Bairong Shen

发表

PON-tstab: Protein Variant Stability Predictor. Importance of Training Data Quality

Yang Yang, Siddhaling Urolagin, Abhishek Niroula, 2018, International journal of molecular sciences.

XML, Ontologies, and Their Clinical Applications.

Bairong Shen, Chunjiang Yu, Bairong Shen, 2016, Advances in experimental medicine and biology.

Decoding competing endogenous RNA networks for cancer biomarker discovery

Xin Qi, Jiajia Chen, Bairong Shen, 2020, Briefings Bioinform..

Node-Weighted Amino Acid Network Strategy for Characterization and Identification of Protein Functional Residues

Jiajia Chen, Bairong Shen, Wenying Yan, 2018, J. Chem. Inf. Model..

Stepping Optimal Controlling of a Rucklidge-Like Chaotic System

Zhi Yang, Bairong Shen, Binhua Tang, 2007, 2007 International Conference on Wireless Communications, Networking and Mobile Computing.

Combined SVM-CRFs for Biological Named Entity Recognition with Maximal Bidirectional Squeezing

Bairong Shen, Fei Zhu, Bairong Shen, 2012, PloS one.

Phenotype–genotype network construction and characterization: a case study of cardiovascular diseases and associated non-coding RNAs

Bairong Shen, Yuxin Lin, Xingyun Liu, 2020, Database J. Biol. Databases Curation.

Modeling and Simulation Studies of Complex Biological Systems for Precision Medicine and Healthcare

Xiaoqian Jiang, Bairong Shen, Xingming Zhao, 2019, TCBB.

Yeast Network and Report of New Stochastic-Credibility Cell Cycle Models

Bairong Shen, Oana Chis, Opris Dumitru, 2011 .

Bibliome Mining Platform and Application for Building Metabolic Interaction Network

Bairong Shen, Preecha Patumcharoenpol, Jonathan H. Chan, 2012, CSBio.

Identification of Intrinsic Disorder in Complexes from the Protein Data Bank

Jianhong Zhou, Bairong Shen, Fei Huang, 2018, 2018 IEEE 8th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS).

Translational Bioinformatics and Computational Systems Medicine

Hong-Bin Shen, Bairong Shen, Tianhai Tian, 2013, Comput. Math. Methods Medicine.

Molecular Signature of Cancer at Gene Level or Pathway Level? Case Studies of Colorectal Cancer and Prostate Cancer Microarray Data

Ying Wang, Daqing Zhang, Jiajia Chen, 2013, Comput. Math. Methods Medicine.

RNA Bioinformatics for Precision Medicine.

Bairong Shen, Jiajia Chen, Bairong Shen, 2016, Advances in experimental medicine and biology.

Translational Informatics in Smart Healthcare

Bairong Shen, Bairong Shen, Bairong Shen, 2017, Advances in Experimental Medicine and Biology.

LIMS and Clinical Data Management.

Bairong Shen, Yuxin Lin, Yalan Chen, 2016, Advances in experimental medicine and biology.

NGS-FC: A Next-Generation Sequencing Data Format Converter

Yang Yang, Jiajia Chen, Bairong Shen, 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Protein-Protein Interaction Network Constructing Based on Text Mining and Reinforcement Learning with Application to Prostate Cancer

Xiaofang Zhang, Quan Liu, Bairong Shen, 2014, 2015 IEEE Trustcom/BigDataSE/ISPA.

Towards patterns tree of gene coexpression in eukaryotic species

Xia Li, Qi Wang, Bairong Shen, 2008, Bioinform..

PON-Sol: prediction of effects of amino acid substitutions on protein solubility

Yang Yang, Abhishek Niroula, Bairong Shen, 2016, Bioinform..

ANCA: A Web Server for Amino Acid Networks Construction and Analysis

Bairong Shen, Chunjiang Yu, Wenying Yan, 2020, Frontiers in Molecular Biosciences.

Identification and Functional Annotation of Genome-Wide ER-Regulated Genes in Breast Cancer Based on ChIP-Seq Data

Jiajia Chen, Bairong Shen, Zhonghua Xu, 2012, Comput. Math. Methods Medicine.

Physiological Informatics: Collection and Analyses of Data from Wearable Sensors and Smartphone for Healthcare.

