史鸿博｜江苏大学｜学者主页

2025

BioWalk-MDA: a novel approach for large-scale predicting metabolite-drug associations based on multi layered biomedical knowledge graphs

Xiao-Liang Wu, Meitao Wu, Yetong Yang, Shuo Jiang, Gen Li, Yanghe Fu, Zhuoxin Liu, Ying-Li Lv, Hongbo Shi

Briefings Bioinform.

2025

Multi-omics integration reveals functional signatures of gut microbiome in atherosclerosis

Hongbo Shi, Meitao Wu, Xiao-Liang Wu, Zhuoxin Liu, Shuo Jiang, Gen Li, Yetong Yang, Yanghe Fu, Qiuping Wang, Guangde Zhang, Liang Cheng

Gut microbes

DOI

2024

Identification of miRNA-TF Regulatory Pathways Related to Diseases from a Neuroendocrine-Immune Perspective

Chengyi Wang, Meitao Wu, Ziyang Wang, Xiao-Liang Wu, H. Yuan, Shuo Jiang, Gen Li, Rifang Lan, Qiuping Wang, Guangde Zhang, Ying-Li Lv, Hongbo Shi

Cellular and molecular neurobiology

DOI

2024

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

Yingli Lv, Guo-Kai Feng, Lei Yang, Xiao-Liang Wu, Chengyi Wang, Aokun Ye, Shu-Yuan Wang, Chaohan Xu, Hongbo Shi

Heliyon

DOI

2023

MultiDS-MDA: Integrating multiple data sources into heterogeneous network for predicting novel metabolite-drug associations

Xiuhong Li, Hao Yuan, Xiaoliang Wu, Chengyi Wang, Meitao Wu, Hongbo Shi, Yingli Lv

Comput. Biol. Medicine

DOI

2023

Identification of immune-related signatures and pathogenesis differences between thoracic aortic aneurysm patients with bicuspid versus tricuspid valves via weighted gene co-expression network analysis

Min Huang, Rong Guan, Jiawei Qiu, Abla Judith Estelle Gnamey, Yusi Wang, Hai Tian, Haoran Sun, Hongbo Shi, Wen-Jing Sun, Xue-Yuan Jia, Jie Wu

PLoS ONE

DOI

2022

Comparative study of disease progression for heart failure with different etiologies via time-ordered network analysis.

Haoran Sun, Xiuhong Li, Hao Yuan, Chengyi Wang, Guangde Zhang, Hongbo Shi

American journal of translational research

2021

Inhibition of lncRNA TCONS_00077866 Ameliorates the High Stearic Acid Diet-Induced Mouse Pancreatic β-Cell Inflammatory Response by Increasing miR-297b-5p to Downregulate SAA3 Expression

Hui-Min Lu, Rui Guo, Yunjin Zhang, Sheng-chang Su, Qingrui Zhao, Yue Yu, Hongbo Shi, Haoran Sun, Yong-Jian Zhang, Sheng-Long Li, Dan Shi, Xia Chu, Chang-Hao Sun

Diabetes

DOI

2021

Time-ordered dysregulated ceRNA networks reveal disease progression and diagnostic biomarkers in ischemic and dilated cardiomyopathy

Ziyi Bai, Haoran Sun, Xiuhong Li, Jie Wu, Hao Yuan, Guangde Zhang, Haixiu Yang, Hongbo Shi

Cell Death Discovery

DOI

2020

ncDRMarker: a computational method for identifying non-coding RNA signatures of drug resistance based on heterogeneous network

Haixiu Yang, Yanjun Xu, D. Shang, Hongbo Shi, Chunlong Zhang, Qun Dong, Yizheng Zhang, Ziyi Bai, Shujun Cheng, Xia Li

Annals of Translational Medicine

DOI

2020

miRNA-mRNA profile and regulatory network in stearic acid-treated β-cell dysfunction.

Yue Yu, Rui Guo, Yunjin Zhang, Hongbo Shi, Haoran Sun, Xia Chu, Xiao-Yan Wu, Hui-Min Lu, Chang-Hao Sun

Journal of Endocrinology

DOI

2020

Systematic analysis of lncRNA and microRNA dynamic features reveals diagnostic and prognostic biomarkers of myocardial infarction

Hongbo Shi, Haoran Sun, Jiayao Li, Ziyi Bai, Jie Wu, Xiuhong Li, Yingli Lv, Guangde Zhang

Aging

DOI

2019

MetSigDis: a manually curated resource for the metabolic signatures of diseases

Liang Cheng, Haixiu Yang, Hengqiang Zhao, Xiaoya Pei, Hongbo Shi, Jie Sun, Yunpeng Zhang, Zhenzhen Wang, Meng Zhou

Briefings Bioinform.

