RankViaContact: ranking and visualization of amino acid contacts. - Bairong Shen; Mauno Vihinen (Bioinform., 2003)

System Stability Via Stepping Optimal Control: Theory and Applications. - Binhua Tang; Li He; Sushing Chen; Bairong Shen (EPIA Workshops, 2007)

Towards patterns tree of gene coexpression in eukaryotic species. - Haiyun Wang; Qi Wang; Xia Li 004; Bairong Shen; Min Ding 006; Ziyin Shen (Bioinform., 2008)

Clinical Information Driven Ensemble Clustering for Inferring Robust Tumor Subtypes. - Haiyun Wang; Min Ding 006; Xia Li 004; Bairong Shen (BMEI, 2009)

Model-Based Identification and Adaptive Control of the Core Module in a Typical Cell Cycle Pathway via Network and System Control Theories. - Binhua Tang; Li He; Qing Jing; Bairong Shen (Adv. Complex Syst., 2009)

Traditional Chinese Medicine data mining: Associating clinical cancer case studies with Traditional Chinese Medicine therapies. - Sushing Chen; Bairong Shen; Jiajia Chen; Yang Yang; Yuan Li (BIBM Workshops, 2010)

Computational inference and analysis of genetic regulatory networks via a supervised combinatorial-optimization pattern. - Binhua Tang; Xuechen Wu; Ge Tan; Su-Shing Chen; Qing Jing; Bairong Shen (BMC Syst. Biol., 2010)

Pathway analysis of microRNAs in mouse heart development. - Ganqiang Liu; Min Ding 006; Haiyun Wang; Jinyan Huang; Qing Jing; Bairong Shen (Int. J. Bioinform. Res. Appl., 2010)

Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs. - Bingchuan Liu; Jiajia Chen; Bairong Shen (BMC Syst. Biol., 2011)

Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. - Ying Wang 053; Jiajia Chen; Qinghui Li; Haiyun Wang; Ganqiang Liu; Qing Jing; Bairong Shen (Comput. Biol. Chem., 2011)

An integrative framework for identifying consistent microRNA expression signatures associated with clear cell renal cell carcinoma. - Jiajia Chen; Daqing Zhang 001; Wenyu Zhang; Yifei Tang; Lingchuan Guo; Bairong Shen (ISB, 2012)

Identifying novel glioma associated pathways based on integrated 'omics' data. - Yangfan Hu; Jinquan Li; Jiajia Chen; Guang Hu 001; Bairong Shen (ISB, 2012)

The preservation of bidirectional promoter architecture in eukaryotes: what is the driving force? - Chao Xu; Jiajia Chen; Bairong Shen (BMC Syst. Biol., 2012)

Identification and Functional Annotation of Genome-Wide ER-Regulated Genes in Breast Cancer Based on ChIP-Seq Data. - Min Ding 006; Haiyun Wang; Jiajia Chen; Bairong Shen; Zhonghua Xu (Comput. Math. Methods Medicine, 2012)

Bibliome Mining Platform and Application for Building Metabolic Interaction Network. - Preecha Patumcharoenpol; Jonathan Hoyin Chan; Asawin Meechai; Bairong Shen; Wanwipa Vongsangnak (CSBio, 2012)

Identifying novel glioma associated pathways based on systems biology level meta-analysis. - Yangfan Hu; Jinquan Li; Wenying Yan; Jiajia Chen; Yin Li; Guang Hu 001; Bairong Shen (BMC Syst. Biol., 2013)

InCoB2013 introduces Systems Biology as a major conference theme. - Christian Schönbach; Bairong Shen; Tin Wee Tan; Shoba Ranganathan (BMC Syst. Biol., 2013)

Identification of novel microRNA regulatory pathways associated with heterogeneous prostate cancer. - Yifei Tang; Wenying Yan; Jiajia Chen; Cheng Luo; Antti Kaipia; Bairong Shen (BMC Syst. Biol., 2013)

Molecular Signature of Cancer at Gene Level or Pathway Level? Case Studies of Colorectal Cancer and Prostate Cancer Microarray Data. - Jiajia Chen; Ying Wang 053; Bairong Shen; Daqing Zhang 001 (Comput. Math. Methods Medicine, 2013)

Translational Bioinformatics and Computational Systems Medicine. - Bairong Shen; Hong-Bin Shen; Tianhai Tian; Qiang Lü; Guang Hu 001 (Comput. Math. Methods Medicine, 2013)