Bairong Shen, Li Shen, Jinwei Bai, 2017, Advances in experimental medicine and biology.

Translational Bioinformatics for Cholangiocarcinoma: Opportunities and Challenges

Bairong Shen, Zhi Jiang, Fuliang Qian, 2018, International journal of biological sciences.

RankViaContact: ranking and visualization of amino acid contacts

Bairong Shen, Mauno Vihinen, Bairong Shen, 2003, Bioinform..

Electrocardiogram generation with a bidirectional LSTM-CNN generative adversarial network

Quan Liu, Yuchen Fu, Bairong Shen, 2019, Scientific Reports.

Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs

Jiajia Chen, Bairong Shen, Bingchuan Liu, 2011, BMC Systems Biology.

Network-Based Biomedical Data Analysis.

Bairong Shen, Yuxin Lin, Xuye Yuan, 2016, Advances in experimental medicine and biology.

Biobanks and Their Clinical Application and Informatics Challenges.

Lan Yang, Bairong Shen, Chunjiang Yu, 2016, Advances in experimental medicine and biology.

Computer-aided biomarker discovery for precision medicine: data resources, models and applications

Bairong Shen, Li Shen, Yuxin Lin, 2019, Briefings Bioinform..

Model-Based Identification and Adaptive Control of the Core Module in a Typical Cell Cycle Pathway via Network and System Control Theories

Bairong Shen, Li He, Binhua Tang, 2009, Adv. Complex Syst..

Protein-protein interaction network constructing based on text mining and reinforcement learning with application to prostate cancer

Xiaofang Zhang, Quan Liu, Bairong Shen, 2015, 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

CHDGKB: a knowledgebase for systematic understanding of genetic variations associated with non-syndromic congenital heart disease

Bairong Shen, Yang Yang, Yuxin Lin, 2020, Database J. Biol. Databases Curation.

MIRKB: a myocardial infarction risk knowledge base

Bairong Shen, Xingyun Liu, Rongrong Wu, 2019, Database J. Biol. Databases Curation.

Data-driven translational prostate cancer research: from biomarker discovery to clinical decision

Bairong Shen, Yuxin Lin, Xiaojun Zhao, 2020, Journal of Translational Medicine.

Computational inference and analysis of genetic regulatory networks via a supervised combinatorial-optimization pattern

Bairong Shen, Su-Shing Chen, Binhua Tang, 2010, BMC Systems Biology.

Identification of novel microRNA regulatory pathways associated with heterogeneous prostate cancer

Jiajia Chen, Bairong Shen, Cheng Luo, 2013, BMC Systems Biology.

Protein interaction network constructing based on text mining and reinforcement learning with application to prostate cancer.

Bairong Shen, Fei Zhu, Quan Liu, 2015, IET systems biology.

System Stability Via Stepping Optimal Control: Theory and Applications

Li He, Bairong Shen, Binhua Tang, 2007, EPIA Workshops.

Translational Informatics for Parkinson’s Disease: from Big Biomedical Data to Small Actionable Alterations

Bairong Shen, Yuxin Lin, Jing Zhou, 2019, Genom. Proteom. Bioinform..

The preservation of bidirectional promoter architecture in eukaryotes: what is the driving force?

Chao Xu, Jiajia Chen, Bairong Shen, 2012, BMC Systems Biology.

Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach

Chuang Liu, Zhongming Zhao, Feixiong Cheng, 2016, BMC Systems Biology.

Translational Biomedical Informatics in the Cloud: Present and Future

Bairong Shen, Wenying Yan, Jiajia Chen, 2013, BioMed research international.

Disease associated protein-protein interaction network reconstruction based on comprehensive influence analysis

Feifei Li, Bairong Shen, Fei Zhu, 2019, bioRxiv.

PCaLiStDB: a lifestyle database for precision prevention of prostate cancer

Lan Yang, Bairong Shen, Chunjiang Yu, 2020, Database J. Biol. Databases Curation.

Identifying novel prostate cancer associated pathways based on integrative microarray data analysis

Ying Wang, Jiajia Chen, Bairong Shen, 2011, Comput. Biol. Chem..

ECG Generation With Sequence Generative Adversarial Nets Optimized by Policy Gradient

Yuchen Fu, Bairong Shen, Fei Zhu, 2019, IEEE Access.

