许超汉｜哈尔滨医科大学｜学者主页

2026

基于snRNA-seq与scATAC-seq整合分析的结直肠癌恶性上皮细胞关键转录因子筛选及功能与预后研究

张清，业佳依，瞿媛媛，陈康楠，王子怡，许超汉

《实用肿瘤学杂志》

2025

RNAPaceDB : a dedicated database to dissect RNA velocity across diverse cell types

Hui Liu, Honghan Zhou, Siru Yang, Weicheng Ma, Jun Wang, Nan Zhang, Huicheng Zhang, Wen Long Huang, Xin Zhong, Chaohan Xu, Shuyuan Wang

Nucleic Acids Research

DOI

2024

Discovery and validation of a 10-gene predictive signature for response to adjuvant chemotherapy in stage II and III colon cancer

Chaohan Xu, Peng Xia, Jie Li, Keeli B. Lewis, Kristen Keon Ciombor, Lily Wang, Jesse Joshua Smith, R. Daniel Beauchamp, Xi Chen

Cell Reports Medicine

DOI

2024

Differential whole-genome doubling based signatures for improvement on clinical outcomes and drug response in patients with breast cancer

Yingli Lv, Guotao Feng, Lei Yang, Xiaoliang Wu, Chengyi Wang, Aokun Ye, Shuyuan Wang, Chaohan Xu, Hongbo Shi

Heliyon

DOI

2024

ncStem: a comprehensive resource of curated and predicted ncRNAs in cancer stemness

Hui Liu, Nan Zhang, Yijie Jia, Jun Wang, Aokun Ye, Siru Yang, Honghan Zhou, Yingli Lv, Chaohan Xu, Shuyuan Wang

Database

DOI

2023

Establishment of comorbidity target pools and prediction of drugs candidate for multiple sclerosis and autoimmune thyroid diseases based on GWAS and transcriptome data

Xin Wang, Yifei Wang, Xuemei Zhang, Xiangxiang Hong, Xinming Rang, Dan Yang, SHAN HU HUANG, Chaohan Xu, Jin Fu

Multiple Sclerosis and Related Disorders

DOI

2023

Systemically Identifying Triple-Negative Breast Cancer Subtype-Specific Prognosis Signatures, Based on Single-Cell RNA-Seq Data

Kaiyuan Xing, Bo Zhang, Zixuan Wang, Yanru Zhang, Tengyue Chai, Jingkai Geng, Xuexue Qin, Xi Chen, Xinxin Zhang, Chaohan Xu

Cells

DOI

2023

Single-cell RNA sequencing identifies critical transcription factors of tumor cell invasion induced by hypoxia microenvironment in glioblastoma

Yanru Zhang, Bo Zhang, Chengqian Lv, Nan Zhang, Kaiyuan Xing, Zixuan Wang, Rongkai Lv, Mingchen Yu, Chaohan Xu, Yihan Wang

Theranostics

DOI

2022

Immune cells transcriptome-based drug repositioning for multiple sclerosis

Xinyue Yin, Xinming Rang, Xiangxiang Hong, Yinglian Zhou, Chaohan Xu, Jin Fu

Frontiers in Immunology

DOI

2022

Identification of Prognostic Gene Signatures by Developing a scRNA-Seq-Based Integration Approach to Predict Recurrence and Chemotherapy Benefit in Stage II–III Colorectal Cancer

Zixuan Wang, Kaiyuan Xing, Bo Zhang, Yanru Zhang, Tengyue Chai, Jingkai Geng, Xuexue Qin, Xinxin Zhang, Chaohan Xu

International Journal of Molecular Sciences

DOI

2022

Identification of potential key genes and immune infiltration in Multiple sclerosis

Yang Liu, Yinglian Zhou, Hui Yue, Haitong Dou, Xinming Rang, Xin Wang, Chaohan Xu, Jin Fu

Multiple Sclerosis and Related Disorders

DOI

2022

Identification of multiple sclerosis-related genes regulated by EBV-encoded microRNAs in B cells