DOI

2018

Characterization of dysregulated lncRNA-mRNA network based on ceRNA hypothesis to reveal the occurrence and recurrence of myocardial infarction

Guangde Zhang, Haoran Sun, Yawei Zhang, Hengqiang Zhao, Wenjing Fan, Jianfei Li, Yingli Lv, Qiong Song, Jiayao Li, M. Zhang, Hongbo Shi

Cell Death Discovery

DOI

2018

Systematic identification and analysis of dysregulated miRNA and transcription factor feed‐forward loops in hypertrophic cardiomyopathy

Hongbo Shi, Jiayao Li, Qiong Song, Liang Cheng, Haoran Sun, Wenjing Fan, Jianfei Li, Zhenzhen Wang, Guangde Zhang

Journal of Cellular and Molecular Medicine

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

Large-scale identification of adverse drug reaction-related proteins through a random walk model

Xiaowen Chen, Hongbo Shi, Feng Yang, Lei Yang, Yingli Lv, Shuyuan Wang, Enyu Dai, Dianjun Sun, Wei Jiang

Scientific Reports

DOI

2016

Studying Dynamic Features in Myocardial Infarction Progression by Integrating miRNA-Transcription Factor Co-Regulatory Networks and Time-Series RNA Expression Data from Peripheral Blood Mononuclear Cells

Hongbo Shi, Guangde Zhang, Jing Wang, Zhenzhen Wang, Xiaoxia Liu, Liang Cheng, Wei-min Li

PLoS ONE

DOI

2016

AKT1 as the PageRank hub gene is associated with melanoma and its functional annotation is highly related to the estrogen signaling pathway that may regulate the growth of melanoma.

Jingjing Zhao, Xue Zeng, Ping Song, Xiaohong Wu, Hongbo Shi

Oncology Report

DOI

2016

DisSetSim: an online system for calculating similarity between disease sets

Yang Hu, Lingling Zhao, Zhiyan Liu, Hong Ju, Hongbo Shi, Peigang Xu, Ya-Dong Wang, Liang Cheng

Journal of Biomedical Semantics

DOI

2016

PageRank analysis reveals topologically expressed genes correspond to psoriasis and their functions are associated with apoptosis resistance.

Xue Zeng, Jingjing Zhao, Xiaohong Wu, Hongbo Shi, Wali Liu, Bingnan Cui, Li Yang, Xu Ding, Ping Song

Molecular Medicine Reports

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

A potential panel of six-long non-coding RNA signature to improve survival prediction of diffuse large-B-cell lymphoma

Jie Sun, Liang Cheng, Hongbo Shi, Zhaoyue Zhang, Hengqiang Zhao, Zhenzhen Wang, Meng Zhou

Scientific Reports

DOI

2016

IntNetLncSim: an integrative network analysis method to infer human lncRNA functional similarity

Liang Cheng, Hongbo Shi, Zhenzhen Wang, Yang Hu, Haixiu Yang, Chen Zhou, Jie Sun, Meng Zhou

OncoTarget

DOI

2016

Relapse-related long non-coding RNA signature to improve prognosis prediction of lung adenocarcinoma

Meng Zhou, Wan-Ying Xu, Xiao-Long Yue, Hengqiang Zhao, Zhenzhen Wang, Hongbo Shi, Liang Cheng, Jie Sun

OncoTarget

DOI

2016

DisSim: an online system for exploring significant similar diseases and exhibiting potential therapeutic drugs

Liang Cheng, Yue Jiang, Zhenzhen Wang, Hongbo Shi, Jie Sun, Haixiu Yang, Shuo Zhang, Yang Hu, Meng Zhou

Scientific Reports

DOI

2016

Integration of Multiple Genomic and Phenotype Data to Infer Novel miRNA-Disease Associations

Hongbo Shi, Guangde Zhang, Meng Zhou, Liang Cheng, Haixiu Yang, Jing Wang, Jie Sun, Zhenzhen Wang

PLoS ONE

DOI

2016

Characterization of long non-coding RNA-associated ceRNA network to reveal potential prognostic lncRNA biomarkers in human ovarian cancer

Meng Zhou, Xiaojun Wang, Hongbo Shi, Liang Cheng, Zhenzhen Wang, Hengqiang Zhao, Lei Yang, Jie Sun

OncoTarget

DOI

2015

A potential prognostic long non-coding RNA signature to predict metastasis-free survival of breast cancer patients

Jie Sun, Xi-Hai Chen, Zhenzhen Wang, Maoni Guo, Hongbo Shi, Xiaojun Wang, Liang Cheng, Meng Zhou

Scientific Reports

DOI

2015

Identification and validation of potential prognostic lncRNA biomarkers for predicting survival in patients with multiple myeloma

Meng Zhou, Hengqiang Zhao, Zhenzhen Wang, Liang Cheng, Lei Yang, Hongbo Shi, Haixiu Yang, Jie Sun

Journal of experimental & clinical cancer research : CR

DOI

2015

Prioritizing candidate disease-related long non-coding RNAs by walking on the heterogeneous lncRNA and disease network.