Abstract 1320: An integrative and interactive colorectal cancer biomarker database

Bairong Shen, Yang Cao, Xingyun Liu, 2018 .

Biomedical text mining and its applications in cancer research

Cheng Zhang, Yang Yang, Bairong Shen, 2013, J. Biomed. Informatics.

Identifying novel glioma associated pathways based on systems biology level meta-analysis

Yin Li, Jiajia Chen, Bairong Shen, 2013, BMC Systems Biology.

Deciphering oncogenic drivers: from single genes to integrated pathways

Jiajia Chen, Bairong Shen, Maomin Sun, 2015, Briefings Bioinform..

NDDVD: an integrated and manually curated Neurodegenerative Diseases Variation Database

Chao Xu, Yuanyuan Zhang, Li Shen, 2018, Database J. Biol. Databases Curation.

InCoB2013 introduces Systems Biology as a major conference theme

Tin Wee Tan, Bairong Shen, Shoba Ranganathan, 2013, BMC Systems Biology.

USEDAT: USA-Europe Data Analysis Training Worldwide Program, 2019 ed.

Yasset Perez-Riverol, Sonia Arrasate, Nuria Sotomayor, 2019 .

CBD: a biomarker database for colorectal cancer

Hong Zhang, Bairong Shen, Yang Cao, 2018, Database J. Biol. Databases Curation.

Biomarker Discovery with Text Mining and Literature Based Discovery

Bairong Shen, Fei Zhu, Bairong Shen, 2013 .

Identifying novel glioma associated pathways based on integrated ‘omics’ data

Jiajia Chen, Bairong Shen, Guang Hu, 2012, 2012 IEEE 6th International Conference on Systems Biology (ISB).

Clinical Information Driven Ensemble Clustering for Inferring Robust Tumor Subtypes

Xia Li, Bairong Shen, Haiyun Wang, 2009, 2009 2nd International Conference on Biomedical Engineering and Informatics.

An integrative framework for identifying consistent microRNA expression signatures associated with clear cell renal cell carcinoma

Daqing Zhang, Wenyu Zhang, Jiajia Chen, 2012, 2012 IEEE 6th International Conference on Systems Biology (ISB).

HFBD: a biomarker knowledge database for heart failure heterogeneity and personalized applications

Bairong Shen, Yuxin Lin, Xingyun Liu, 2021, Bioinform..

CMBD: a manually curated cancer metabolic biomarker knowledge database

Bairong Shen, Yuxin Lin, Xingyun Liu, 2021, Database J. Biol. Databases Curation.

The fourth scientific discovery paradigm for precision medicine and healthcare: Challenges ahead

Bairong Shen, Li Shen, Jinwei Bai, 2021, Precision clinical medicine.

Network modelling reveals the mechanism underlying colitis-associated colon cancer and identifies novel combinatorial anti-cancer targets

Cheng Luo, Bairong Shen, Zhongjie Liang, 2015, Scientific Reports.

New genes drive the evolution of gene interaction networks in the human and mouse genomes

Bairong Shen, Manyuan Long, M. Long, 2015, Genome Biology.

Residue interaction network analysis of Dronpa and a DNA clamp.

Bairong Shen, Wenying Yan, Guang Hu, 2014, Journal of theoretical biology.

Network Biomarkers Constructed from Gene Expression and Protein-Protein Interaction Data for Accurate Prediction of Leukemia

Jiajia Chen, Bairong Shen, Yuxin Lin, 2017, Journal of Cancer.

NF-Y influences directionality of transcription from the bidirectional Mrps12/Sarsm promoter in both mouse and human cells.

Bairong Shen, Antti Häkkinen, Gabriel N. Teku, 2009, Biochimica et biophysica acta.

Amino acid network for the discrimination of native protein structures from decoys.

Bairong Shen, Wenying Yan, Guang Hu, 2014, Current protein & peptide science.

Computationally Comparative Analysis of CpG Islands in Human Bidirectional and Unidirectional Promoters

Jiajia Chen, Bairong Shen, Jiajia Chen, 2010, 2010 4th International Conference on Bioinformatics and Biomedical Engineering.

Systems Health: A Transition from Disease Management Toward Health Promotion.