Xinming Rang, Yuan Liu, Jingguo Wang, Yifei Wang, Chaohan Xu, Jin Xiang Fu

Multiple Sclerosis and Related Disorders

DOI

2022

Identification of common susceptibility genes and drug target genes in multiple sclerosis, systemic lupus erythematosus, and rheumatoid arthritis and its value to guide clinical treatment

Yang Liu, Xinming Rang, Xiaowei Zou, Xin Wang, Xuemei Zhang, Yifei Wang, Chaohan Xu, Jin Xiang Fu

Multiple Sclerosis and Related Disorders

DOI

2021

A Comparison for Dimensionality Reduction Methods of Single-Cell RNA-seq Data

Ruizhi Xiang, Wencan Wang, Lei Yang, Shiyuan Wang, Chaohan Xu, Xiaowen Chen

Frontiers in Genetics

DOI

2020

Revealing the subtyping of non‐small cell lung cancer based on genomic evolutionary patterns by multi‐region sequencing

Gaoming Liao, Xin Liang, Yanyan Ping, Yong Zhang, Jianlong Liao, Yihan Wang, Xiaobo Hou, Zedong Jiang, Xiaoqiu Dong, Chaohan Xu, Yun Xiao

Cancer Medicine

DOI

2020

Dissecting the Functional Mechanisms of Somatic Copy-Number Alterations Based on Dysregulated ceRNA Networks across Cancers

Yanyan Ping, Yao Zhou, Jing Rong Hu, Lin Pang, Chaohan Xu, Yun Xiao

Molecular Therapy — Nucleic Acids

DOI

2020

Context-Specific Coordinately Regulatory Network Prioritize Breast Cancer Genetic Risk Factors

Shuyuan Wang, Wencan Wang, Weida Wang, Peng Xia, Lei Yu, Ye Feng Lu, Xiaowen Chen, Chaohan Xu, Hui Liu

Frontiers in Genetics

DOI

2020

Identification and functional analysis of specific MS risk miRNAs and their target genes

Deling Luo, Jingguo Wang, Xuemei Zhang, Xinming Rang, Chaohan Xu, Jin Fu

Multiple Sclerosis and Related Disorders

DOI

2020

Prioritizing Gene Cascading Paths to Model Colorectal Cancer Through Engineered Organoids

Yanyan Ping, Chaohan Xu, Liwen Xu, Gaoming Liao, Yao Zhou, Chunyu Deng, Yujia Lan, Fulong Yu, Jian Shi, Li Wang, Yun Xiao, Xia Li

Frontiers in Bioengineering and Biotechnology

DOI

2020

Systematical identification of cell-specificity of CTCF-gene binding based on epigenetic modifications

Jie Wu, Li Zhang, Qian Song, Lei Yu, Shuyuan Wang, Bo Zhang, Weida Wang, Peng Xia, Xiaowen Chen, Yun Xiao, Chaohan Xu

Briefings in Bioinformatics

DOI

2019

Identification of Dysregulated Competitive Endogenous RNA Networks Driven by Copy Number Variations in Malignant Gliomas

Jinyuan Xu, Xiaobo Hou, Lin Pang, Shangqin Sun, Shengyuan He, Yiran Yang, Kun Liu, Linfu Xu, Wenkang Yin, Chaohan Xu, Yun Xiao

Frontiers in Genetics

DOI

2019

Dissecting the m6A methylation affection on afatinib resistance in non-small cell lung cancer

Qianqian Meng, Shuyuan Wang, Shunheng Zhou, Haizhou Liu, Xueyan Ma, Xu Zhou, Hui Liu, Chaohan Xu, Wei Jiang

The Pharmacogenomics Journal

DOI

2019

Identification of a Combined RNA Prognostic Signature in Adenocarcinoma of the Lung

Si-Yu He, Wenjing Xi, Xin Wang, Chaohan Xu, Liang Cheng, Si-Yao Liu, Qianqian Meng, Boyan Li, Yahui Wang, Hongbo Shi, Hongjiu Wang, Zhenzhen Wang