Biomedical text mining and its applications in cancer research. - Fei Zhu 003; Preecha Patumcharoenpol; Cheng Zhang; Yang Yang; Jonathan H. Chan; Asawin Meechai; Wanwipa Vongsangnak; Bairong Shen (J. Biomed. Informatics, 2013)

Protein-protein interaction network constructing based on text mining and reinforcement learning with application to prostate cancer. - Fei Zhu 003; Quan Liu 004; Xiaofang Zhang; Bairong Shen (BIBM, 2014)

Deciphering oncogenic drivers: from single genes to integrated pathways. - Jiajia Chen; Maomin Sun; Bairong Shen (Briefings Bioinform., 2015)

PON-Sol: prediction of effects of amino acid substitutions on protein solubility. - Yang Yang; Abhishek Niroula; Bairong Shen; Mauno Vihinen (Bioinform., 2016)

Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach. - Feixiong Cheng; Chuang Liu; Bairong Shen; Zhongming Zhao (BMC Syst. Biol., 2016)

Identification of intrinsic disorder in complexes from Protein Data Bank. - Jianhong Zhou; Christopher J. Oldfield; Fei Huang; Wenying Yan; Bairong Shen; A. Keith Dunker (ICCABS, 2018)

NDDVD: an integrated and manually curated Neurodegenerative Diseases Variation Database. - Yang Yang; Chen Xu; Xingyun Liu; Chao Xu; Yuanyuan Zhang; Li Shen; Mauno Vihinen; Bairong Shen (Database J. Biol. Databases Curation, 2018)

CBD: a biomarker database for colorectal cancer. - Xueli Zhang; Xiao-Feng Sun; Yang Cao 009; Benchen Ye; Qiliang Peng; Xingyun Liu; Bairong Shen; Hong Zhang (Database J. Biol. Databases Curation, 2018)

Node-Weighted Amino Acid Network Strategy for Characterization and Identification of Protein Functional Residues. - Wenying Yan; Guang Hu 001; Zhongjie Liang; Jianhong Zhou; Yang Yang; Jiajia Chen; Bairong Shen (J. Chem. Inf. Model., 2018)

NGS-FC: A Next-Generation Sequencing Data Format Converter. - Chunjiang Yu; Wentao Wu 004; Jing Wang; Yuxin Lin; Yang Yang; Jiajia Chen; Fei Zhu 003; Bairong Shen (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

ECG Generation With Sequence Generative Adversarial Nets Optimized by Policy Gradient. - Fei Ye; Fei Zhu 003; Yuchen Fu; Bairong Shen (IEEE Access, 2019)

Computer-aided biomarker discovery for precision medicine: data resources, models and applications. - Yuxin Lin; Fuliang Qian; Li Shen; Feifei Chen; Jiajia Chen; Bairong Shen (Briefings Bioinform., 2019)

MIRKB: a myocardial infarction risk knowledge base. - Chaoying Zhan; Manhong Shi; Rongrong Wu; Hongxin He; Xingyun Liu; Bairong Shen (Database J. Biol. Databases Curation, 2019)

Translational Informatics for Parkinson's Disease: from Big Biomedical Data to Small Actionable Alterations. - Bairong Shen; Yuxin Lin; Cheng Bi; Shengrong Zhou; Zhongchen Bai; Guangmin Zheng 002; Jing Zhou (Genom. Proteom. Bioinform., 2019)

Modeling and Simulation Studies of Complex Biological Systems for Precision Medicine and Healthcare. - Bairong Shen; Xiaoqian Jiang; Xingming Zhao (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Decoding competing endogenous RNA networks for cancer biomarker discovery. - Xin Qi; Yuxin Lin; Jiajia Chen; Bairong Shen (Briefings Bioinform., 2020)

PCaLiStDB: a lifestyle database for precision prevention of prostate cancer. - Yalan Chen; Xingyun Liu; Yijun Yu; Chunjiang Yu; Lan Yang; Yuxin Lin; Ting Xi; Ziyun Ye; Zhe Feng 006; Bairong Shen (Database J. Biol. Databases Curation, 2020)

Phenotype-genotype network construction and characterization: a case study of cardiovascular diseases and associated non-coding RNAs. - Rongrong Wu; Yuxin Lin; Xingyun Liu; Chaoying Zhan; Hongxin He; Manhong Shi; Zhi Jiang; Bairong Shen (Database J. Biol. Databases Curation, 2020)

