Yang Zhou, Jin-Liang Li, Xi-Yun Jin, Zhao-Chun Xu, Liran Juan, Zheng Zhang, Yu-Ou Li, Renqiang Liu, Yiqun Li, Chang Xu, Kexin Ma, Huimin Cao, Jing-Wei Wang, Pingping Wang, Z. Bu, Qinghua Jiang

Protein & Cell

DOI

2020

Prediction of transcription factors binding events based on epigenetic modifications in different human cells.

Yan Huang, Dianshuang Zhou, Yihan Wang, Xing-Da Zhang, Mu Su, Cong Wang, Zhongyi Sun, Qinghua Jiang, Baoqing Sun, Yan Zhang

Epigenomics

DOI

2019

SCIA: A Novel Gene Set Analysis Applicable to Data With Different Characteristics

Yiqun Li, Ying Wu, Xiaohan Zhang, Yun-Fan Bai, Luqman Muhammad Akthar, Xin Lu, M. Shi, Jian-Xiang Zhao, Qinghua Jiang, Yu Li

Frontiers in Genetics

DOI

2019

Supplementary document of “ A learning-based framework for miRNA-disease association identification using neural networks ”

Jia-Jie Peng, Weiwei Hui, Qianqian Li, Bolin Chen, Jian-Ye Hao, Qinghua Jiang, Xue-Qun Shang, Zhongyu Wei

2019

SpliVert: A Protein Multiple Sequence Alignment Refinement Method Based on Splitting-Splicing Vertically.

Qing Zhan, Yi-Lei Fu, Qinghua Jiang, Bo Liu, Jia-Jie Peng, Ya-Dong Wang

Protein Peptide Letters

DOI

2019

Computational Methods for Identifying Similar Diseases

Liang Cheng, Hengqiang Zhao, Pingping Wang, Wen-Yang Zhou, Meng Luo, Tianxing Li, Junwei Han, Shu-Lin Liu, Qinghua Jiang

Molecular Therapy: Nucleic Acids

DOI

2019

ProbPFP: a multiple sequence alignment algorithm combining hidden Markov model optimized by particle swarm optimization with partition function

Qing Zhan, Nan Wang, Shuilin Jin, Renjie Tan, Qinghua Jiang, Ya-Dong Wang

BMC Bioinformatics

DOI

2018

ProbPFP: A Multiple Sequence Alignment Algorithm Combining Partition Function and Hidden Markov Model with Particle Swarm Optimization

Qing Zhan, Nan Wang, Shuilin Jin, Renjie Tan, Qinghua Jiang, Ya-Dong Wang

IEEE International Conference on Bioinformatics and Biomedicine

DOI

2018

An online tool for measuring and visualizing phenotype similarities using HPO

Jia-Jie Peng, Hansheng Xue, Weiwei Hui, Junya Lu, Bolin Chen, Qinghua Jiang, Xue-Qun Shang, Ya-Dong Wang

BMC Genomics

DOI

2018

CircR2Disease: a manually curated database for experimentally supported circular RNAs associated with various diseases

Chun-Yan Fan, Xiujuan Lei, Zengqiang Fang, Qinghua Jiang, Fang-Xiang Wu

Database J. Biol. Databases Curation

DOI

2018

DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function

Liang Cheng, Yang Hu, Jie Sun, Meng Zhou, Qinghua Jiang

Bioinform.

DOI

2018

LncRNA2Target v2.0: a comprehensive database for target genes of lncRNAs in human and mouse

Liang Cheng, Pingping Wang, Rui Tian, Song Wang, Qinghua Guo, Meng Luo, Wen-Yang Zhou, Guiyou Liu, Hui-Jie Jiang, Qinghua Jiang

Nucleic Acids Res.

DOI

2018

EWAS: epigenome-wide association study software 2.0

Jing Xu, Linna Zhao, Di Liu, Simeng Hu, Xiuling Song, Jin Li, Hongchao Lv, Lian Duan, Ming-Ming Zhang, Qinghua Jiang, Guiyou Liu, Shuilin Jin, Mingzhi Liao, Meng Zhang, R. Feng, Fanwu Kong, Liang-De Xu, Yongshuai Jiang

Bioinform.