Medical Science Monitor

DOI

2019

Systematical Identification of Breast Cancer-Related Circular RNA Modules for Deciphering circRNA Functions Based on the Non-Negative Matrix Factorization Algorithm

Shuyuan Wang, Peng Xia, Li Zhang, Lei Yu, Hui Liu, Qianqian Meng, Siyao Liu, Jie Li, Qian Song, Jie Wu, Weida Wang, Lei Yang, Yun Xiao, Chaohan Xu

International Journal of Molecular Sciences

DOI

2018

Inference of patient‐specific subpathway activities reveals a functional signature associated with the prognosis of patients with breast cancer

Junwei Han, Siyao Liu, Ying Jiang, Chaohan Xu, Baotong Zheng, Minghao Jiang, Haixiu Yang, Fei Su, Chunquan Li, Yunpeng Zhang

Journal of Cellular and Molecular Medicine

DOI

2018

Identification of a five‐lncRNA signature for predicting the risk of tumor recurrence in patients with breast cancer

Jie Li, Weida Wang, Peng Xia, Linyun Wan, Li Zhang, Lei Yu, Lily Hui-Ching Wang, Xi Chen, Yun Xiao, Chaohan Xu

International Journal of Cancer

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

2017

Optimizing prognosis-related key miRNA-target interactions responsible for cancer metastasis

Hongying Zhao, Huating Yuan, Jing Rong Hu, Chaohan Xu, Gaoming Liao, Wenkang Yin, Liwen Xu, Li Wang, Xinxin Zhang, Aiai Shi, Jing Li, Yun Xiao

Oncotarget

DOI

2017

Systemically identifying and prioritizing risk lncRNAs through integration of pan-cancer phenotype associations

Chaohan Xu, Rui Qi, Yanyan Ping, Jie Li, Hongying Zhao, Li Wang, Michael Yifei Du, Yun Xiao, Xia Li

Oncotarget

DOI

2016

Cooperative genomic alteration network reveals molecular classification across 12 major cancer types

Hongyi Zhang, Yulan Deng, Yong Zhang, Yanyan Ping, Hongying Zhao, Lin Pang, Xinxin Zhang, Li Wang, Chaohan Xu, Yun Xiao, Xia Li

Nucleic Acids Research

DOI

2016

Systematically characterizing dysfunctional long intergenic non-coding RNAs in multiple brain regions of major psychosis

Jing Rong Hu, Jinyuan Xu, Lin Pang, Hongying Zhao, Feng Li, Yulan Deng, Ling Liu, Yujia Lan, Xinxin Zhang, Tingting Zhao, Chaohan Xu, Chun Di Xu, Yun Xiao, Xia Li

Oncotarget

DOI

2016

Identifying the crosstalk of dysfunctional pathways mediated by lncRNAs in breast cancer subtypes

Li Wang, Jing Li, Hongying Zhao, Jing Rong Hu, Yanyan Ping, Feng Li, Yujia Lan, Chaohan Xu, Yun Xiao, Xia Li

Molecular BioSystems

DOI

2015

Systematically Prioritizing Functional Differentially Methylated Regions (fDMRs) by Integrating Multi-omics Data in Colorectal Cancer

Huihui Fan, Hongying Zhao, Lin Pang, Ling Liu, Guanxiong Zhang, Fulong Yu, Tingting Liu, Chaohan Xu, Yun Xiao, Xia Li

Scientific Reports

DOI

2015

Chromatin states modify network motifs contributing to cell-specific functions

Hongying Zhao, Tingting Liu, Ling Liu, Guanxiong Zhang, Lin Pang, Fulong Yu, Huihui Fan, Yanyan Ping, Li Wang, Chaohan Xu, Yun Xiao, Xia Li

Scientific Reports

DOI

2015

Identifying core gene modules in glioblastoma based on multilayer factor-mediated dysfunctional regulatory networks through integrating multi-dimensional genomic data

Yanyan Ping, Yulan Deng, Li Wang, Hongyi Zhang, Yong Zhang, Chaohan Xu, Hongying Zhao, Huihui Fan, Fulong Yu, Yun Xiao, Xia Li