Meng Zhou, Xiaojun Wang, Jia-Wei Li, D. Hao, Zhenzhen Wang, Hongbo Shi, Lu Han, Hui Zhou, Jie Sun

Molecular Biosystems

DOI

2015

MicroRNA and Transcription Factor Mediated Regulatory Network Analysis Reveals Critical Regulators and Regulatory Modules in Myocardial Infarction

Guangde Zhang, Hongbo Shi, Lin Wang, Meng Zhou, Zhenzhen Wang, Xiaoxia Liu, Liang Cheng, Wei-Min Li, Xue-Qi Li

PLoS ONE

DOI

2014

Inferring novel lncRNA-disease associations based on a random walk model of a lncRNA functional similarity network.

Jie Sun, Hongbo Shi, Zhenzhen Wang, Chang-Jian Zhang, Lin Liu, Le-Tian Wang, Weiwei He, D. Hao, Shu-Lin Liu, Meng Zhou

Molecular Biosystems

DOI

2013

Walking the interactome to identify human miRNA-disease associations through the functional link between miRNA targets and disease genes

Hongbo Shi, Juan Xu, Guangde Zhang, Liang-De Xu, Chunquan Li, Li Wang, Zheng Zhao, Wei Jiang, Zheng Guo, Xia Li

BMC Systems Biology

DOI

2013

Classification of topological domains based on gene expression and regulation

Jingjing Zhao, Hongbo Shi, N. Ahituv

Genome

DOI

2012

Community of protein complexes impacts disease association

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

European Journal of Human Genetics

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, Liang-De Xu, Haixiu Yang, Hongbo Shi, Shang-Wei Ning, Li Chen, Yan Li, Taotao He, Yan Zheng

Genomics

DOI

史鸿博

精选作品

期刊论文

BioWalk-MDA: a novel approach for large-scale predicting metabolite-drug associations based on multi layered biomedical knowledge graphs

Multi-omics integration reveals functional signatures of gut microbiome in atherosclerosis

Identification of miRNA-TF Regulatory Pathways Related to Diseases from a Neuroendocrine-Immune Perspective

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

MultiDS-MDA: Integrating multiple data sources into heterogeneous network for predicting novel metabolite-drug associations

Identification of immune-related signatures and pathogenesis differences between thoracic aortic aneurysm patients with bicuspid versus tricuspid valves via weighted gene co-expression network analysis

Comparative study of disease progression for heart failure with different etiologies via time-ordered network analysis.

Inhibition of lncRNA TCONS_00077866 Ameliorates the High Stearic Acid Diet-Induced Mouse Pancreatic β-Cell Inflammatory Response by Increasing miR-297b-5p to Downregulate SAA3 Expression

Time-ordered dysregulated ceRNA networks reveal disease progression and diagnostic biomarkers in ischemic and dilated cardiomyopathy

ncDRMarker: a computational method for identifying non-coding RNA signatures of drug resistance based on heterogeneous network

miRNA-mRNA profile and regulatory network in stearic acid-treated β-cell dysfunction.

Systematic analysis of lncRNA and microRNA dynamic features reveals diagnostic and prognostic biomarkers of myocardial infarction

MetSigDis: a manually curated resource for the metabolic signatures of diseases

Characterization of dysregulated lncRNA-mRNA network based on ceRNA hypothesis to reveal the occurrence and recurrence of myocardial infarction

Systematic identification and analysis of dysregulated miRNA and transcription factor feed‐forward loops in hypertrophic cardiomyopathy

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

Large-scale identification of adverse drug reaction-related proteins through a random walk model

Studying Dynamic Features in Myocardial Infarction Progression by Integrating miRNA-Transcription Factor Co-Regulatory Networks and Time-Series RNA Expression Data from Peripheral Blood Mononuclear Cells

AKT1 as the PageRank hub gene is associated with melanoma and its functional annotation is highly related to the estrogen signaling pathway that may regulate the growth of melanoma.

DisSetSim: an online system for calculating similarity between disease sets

PageRank analysis reveals topologically expressed genes correspond to psoriasis and their functions are associated with apoptosis resistance.

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

A potential panel of six-long non-coding RNA signature to improve survival prediction of diffuse large-B-cell lymphoma

IntNetLncSim: an integrative network analysis method to infer human lncRNA functional similarity

Relapse-related long non-coding RNA signature to improve prognosis prediction of lung adenocarcinoma

DisSim: an online system for exploring significant similar diseases and exhibiting potential therapeutic drugs

Integration of Multiple Genomic and Phenotype Data to Infer Novel miRNA-Disease Associations

Characterization of long non-coding RNA-associated ceRNA network to reveal potential prognostic lncRNA biomarkers in human ovarian cancer

A potential prognostic long non-coding RNA signature to predict metastasis-free survival of breast cancer patients

Identification and validation of potential prognostic lncRNA biomarkers for predicting survival in patients with multiple myeloma

Prioritizing candidate disease-related long non-coding RNAs by walking on the heterogeneous lncRNA and disease network.

MicroRNA and Transcription Factor Mediated Regulatory Network Analysis Reveals Critical Regulators and Regulatory Modules in Myocardial Infarction

Inferring novel lncRNA-disease associations based on a random walk model of a lncRNA functional similarity network.

Walking the interactome to identify human miRNA-disease associations through the functional link between miRNA targets and disease genes

Classification of topological domains based on gene expression and regulation

Community of protein complexes impacts disease association

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