DOI

2017

Erratum to: InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology

Jia-Jie Peng, Hong-Xiang Li, Yong-Zhuang Liu, Liran Juan, Qinghua Jiang, Ya-Dong Wang, Jin Chen

BMC Genomics

DOI

2017

The Complexity of Promoter Regions Based on a Vector Topological Entropy

Shuilin Jin, Zhuo Wang, Junyu Lin, Jia Wang, Xiurui Zhang, Renjie Tan, Chuan-xin Zhang, Zhe Wang, Wanqian Guo, Yang Hu, Li Xu, Lejun Zhang, Guiyou Liu, Qinghua Jiang

DOI

2017

DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data

Zhuo Wang, Shuilin Jin, Guiyou Liu, Xiurui Zhang, Nan Wang, Deliang Wu, Yang Hu, Chiping Zhang, Qinghua Jiang, Li Xu, Ya-Dong Wang

BMC Bioinformatics

DOI

2017

Measuring disease similarity and predicting disease-related ncRNAs by a novel method

Yang Hu, Meng Zhou, Hongbo Shi, Hong Ju, Qinghua Jiang, Liang Cheng

BMC Medical Genomics

DOI

2016

ERDS-pe: A paired hidden Markov model for copy number variant detection from whole-exome sequencing data

Renjie Tan, Jixuan Wang, Xiaoliang Wu, Guoqiang Wan, Rongjie Wang, Rui Ma, Zhijie Han, Wen-Yang Zhou, Shuilin Jin, Qinghua Jiang, Ya-Dong Wang

IEEE International Conference on Bioinformatics and Biomedicine

DOI

2016

InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology

Jia-Jie Peng, Hong-Xiang Li, Yong-Zhuang Liu, Liran Juan, Qinghua Jiang, Ya-Dong Wang, Jin Chen

BMC Genomics

DOI

2016

InfDisSim: A novel method for measuring disease similarity based on information flow

Yang Hu, Meng Zhou, Hongbo Shi, Hong Ju, Qinghua Jiang, Liang Cheng

IEEE International Conference on Bioinformatics and Biomedicine

DOI

2016

Identifying Liver Cancer-Related Enhancer SNPs by Integrating GWAS and Histone Modification ChIP-seq Data

Tianjiao Zhang, Yang Hu, Xiaoliang Wu, Rui Ma, Qinghua Jiang, Ya-Dong Wang

BioMed Research International

DOI

2016

Preface

Ya-Dong Wang, Kevin Burrage, Yunlong Liu, Shinichi Morishita, Tianhai Tian, Qinghua Jiang, Jiangning Song, Guo-Hua Wang, Qian Zhu, Xiao-Hua Hu

IEEE International Conference on Bioinformatics and Biomedicine

2015

Identification Exon Skipping Events From High-Throughput RNA Sequencing Data

Yang Bai, Shufan Ji, Qinghua Jiang, Ya-Dong Wang

IEEE Transactions on Nanobioscience

DOI

2015

Bioinformatics Research and Applications

Jia-Jie Peng, Hong-Xiang Li, Yong-Zhuang Liu, Liran Juan, Qinghua Jiang, Ya-Dong Wang, Jin Chen

Lecture Notes in Computer Science

DOI

2015

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads

Xiao Zhu, H. Leung, Rongjie Wang, F. Chin, Siu-Ming Yiu, Guangri Quan, Ya-Jie Li, Rui Zhang, Qinghua Jiang, Bo Liu, Yucui Dong, Guohui Zhou, Ya-Dong Wang

BMC Bioinformatics

DOI

2015

LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data

Qinghua Jiang, Rui Ma, Jixuan Wang, Xiaoliang Wu, Shuilin Jin, Jia-Jie Peng, Renjie Tan, Tianjiao Zhang, Yu Li, Ya-Dong Wang

BMC Genomics

DOI

2014

An Evaluation of Copy Number Variation Detection Tools from Whole‐Exome Sequencing Data

Renjie Tan, Ya-Dong Wang, S. Kleinstein, Yong-Zhuang Liu, Xiaolin Zhu, Hongzhe Guo, Qinghua Jiang, A. Allen, Mingfu Zhu

Human Mutation

DOI

2014

Pathway analysis of genome-wide association study and transcriptome data highlights new biological pathways in colorectal cancer

Bao-Ku Quan, Xingsi Qi, Zhi-Hui Yu, Yongshuai Jiang, Mingzhi Liao, Guangyu Wang, R. Feng, Liangcai Zhang, Zugen Chen, Qinghua Jiang, Guiyou Liu

Zeitschrift für Induktive Abstammungs- und Vererbungslehre

DOI

2014

LncRNA2Target: a database for differentially expressed genes after lncRNA knockdown or overexpression

Qinghua Jiang, Jixuan Wang, Xiaoliang Wu, Rui Ma, Tianjiao Zhang, Shuilin Jin, Zhijie Han, Renjie Tan, Jia-Jie Peng, Guiyou Liu, Yu Li, Ya-Dong Wang

Nucleic Acids Res.