Nucleic Acids Research

DOI

2014

Identification of cancer-related lncRNAs through integrating genome, regulome and transcriptome features

Tingting Zhao, Jinyuan Xu, Ling Liu, Jing Bai, Chaohan Xu, Yun Xiao, Xia Li, Liming Zhang

Molecular BioSystems

DOI

2014

Prioritizing candidate disease miRNAs by integrating phenotype associations of multiple diseases with matched miRNA and mRNA expression profiles

Chaohan Xu, Yanyan Ping, Xiang Li, Xiang Li, Hongying Zhao, Li Wang, Huihui Fan, Yun Xiao, Xia Li, Xia Li

Molecular BioSystems

DOI

2014

Integrating epigenetic marks for identification of transcriptionally active miRNAs

Yun Xiao, Tingting Liu, Hongying Zhao, Xiang Li, Xiang Li, Jinxia Guan, Chaohan Xu, Yanyan Ping, Huihui Fan, Li Wang, Tingting Zhao, Yanling Lv, Jing Rong Hu, Xin Yu, Yan Jin, Xia Li, Xia Li

Genomics

DOI

2014

IndividualizedPath: identifying genetic alterations contributing to the dysfunctional pathways in glioblastoma individuals

Yanyan Ping, Hongyi Zhang, Yulan Deng, Li Wang, Hongying Zhao, Lin Pang, Huihui Fan, Chaohan Xu, Feng Li, Yong Zhang, Yonghui Gong, Yun Xiao, Xia Li

Molecular BioSystems

DOI

2014

The DNA Methylome and Transcriptome of Different Brain Regions in Schizophrenia and Bipolar Disorder

Yun Xiao, Cynthia Camarillo, Yanyan Ping, Tania Bedard Arana, Hongying Zhao, Peter M. Thompson, Chaohan Xu, Chaohan Xu, Bin Su, Huihui Fan, Javier Ordoñez, Li Wang, Chunxiang Mao, Yunpeng Zhang, Dianne A. Cruz, Michael Escamilla, Xia Li, Chun Di Xu, Chun Di Xu

PLoS ONE

DOI

2014

Features of DMRs.

Yun Xiao, C. Cynthia, Y. Ping, Bedard Arana Tania, Hongying Zhao, M. ThompsonPeter, Chaohan Xu, Brenda Su Bin, Huihui Fan, Ordoñez Javier, Li Wang, Chun-Xiang Mao, Yun-Peng Zhang, C. Dianne, A. Michael, Xia Li, Chun Xu

DOI

2014

The distribution of hyper- and hypomethylated DMRs.

Yun Xiao, C. Cynthia, Y. Ping, Bedard Arana Tania, Hongying Zhao, M. ThompsonPeter, Chaohan Xu, Brenda Su Bin, Huihui Fan, Ordoñez Javier, Li Wang, Chun-Xiang Mao, Yun-Peng Zhang, C. Dianne, A. Michael, Xia Li, Chun-Hong Xu

DOI

2014

Comparisons of biological processes between different brain regions of SC and BP.

Yun Xiao, C. Cynthia, Y. Ping, Bedard Arana Tania, Hongying Zhao, M. ThompsonPeter, Chaohan Xu, Brenda Su Bin, Huihui Fan, Ordoñez Javier, Li Wang, Chun-Xiang Mao, Yun-Peng Zhang, C. Dianne, A. Michael, Xia Li, Chun Xu

DOI

2014

Cross cluster analyses.

Yun Xiao, C. Cynthia, Y. Ping, Bedard Arana Tania, Hongying Zhao, M. ThompsonPeter, Chaohan Xu, Brenda Su Bin, Huihui Fan, Ordoñez Javier, Li Wang, Chun-Xiang Mao, Yun-Peng Zhang, C. Dianne, A. Michael, Xia Li, Chun-Jie Xu

DOI

2013

Systematic Identification of Core Transcription Factors Mediating Dysregulated Links Bridging Inflammatory Bowel Diseases and Colorectal Cancer

Yun Xiao, Huihui Fan, Yunpeng Zhang, Wenjing Xing, Yanyan Ping, Hongying Zhao, Chaohan Xu, Yiqun Li, Li Wang, Feng Li, Jing Rong Hu, Teng Huang, Yanling Lv, Huan Ren, Xia Li

PLoS ONE

DOI

2013

Identifying dysfunctional miRNA-mRNA regulatory modules by inverse activation, cofunction, and high interconnection of target genes: a case study of glioblastoma.

