Bairong Shen

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 32

Top Topics

Protein Functional

Top Venues

Database J. Biol. Databases Curation

Briefings Bioinform.

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Jianchao Duan, Peiyi Li, Aibin Shao, Xuechao Hao, Ruihao Zhou, Cheng Bi, Xingyun Liu, Weimin Li, Huadong Zhu, Guo Chen, Bairong Shen, Tao Zhu
PPCRKB: a risk factor knowledge base of postoperative pulmonary complications. Database J. Biol. Databases Curation 2024 (2024)
Shumin Ren, Lin Yang, Jiale Du, Mengqiao He, Bairong Shen
DRGKB: a knowledgebase of worldwide diagnosis-related groups' practices for comparison, evaluation and knowledge-guided application. Database J. Biol. Databases Curation 2024 (2024)
Hui Zong, Rongrong Wu, Jiaxue Cha, Erman Wu, Jiakun Li, Liang Tao, Zuofeng Li, Buzhou Tang, Bairong Shen
Advancing Biomedical Text Mining with Community Challenges. CoRR (2024)
Shumin Ren, Jiakun Li, Julián Dorado, Alejandro Pazos Sierra, Humberto González Díaz, Aliuska Duardo-Sánchez, Bairong Shen
From molecular mechanisms of prostate cancer to translational applications: based on multi-omics fusion analysis and intelligent medicine. Health Inf. Sci. Syst. 12 (1) (2024)
Chunjiang Yu, Hui Zong, Yalan Chen, Yibin Zhou, Xingyun Liu, Yuxin Lin, Jiakun Li, Xiaonan Zheng, Hua Min, Bairong Shen
PCAO2: an ontology for integration of prostate cancer associated genotypic, phenotypic and lifestyle data. Briefings Bioinform. 25 (3) (2024)
Ke Shen, Ahmad Ud Din, Baivab Sinha, Yi Zhou, Fuliang Qian, Bairong Shen
Translational informatics for human microbiota: data resources, models and applications. Briefings Bioinform. 24 (3) (2023)
Chaoying Zhan, Kai Liu, Yuxin Zhang, Yingbo Zhang, Mengqiao He, Rongrong Wu, Cheng Bi, Bairong Shen
Myocardial infarction unveiled: Key miRNA players screened by a novel lncRNA-miRNA-mRNA network model. Comput. Biol. Medicine 160 (2023)
Chunjiang Yu, Xin Qi, Wenying Yan, Wentao Wu, Bairong Shen
Next-Generation Sequencing Markup Language (NGSML): A Medium for the Representation and Exchange of NGS Data. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (1) (2023)
Tong Tang, Xingyun Liu, Rongrong Wu, Li Shen, Shumin Ren, Bairong Shen
CTRR-ncRNA: A Knowledgebase for Cancer Therapy Resistance and Recurrence Associated Non-coding RNAs. Genom. Proteom. Bioinform. 21 (2) (2023)
Xiaonan Zheng, Hang Xu, Tianhai Lin, Ping Tan, Qiao Xiong, Xianyanling Yi, Shi Qiu, Lu Yang, Bairong Shen, Jianzhong Ai, Qiang Wei
CD93 orchestrates the tumor microenvironment and predicts the molecular subtype and therapy response of bladder cancer. Comput. Biol. Medicine 147 (2022)
Erman Wu, Xuemeng Fan, Tong Tang, Jingjing Li, Jiao Wang, Xingyun Liu, Zayatta Zungar, Jiaojiao Ren, Cong Wu, Bairong Shen
Biomarkers discovery for endometrial cancer: A graph convolutional sample network method. Comput. Biol. Medicine 150 (2022)
Shumin Ren, Yanwen Jin, Yalan Chen, Bairong Shen
CRPMKB: a knowledge base of cancer risk prediction models for systematic comparison and personalized applications. Bioinform. 38 (6) (2022)
Hongxin He, Manhong Shi, Yuxin Lin, Chaoying Zhan, Rongrong Wu, Cheng Bi, Xingyun Liu, Shumin Ren, Bairong Shen
HFBD: a biomarker knowledge database for heart failure heterogeneity and personalized applications. Bioinform. 37 (23) (2021)
Yalan Chen, Chunjiang Yu, Xingyun Liu, Ting Xi, Guangfei Xu, Yan Sun, Fei Zhu, Bairong Shen
PCLiON: An Ontology for Data Standardization and Sharing of Prostate Cancer Associated Lifestyles. Int. J. Medical Informatics 145 (2021)
Jing Chen, Xingyun Liu, Li Shen, Yuxin Lin, Bairong Shen
CMBD: a manually curated cancer metabolic biomarker knowledge database. Database J. Biol. Databases Curation 2021 (2021)
Chunjiang Yu, Xin Qi, Yuxin Lin, Yin Li, Bairong Shen
iODA: An integrated tool for analysis of cancer pathway consistency from heterogeneous multi-omics data. J. Biomed. Informatics 112 (2020)