CHDGKB: a knowledgebase for systematic understanding of genetic variations associated with non-syndromic congenital heart disease. - Lan Yang; Yang Yang; Xingyun Liu; Yongquan Chen; Yalan Chen; Yuxin Lin; Yan Sun; Bairong Shen (Database J. Biol. Databases Curation, 2020)

iODA: An integrated tool for analysis of cancer pathway consistency from heterogeneous multi-omics data. - Chunjiang Yu; Xin Qi; Yuxin Lin; Yin Li; Bairong Shen (J. Biomed. Informatics, 2020)

CMBD: a manually curated cancer metabolic biomarker knowledge database. - Jing Chen; Xingyun Liu; Li Shen; Yuxin Lin; Bairong Shen (Database J. Biol. Databases Curation, 2021)

HFBD: a biomarker knowledge database for heart failure heterogeneity and personalized applications. - Hongxin He; Manhong Shi; Yuxin Lin; Chaoying Zhan; Rongrong Wu; Cheng Bi; Xingyun Liu; Shumin Ren; Bairong Shen (Bioinform., 2021)

PCLiON: An Ontology for Data Standardization and Sharing of Prostate Cancer Associated Lifestyles. - Yalan Chen; Chunjiang Yu; Xingyun Liu; Ting Xi; Guangfei Xu; Yan Sun; Fei Zhu 003; Bairong Shen (Int. J. Medical Informatics, 2021)

CRPMKB: a knowledge base of cancer risk prediction models for systematic comparison and personalized applications. - Shumin Ren; Yanwen Jin; Yalan Chen; Bairong Shen (Bioinform., 2022)

Biomarkers discovery for endometrial cancer: A graph convolutional sample network method. - Erman Wu; Xuemeng Fan; Tong Tang; Jingjing Li; Jiao Wang; Xingyun Liu; Zayatta Zungar; Jiaojiao Ren; Cong Wu 005; Bairong Shen (Comput. Biol. Medicine, 2022)

CD93 orchestrates the tumor microenvironment and predicts the molecular subtype and therapy response of bladder cancer. - Xiaonan Zheng; Hang Xu; Tianhai Lin; Ping Tan; Qiao Xiong; Xianyanling Yi; Shi Qiu; Lu Yang; Bairong Shen; Jianzhong Ai; Qiang Wei (Comput. Biol. Medicine, 2022)

Next-Generation Sequencing Markup Language (NGSML): A Medium for the Representation and Exchange of NGS Data. - Chunjiang Yu; Xin Qi; Wenying Yan; Wentao Wu 004; Bairong Shen (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

CTRR-ncRNA: A Knowledgebase for Cancer Therapy Resistance and Recurrence Associated Non-coding RNAs. - Tong Tang; Xingyun Liu; Rongrong Wu; Li Shen; Shumin Ren; Bairong Shen (Genom. Proteom. Bioinform., 2023)

Translational informatics for human microbiota: data resources, models and applications. - Ke Shen; Ahmad Ud Din; Baivab Sinha; Yi Zhou; Fuliang Qian; Bairong Shen (Briefings Bioinform., 2023)

Myocardial infarction unveiled: Key miRNA players screened by a novel lncRNA-miRNA-mRNA network model. - Chaoying Zhan; Kai Liu; Yuxin Zhang; Yingbo Zhang; Mengqiao He; Rongrong Wu; Cheng Bi; Bairong Shen (Comput. Biol. Medicine, 2023)

Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome. - Yinhu Li; Guangze Pan; Shuai Wang 036; Zhengtu Li; Ru Yang; Yiqi Jiang; Yu Chen; Shuaicheng Li 001; Bairong Shen (Briefings Bioinform., 2024)

Elevated incidence of somatic mutations at prevalent genetic sites. - Mengyao Wang; Shuai Cheng Li 001; Bairong Shen (Briefings Bioinform., 2024)

scFed: federated learning for cell type classification with scRNA-seq. - Shuang Wang 002; Bochen Shen; Lanting Guo; Mengqi Shang; Jinze Liu; Qi Sun; Bairong Shen (Briefings Bioinform., 2024)

Identify gestational diabetes mellitus by deep learning model from cell-free DNA at the early gestation stage. - Yipeng Wang; Pei Sun; Zicheng Zhao; Yousheng Yan; Wentao Yue; Kai Yang; Ruixia Liu; Hui Huang; Yinan Wang; Yin Chen; Nan Li; Hailong Feng; et al. (Briefings Bioinform., 2024)