Yun Xiao, Y. Ping, Huihui Fan, Chaohan Xu, Jinxia Guan, Hongying Zhao, Yiqun Li, Yanling Lv, Yan Jin, Li-Hua Wang, Xia Li

Neuro-Oncology

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

Prioritizing cancer-related key miRNA–target interactions by integrative genomics

Yun Xiao, Jinxia Guan, Yanyan Ping, Chaohan Xu, Teng Huang, Hongying Zhao, Huihui Fan, Yiqun Li, Yanling Lv, Tingting Zhao, Yucui Dong, Huan Ren, Xia Li

Nucleic Acids Research

DOI

2012

Systematic identification of common functional modules related to heart failure with different etiologies

Yun Xiao, Chaohan Xu, Liangde Xu, Jinxia Guan, Yanyan Ping, Huihui Fan, Yiqun Li, Hongying Zhao, Xia Li

Gene

DOI

2012

Discovering Dysfunction of Multiple MicroRNAs Cooperation in Disease by a Conserved MicroRNA Co-Expression Network

Yun Xiao, Chaohan Xu, Jinxia Guan, Yanyan Ping, Huihui Fan, Yiqun Li, Hongying Zhao, Xia Li

PLoS ONE

DOI

2011

Differential expression pattern-based prioritization of candidate genes through integrating disease-specific expression data

Yun Xiao, Chaohan Xu, Yanyan Ping, Jinxia Guan, Huihui Fan, Yiqun Li, Xia Li

Genomics

DOI

2010

Functional Homogeneity in microRNA Target Heterogeneity—a New Sight into Human microRNomics

Yingying Wang, Lei Du, Xia Li, Shaojun Zhang, Yun Xiao, Binsheng Gong, Qianghu Wang, Meng Zhou, Chaohan Xu, Xin Chen, Sali Lv, Shaoqi Rao

OMICS A Journal of Integrative Biology

DOI

精选作品

期刊论文

基于snRNA-seq与scATAC-seq整合分析的结直肠癌恶性上皮细胞关键转录因子筛选及功能与预后研究

RNAPaceDB : a dedicated database to dissect RNA velocity across diverse cell types

Discovery and validation of a 10-gene predictive signature for response to adjuvant chemotherapy in stage II and III colon cancer

Differential whole-genome doubling based signatures for improvement on clinical outcomes and drug response in patients with breast cancer

ncStem: a comprehensive resource of curated and predicted ncRNAs in cancer stemness

Establishment of comorbidity target pools and prediction of drugs candidate for multiple sclerosis and autoimmune thyroid diseases based on GWAS and transcriptome data

Systemically Identifying Triple-Negative Breast Cancer Subtype-Specific Prognosis Signatures, Based on Single-Cell RNA-Seq Data

Single-cell RNA sequencing identifies critical transcription factors of tumor cell invasion induced by hypoxia microenvironment in glioblastoma

Immune cells transcriptome-based drug repositioning for multiple sclerosis

Identification of Prognostic Gene Signatures by Developing a scRNA-Seq-Based Integration Approach to Predict Recurrence and Chemotherapy Benefit in Stage II–III Colorectal Cancer

Identification of potential key genes and immune infiltration in Multiple sclerosis

Identification of multiple sclerosis-related genes regulated by EBV-encoded microRNAs in B cells

Identification of common susceptibility genes and drug target genes in multiple sclerosis, systemic lupus erythematosus, and rheumatoid arthritis and its value to guide clinical treatment