DOI

2014

An integrative approach for measuring semantic similarities using gene ontology

Jia-Jie Peng, Hong-Xiang Li, Qinghua Jiang, Ya-Dong Wang, Jin Chen

BMC Systems Biology

DOI

2014

TF2LncRNA: Identifying Common Transcription Factors for a List of lncRNA Genes from ChIP-Seq Data

Qinghua Jiang, Jixuan Wang, Ya-Dong Wang, Rui Ma, Xiaoliang Wu, Yu Li

BioMed Research International

DOI

2014

A Generalized Topological Entropy for Analyzing the Complexity of DNA Sequences

Shuilin Jin, Renjie Tan, Qinghua Jiang, Li Xu, Jia-Jie Peng, Yong Wang, Ya-Dong Wang

PLoS ONE

DOI

2011

Chromatin structure characteristics of pre-miRNA genomic sequences

Shijia Zhu, Qinghua Jiang, Guohua Wang, Bo Liu, Mingxiang Teng, Ya-Dong Wang

BMC Genomics

DOI

2010

Predicting human microRNA-disease associations based on support vector machine

Qinghua Jiang, Guohua Wang, Tianjiao Zhang, Ya-Dong Wang

IEEE International Conference on Bioinformatics and Biomedicine

DOI

2010

An approach for prioritizing disease-related microRNAs based on genomic data integration

Qinghua Jiang, Guohua Wang, Ya-Dong Wang

International Conference on BioMedical Engineering and Informatics

DOI

2010

Weighted Network-Based Inference of Human MicroRNA-Disease Associations

Qinghua Jiang, Yangyang Hao, Guohua Wang, Tianjiao Zhang, Ya-Dong Wang

2010 Fifth International Conference on Frontier of Computer Science and Technology

DOI

2010

Prioritization of disease microRNAs through a human phenome-microRNAome network

Qinghua Jiang, Yangyang Hao, Guo-Hua Wang, Liran Juan, Tianjiao Zhang, Mingxiang Teng, Yunlong Liu, Ya-Dong Wang

BMC Systems Biology

DOI

2008

miR2Disease: a manually curated database for microRNA deregulation in human disease

Qinghua Jiang, Ya-Dong Wang, Yangyang Hao, Liran Juan, Mingxiang Teng, Xinjun Zhang, Meimei Li, Guohua Wang, Yunlong Liu

Nucleic Acids Res.

DOI

精选作品

期刊论文

From the Dark Genome to Immunotherapy Targets: Artificial Intelligence Enables the Identification of Noncanonical Neoantigens

AI-driven computational methods and benchmarking for T-cell antigen identification

Systematic evaluation of computational methods for cell segmentation

Identifying T cell antigen at the atomic level with graph convolutional network

Multi-omics-guided characterization of neoantigens improves patient stratification and potentiates combinatorial immunotherapy in glioma

Pan-cancer neural regulation pattern with implications for patient stratification and immunotherapy

TriCLFF: a multi-modal feature fusion framework using contrastive learning for spatial domain identification

A comparative analysis of TCR immune repertoire in COVID-19 patients.

Deciphering cell–cell communication at single-cell resolution for spatial transcriptomics with subgraph-based graph attention network

stSNV: a comprehensive resource of SNVs in spatial transcriptome

Supplementary Figures S1-S8 from The Deep Learning Framework iCanTCR Enables Early Cancer Detection Using the T-cell Receptor Repertoire in Peripheral Blood

The Deep Learning Framework iCanTCR Enables Early Cancer Detection Using the T-cell Receptor Repertoire in Peripheral Blood

Functional requirement of alternative splicing in epithelial-mesenchymal transition of pancreatic circulating tumor

Dimension reduction, cell clustering, and cell–cell communication inference for single-cell transcriptomics with DcjComm

An interpretable single-cell RNA sequencing data clustering method based on latent Dirichlet allocation

Identification of shared characteristics in tumor-infiltrating T cells across 15 cancers

Global Characterization of Peripheral B Cells in Parkinson’s Disease by Single-Cell RNA and BCR Sequencing

MutCov: A pipeline for evaluating the effect of mutations in spike protein on infectivity and antigenicity of SARS-CoV-2

DeepCCI: a deep learning framework for identifying cell–cell interactions from single-cell RNA sequencing data

DeepST: identifying spatial domains in spatial transcriptomics by deep learning

Regional transcriptional vulnerability to basal forebrain functional dysconnectivity in mild cognitive impairment patients.