Rongrong Wu, Yuxin Lin, Xingyun Liu, Chaoying Zhan, Hongxin He, Manhong Shi, Zhi Jiang, Bairong Shen
Phenotype-genotype network construction and characterization: a case study of cardiovascular diseases and associated non-coding RNAs. Database J. Biol. Databases Curation 2020 (2020)
Xin Qi, Yuxin Lin, Jiajia Chen, Bairong Shen
Decoding competing endogenous RNA networks for cancer biomarker discovery. Briefings Bioinform. 21 (2) (2020)
Lan Yang, Yang Yang, Xingyun Liu, Yongquan Chen, Yalan Chen, Yuxin Lin, Yan Sun, Bairong Shen
CHDGKB: a knowledgebase for systematic understanding of genetic variations associated with non-syndromic congenital heart disease. Database J. Biol. Databases Curation 2020 (2020)
Yalan Chen, Xingyun Liu, Yijun Yu, Chunjiang Yu, Lan Yang, Yuxin Lin, Ting Xi, Ziyun Ye, Zhe Feng, Bairong Shen
PCaLiStDB: a lifestyle database for precision prevention of prostate cancer. Database J. Biol. Databases Curation 2020 (2020)
Chaoying Zhan, Manhong Shi, Rongrong Wu, Hongxin He, Xingyun Liu, Bairong Shen
MIRKB: a myocardial infarction risk knowledge base. Database J. Biol. Databases Curation 2019 (2019)
Fei Ye, Fei Zhu, Yuchen Fu, Bairong Shen
ECG Generation With Sequence Generative Adversarial Nets Optimized by Policy Gradient. IEEE Access 7 (2019)
Bairong Shen, Xiaoqian Jiang, Xingming Zhao
Modeling and Simulation Studies of Complex Biological Systems for Precision Medicine and Healthcare. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (1) (2019)
Bairong Shen, Yuxin Lin, Cheng Bi, Shengrong Zhou, Zhongchen Bai, Guangmin Zheng, Jing Zhou
Translational Informatics for Parkinson's Disease: from Big Biomedical Data to Small Actionable Alterations. Genom. Proteom. Bioinform. 17 (4) (2019)
Yuxin Lin, Fuliang Qian, Li Shen, Feifei Chen, Jiajia Chen, Bairong Shen
Computer-aided biomarker discovery for precision medicine: data resources, models and applications. Briefings Bioinform. 20 (3) (2019)
Yang Yang, Chen Xu, Xingyun Liu, Chao Xu, Yuanyuan Zhang, Li Shen, Mauno Vihinen, Bairong Shen
NDDVD: an integrated and manually curated Neurodegenerative Diseases Variation Database. Database J. Biol. Databases Curation 2018 (2018)
Xueli Zhang, Xiao-Feng Sun, Yang Cao, Benchen Ye, Qiliang Peng, Xingyun Liu, Bairong Shen, Hong Zhang
CBD: a biomarker database for colorectal cancer. Database J. Biol. Databases Curation 2018 (2018)
Wenying Yan, Guang Hu, Zhongjie Liang, Jianhong Zhou, Yang Yang, Jiajia Chen, Bairong Shen
Node-Weighted Amino Acid Network Strategy for Characterization and Identification of Protein Functional Residues. J. Chem. Inf. Model. 58 (9) (2018)
Jianhong Zhou, Christopher J. Oldfield, Fei Huang, Wenying Yan, Bairong Shen, A. Keith Dunker
Identification of intrinsic disorder in complexes from Protein Data Bank. ICCABS (2018)
Chunjiang Yu, Wentao Wu, Jing Wang, Yuxin Lin, Yang Yang, Jiajia Chen, Fei Zhu, Bairong Shen
NGS-FC: A Next-Generation Sequencing Data Format Converter. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (5) (2018)
Yang Yang, Abhishek Niroula, Bairong Shen, Mauno Vihinen
PON-Sol: prediction of effects of amino acid substitutions on protein solubility. Bioinform. 32 (13) (2016)
Feixiong Cheng, Chuang Liu, Bairong Shen, Zhongming Zhao
Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach. BMC Syst. Biol. 10 (S-3) (2016)
Fei Zhu, Quan Liu, Xiaofang Zhang, Bairong Shen
Protein-Protein Interaction Network Constructing Based on Text Mining and Reinforcement Learning with Application to Prostate Cancer. TrustCom/BigDataSE/ISPA (1) (2015)
Jiajia Chen, Maomin Sun, Bairong Shen
Deciphering oncogenic drivers: from single genes to integrated pathways. Briefings Bioinform. 16 (3) (2015)
Fei Zhu, Quan Liu, Xiaofang Zhang, Bairong Shen
Protein-protein interaction network constructing based on text mining and reinforcement learning with application to prostate cancer. BIBM (2014)