A Comparison for Dimensionality Reduction Methods of Single-Cell RNA-seq Data

Revealing the subtyping of non‐small cell lung cancer based on genomic evolutionary patterns by multi‐region sequencing

Dissecting the Functional Mechanisms of Somatic Copy-Number Alterations Based on Dysregulated ceRNA Networks across Cancers

Context-Specific Coordinately Regulatory Network Prioritize Breast Cancer Genetic Risk Factors

Identification and functional analysis of specific MS risk miRNAs and their target genes

Prioritizing Gene Cascading Paths to Model Colorectal Cancer Through Engineered Organoids

Systematical identification of cell-specificity of CTCF-gene binding based on epigenetic modifications

Identification of Dysregulated Competitive Endogenous RNA Networks Driven by Copy Number Variations in Malignant Gliomas

Dissecting the m6A methylation affection on afatinib resistance in non-small cell lung cancer

Identification of a Combined RNA Prognostic Signature in Adenocarcinoma of the Lung

Systematical Identification of Breast Cancer-Related Circular RNA Modules for Deciphering circRNA Functions Based on the Non-Negative Matrix Factorization Algorithm

Inference of patient‐specific subpathway activities reveals a functional signature associated with the prognosis of patients with breast cancer

Identification of a five‐lncRNA signature for predicting the risk of tumor recurrence in patients with breast cancer

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

Optimizing prognosis-related key miRNA-target interactions responsible for cancer metastasis

Systemically identifying and prioritizing risk lncRNAs through integration of pan-cancer phenotype associations

Cooperative genomic alteration network reveals molecular classification across 12 major cancer types

Systematically characterizing dysfunctional long intergenic non-coding RNAs in multiple brain regions of major psychosis

Identifying the crosstalk of dysfunctional pathways mediated by lncRNAs in breast cancer subtypes

Systematically Prioritizing Functional Differentially Methylated Regions (fDMRs) by Integrating Multi-omics Data in Colorectal Cancer

Chromatin states modify network motifs contributing to cell-specific functions

Identifying core gene modules in glioblastoma based on multilayer factor-mediated dysfunctional regulatory networks through integrating multi-dimensional genomic data

Identification of cancer-related lncRNAs through integrating genome, regulome and transcriptome features

Prioritizing candidate disease miRNAs by integrating phenotype associations of multiple diseases with matched miRNA and mRNA expression profiles

Integrating epigenetic marks for identification of transcriptionally active miRNAs

IndividualizedPath: identifying genetic alterations contributing to the dysfunctional pathways in glioblastoma individuals

The DNA Methylome and Transcriptome of Different Brain Regions in Schizophrenia and Bipolar Disorder

Features of DMRs.

The distribution of hyper- and hypomethylated DMRs.

Comparisons of biological processes between different brain regions of SC and BP.

Cross cluster analyses.

Systematic Identification of Core Transcription Factors Mediating Dysregulated Links Bridging Inflammatory Bowel Diseases and Colorectal Cancer

Identifying dysfunctional miRNA-mRNA regulatory modules by inverse activation, cofunction, and high interconnection of target genes: a case study of glioblastoma.

Prioritising risk pathways of complex human diseases based on functional profiling

Prioritizing cancer-related key miRNA–target interactions by integrative genomics

Systematic identification of common functional modules related to heart failure with different etiologies

Discovering Dysfunction of Multiple MicroRNAs Cooperation in Disease by a Conserved MicroRNA Co-Expression Network

Differential expression pattern-based prioritization of candidate genes through integrating disease-specific expression data

Functional Homogeneity in microRNA Target Heterogeneity—a New Sight into Human microRNomics

预印本

Circulating Tumor DNA Mutation Profiling Reveals Prognostic Signatures in Breast Cancer

Exploring of mechanisms and predicting of potential drugs of the comorbidity between migraine and multiple sclerosis based on bioinformatics analysis of transcriptome data

Single-cell RNA-seq data reveals TNBC tumor heterogeneity through characterizing subclone compositions and proportions

Construction of Breast Cancer-Related LncSLGP Models for Systematically Deciphering Their Functions and Improving Prognosis