PCAO2: an ontology for integration of prostate cancer associated genotypic, phenotypic and lifestyle data. - Chunjiang Yu; Hui Zong; Yalan Chen; Yibin Zhou; Xingyun Liu; Yuxin Lin; Jiakun Li; Xiaonan Zheng; Hua Min; Bairong Shen (Briefings Bioinform., 2024)

Advancing Biomedical Text Mining with Community Challenges. - Hui Zong; Rongrong Wu; Jiaxue Cha; Erman Wu; Jiakun Li; Liang Tao; Zuofeng Li; Buzhou Tang; Bairong Shen (CoRR, 2024)

Bridging the Gaps: Utilizing Unlabeled Face Recognition Datasets to Boost Semi-Supervised Facial Expression Recognition. - Jie Song; Mengqiao He; Jinhua Feng; Bairong Shen (CoRR, 2024)

Advancing Chinese biomedical text mining with community challenges. - Hui Zong; Rongrong Wu; Jiaxue Cha; Weizhe Feng; Erman Wu; Jiakun Li; Aibin Shao; Liang Tao; Zuofeng Li; Buzhou Tang; Bairong Shen (J. Biomed. Informatics, 2024)

Medical intelligence for anxiety research: Insights from genetics, hormones, implant science, and smart devices with future strategies. - Faijan Akhtar; Md Belal Bin Heyat; Arshiya Sultana; Saba Parveen; Hafiz Muhammad Zeeshan; Stalin Fathima Merlin; Bairong Shen; Dustin Pomary; Jian Ping Li; Mohamad Sawan (WIREs Data. Mining. Knowl. Discov., 2024)

PPCRKB: a risk factor knowledge base of postoperative pulmonary complications. - Jianchao Duan; Peiyi Li 007; Aibin Shao; Xuechao Hao; Ruihao Zhou; Cheng Bi; Xingyun Liu; Weimin Li 003; Huadong Zhu; Guo Chen; Bairong Shen; Tao Zhu (Database J. Biol. Databases Curation, 2024)

DRGKB: a knowledgebase of worldwide diagnosis-related groups' practices for comparison, evaluation and knowledge-guided application. - Shumin Ren; Lin Yang; Jiale Du; Mengqiao He; Bairong Shen (Database J. Biol. Databases Curation, 2024)

From molecular mechanisms of prostate cancer to translational applications: based on multi-omics fusion analysis and intelligent medicine. - Shumin Ren; Jiakun Li; Julián Dorado; Alejandro Pazos Sierra; Humberto González Díaz; Aliuska Duardo-Sánchez; Bairong Shen (Health Inf. Sci. Syst., 2024)

Development of transient ischemic attack risk prediction model suitable for initializing a learning health system unit using electronic medical records. - Jian Wen; Tianmei Zhang; Shangrong Ye; Cheng Li; Ruobing Han; Ran Huang; Bairong Shen; Anjun Chen; Qinghua Li (BMC Medical Informatics Decis. Mak., 2024)

MIO: An ontology for annotating and integrating medical knowledge in myocardial infarction to enhance clinical decision making. - Chaoying Zhan; Shumin Ren; Yuxin Zhang; Xiaojun Lv; Yalan Chen; Xin Zheng; Rongrong Wu; Erman Wu; Tong Tang; Jiao Wang; Cheng Bi; Mengqiao He; et al. (Comput. Biol. Medicine, 2025)

The comprehensive clinical benefits of digital phenotyping: from broad adoption to full impact. - Yingbo Zhang; Jiao Wang; Hui Zong; Rajeev K. Singla; Amin Ullah; Xingyun Liu; Rongrong Wu; Shumin Ren; Bairong Shen (npj Digit. Medicine, 2025)

Expertise or Hallucination? A Comprehensive Evaluation of ChatGPT's Aptitude in Clinical Genetics. - Yingbo Zhang; Shumin Ren; Jiao Wang; Chaoying Zhan; Mengqiao He; Xingyun Liu; Rongrong Wu; Jing Zhao; Cong Wu 005; Chuanzhu Fan; Bairong Shen (IEEE Trans. Big Data, 2025)

Face-based machine learning diagnostics: applications, challenges and opportunities. - Jie Song; Mengqiao He; Xin Zheng; Yuxin Zhang; Cheng Bi; Jinhua Feng; Jiale Du; Hang Li; Bairong Shen (Artif. Intell. Rev., 2025)