Christian Schönbach, Bairong Shen, Tin Wee Tan, Shoba Ranganathan
InCoB2013 introduces Systems Biology as a major conference theme. BMC Syst. Biol. 7 (S-3) (2013)
Bairong Shen, Hong-Bin Shen, Tianhai Tian, Qiang Lü, Guang Hu
Translational Bioinformatics and Computational Systems Medicine. Comput. Math. Methods Medicine 2013 (2013)
Jiajia Chen, Ying Wang, Bairong Shen, Daqing Zhang
Molecular Signature of Cancer at Gene Level or Pathway Level? Case Studies of Colorectal Cancer and Prostate Cancer Microarray Data. Comput. Math. Methods Medicine 2013 (2013)
Yangfan Hu, Jinquan Li, Wenying Yan, Jiajia Chen, Yin Li, Guang Hu, Bairong Shen
Identifying novel glioma associated pathways based on systems biology level meta-analysis. BMC Syst. Biol. 7 (S-2) (2013)
Yifei Tang, Wenying Yan, Jiajia Chen, Cheng Luo, Antti Kaipia, Bairong Shen
Identification of novel microRNA regulatory pathways associated with heterogeneous prostate cancer. BMC Syst. Biol. 7 (S-3) (2013)
Fei Zhu, Preecha Patumcharoenpol, Cheng Zhang, Yang Yang, Jonathan H. Chan, Asawin Meechai, Wanwipa Vongsangnak, Bairong Shen
Biomedical text mining and its applications in cancer research. J. Biomed. Informatics 46 (2) (2013)
Yangfan Hu, Jinquan Li, Jiajia Chen, Guang Hu, Bairong Shen
Identifying novel glioma associated pathways based on integrated 'omics' data. ISB (2012)
Chao Xu, Jiajia Chen, Bairong Shen
The preservation of bidirectional promoter architecture in eukaryotes: what is the driving force? BMC Syst. Biol. 6 (S-1) (2012)
Preecha Patumcharoenpol, Jonathan Hoyin Chan, Asawin Meechai, Bairong Shen, Wanwipa Vongsangnak
Bibliome Mining Platform and Application for Building Metabolic Interaction Network. CSBio (2012)
Min Ding, Haiyun Wang, Jiajia Chen, Bairong Shen, Zhonghua Xu
Identification and Functional Annotation of Genome-Wide ER-Regulated Genes in Breast Cancer Based on ChIP-Seq Data. Comput. Math. Methods Medicine 2012 (2012)
Jiajia Chen, Daqing Zhang, Wenyu Zhang, Yifei Tang, Lingchuan Guo, Bairong Shen
An integrative framework for identifying consistent microRNA expression signatures associated with clear cell renal cell carcinoma. ISB (2012)
Bingchuan Liu, Jiajia Chen, Bairong Shen
Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs. BMC Syst. Biol. 5 (S-1) (2011)
Ying Wang, Jiajia Chen, Qinghui Li, Haiyun Wang, Ganqiang Liu, Qing Jing, Bairong Shen
Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. Comput. Biol. Chem. 35 (3) (2011)
Ganqiang Liu, Min Ding, Haiyun Wang, Jinyan Huang, Qing Jing, Bairong Shen
Pathway analysis of microRNAs in mouse heart development. Int. J. Bioinform. Res. Appl. 6 (1) (2010)
Binhua Tang, Xuechen Wu, Ge Tan, Su-Shing Chen, Qing Jing, Bairong Shen
Computational inference and analysis of genetic regulatory networks via a supervised combinatorial-optimization pattern. BMC Syst. Biol. 4 (S-2) (2010)
Sushing Chen, Bairong Shen, Jiajia Chen, Yang Yang, Yuan Li
Traditional Chinese Medicine data mining: Associating clinical cancer case studies with Traditional Chinese Medicine therapies. BIBM Workshops (2010)
Haiyun Wang, Min Ding, Xia Li, Bairong Shen
Clinical Information Driven Ensemble Clustering for Inferring Robust Tumor Subtypes. BMEI (2009)
Binhua Tang, Li He, Qing Jing, Bairong Shen
Model-Based Identification and Adaptive Control of the Core Module in a Typical Cell Cycle Pathway via Network and System Control Theories. Adv. Complex Syst. 12 (1) (2009)
Haiyun Wang, Qi Wang, Xia Li, Bairong Shen, Min Ding, Ziyin Shen
Towards patterns tree of gene coexpression in eukaryotic species. Bioinform. 24 (11) (2008)
Binhua Tang, Li He, Sushing Chen, Bairong Shen
System Stability Via Stepping Optimal Control: Theory and Applications. EPIA Workshops (2007)
Bairong Shen, Mauno Vihinen
RankViaContact: ranking and visualization of amino acid contacts. Bioinform. 19 (16) (2003)