Identification of alternative splicing-derived cancer neoantigens for mRNA vaccine development

Network analysis between neuron dysfunction and neuroimmune response based on neural single-cell transcriptome of COVID-19 patients

CBLRR: a cauchy-based bounded constraint low-rank representation method to cluster single-cell RNA-seq data

COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas

Single-cell transcriptome and TCR profiling reveal activated and expanded T cell populations in Parkinson’s disease

Global characterization of B cell receptor repertoire in COVID-19 patients by single-cell V(D)J sequencing

Comprehensive analysis of partial methylation domains in colorectal cancer based on single-cell methylation profiles

A pan-cancer analysis of alternative splicing of splicing factors in 6904 patients

Alternative splicing associated with cancer stemness in kidney renal clear cell carcinoma

Identification of potential vaccine targets for COVID‐19 by combining single‐cell and bulk TCR sequencing

Impact of mutations in SARS-COV-2 spike on viral infectivity and antigenicity

DLpTCR: an ensemble deep learning framework for predicting immunogenic peptide recognized by T cell receptor

N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation

Comprehensive Analysis of Copy Number Variations in Kidney Cancer by Single-Cell Exome Sequencing

Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients

PGsim: A Comprehensive and Highly Customizable Personal Genome Simulator

An Information Gain-based Method for Evaluating the Classification Power of Features Towards Identifying Enhancers

Identification of sub-Golgi protein localization by use of deep representation learning features

ERDS-Exome: A Hybrid Approach for Copy Number Variant Detection from Whole-Exome Sequencing Data

Comprehensive analysis of TCR repertoire in COVID-19 using single cell sequencing

Single cell RNA and immune repertoire profiling of COVID-19 patients reveal novel neutralizing antibody

Prediction of transcription factors binding events based on epigenetic modifications in different human cells.

SCIA: A Novel Gene Set Analysis Applicable to Data With Different Characteristics

Supplementary document of “ A learning-based framework for miRNA-disease association identification using neural networks ”

SpliVert: A Protein Multiple Sequence Alignment Refinement Method Based on Splitting-Splicing Vertically.

Computational Methods for Identifying Similar Diseases

ProbPFP: a multiple sequence alignment algorithm combining hidden Markov model optimized by particle swarm optimization with partition function

ProbPFP: A Multiple Sequence Alignment Algorithm Combining Partition Function and Hidden Markov Model with Particle Swarm Optimization

An online tool for measuring and visualizing phenotype similarities using HPO

CircR2Disease: a manually curated database for experimentally supported circular RNAs associated with various diseases

DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function

LncRNA2Target v2.0: a comprehensive database for target genes of lncRNAs in human and mouse

EWAS: epigenome-wide association study software 2.0

Erratum to: InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology

The Complexity of Promoter Regions Based on a Vector Topological Entropy

DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data

Measuring disease similarity and predicting disease-related ncRNAs by a novel method

ERDS-pe: A paired hidden Markov model for copy number variant detection from whole-exome sequencing data

InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology

InfDisSim: A novel method for measuring disease similarity based on information flow

Identifying Liver Cancer-Related Enhancer SNPs by Integrating GWAS and Histone Modification ChIP-seq Data

Preface

Identification Exon Skipping Events From High-Throughput RNA Sequencing Data

Bioinformatics Research and Applications

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads

LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data

An Evaluation of Copy Number Variation Detection Tools from Whole‐Exome Sequencing Data

Pathway analysis of genome-wide association study and transcriptome data highlights new biological pathways in colorectal cancer

LncRNA2Target: a database for differentially expressed genes after lncRNA knockdown or overexpression

An integrative approach for measuring semantic similarities using gene ontology

TF2LncRNA: Identifying Common Transcription Factors for a List of lncRNA Genes from ChIP-Seq Data

A Generalized Topological Entropy for Analyzing the Complexity of DNA Sequences

Chromatin structure characteristics of pre-miRNA genomic sequences

Predicting human microRNA-disease associations based on support vector machine

An approach for prioritizing disease-related microRNAs based on genomic data integration

Weighted Network-Based Inference of Human MicroRNA-Disease Associations

Prioritization of disease microRNAs through a human phenome-microRNAome network