Bairong Shen, Yuxin Lin, Benchen Ye, 2017, Advances in experimental medicine and biology.

Biomedical Data Integration, Modeling, and Simulation in the Era of Big Data and Translational Medicine

Junfeng Xia, Bairong Shen, Degui Zhi, 2014, BioMed research international.

Renyi Distribution Entropy Analysis of Short-Term Heart Rate Variability Signals and Its Application in Coronary Artery Disease Detection

Bairong Shen, Rongrong Wu, Chaoying Zhan, 2019, Front. Physiol..

Top associated SNPs in prostate cancer are significantly enriched in cis-expression quantitative trait loci and at transcription factor binding sites

Peilin Jia, Zhongming Zhao, Bairong Shen, 2014, Oncotarget.

Physicochemical feature-based classification of amino acid mutations.

Bairong Shen, Mauno Vihinen, Jinwei Bai, 2007, Protein engineering, design & selection : PEDS.

Key regulators in prostate cancer identified by co-expression module analysis

Peilin Jia, Zhongming Zhao, Bairong Shen, 2014, BMC Genomics.

Amino acid contact energy networks impact protein structure and evolution.

Jiajia Chen, Bairong Shen, Wenying Yan, 2014, Journal of theoretical biology.

MiRNA-BD: an evidence-based bioinformatics model and software tool for microRNA biomarker discovery

Bairong Shen, Zhandong Sun, Yuxin Lin, 2018, RNA biology.

A systems biology perspective on rational design of peptide vaccine against virus infections.

Jiajia Chen, Bairong Shen, Ying Wang, 2012, Current topics in medicinal chemistry.

Comparison of Prognostic MicroRNA Biomarkers in Blood and Tissues for Gastric Cancer

Jiajia Chen, Bairong Shen, Wenying Yan, 2016, Journal of Cancer.

Structure-based prediction of the effects of a missense variant on protein stability

Bairong Shen, Mauno Vihinen, Yang Yang, 2012, Amino Acids.

Clear cell renal cell carcinoma associated microRNA expression signatures identified by an integrated bioinformatics analysis

Jiajia Chen, Bairong Shen, Wenying Yan, 2013, Journal of Translational Medicine.

MicroRNA expression analysis reveals significant biological pathways in human prostate cancer

Jiajia Chen, Bairong Shen, Yifei Tang, 2011, 2011 IEEE International Conference on Systems Biology (ISB).

Interactions Between Genetics, Lifestyle, and Environmental Factors for Healthcare.

Jiajia Chen, Bairong Shen, Yuxin Lin, 2017, Advances in experimental medicine and biology.

Genome wide analysis of pathogenic SH2 domain mutations

Bairong Shen, Mauno Vihinen, Ilkka Lappalainen, 2008, Proteins.

Computational analysis of microRNA function in heart development.

Jiajia Chen, Bairong Shen, Qing Jing, 2010, Acta biochimica et biophysica Sinica.

Identification of candidate miRNA biomarkers from miRNA regulatory network with application to prostate cancer

Bairong Shen, Zhandong Sun, Wenying Yan, 2014, Journal of Translational Medicine.

Novel Biomarker MicroRNAs for Subtyping of Acute Coronary Syndrome: A Bioinformatics Approach

Xiaoqian Jiang, Bairong Shen, Zhandong Sun, 2016, BioMed research international.

Biomedical Informatics and Computational Biology for High-Throughput Data Analysis

Bairong Shen, Junbai Wang, Jian Ma, 2014, TheScientificWorldJournal.

Post genome-wide association studies functional characterization of prostate cancer risk loci

Bairong Shen, Guang Hu, Wanwipa Vongsangnak, 2013, BMC Genomics.

Wavelet Transform Based Protein Decoy Discrimination

Minxin Chen, Bairong Shen, Wenying Yan, 2009, 2009 3rd International Conference on Bioinformatics and Biomedical Engineering.

Conservation and covariance in PH domain sequences: physicochemical profile and information theoretical analysis of XLA-causing mutations in the Btk PH domain.

Bairong Shen, Mauno Vihinen, Bairong Shen, 2004, Protein engineering, design & selection : PEDS.

Identification of MicroRNA as Sepsis Biomarker Based on miRNAs Regulatory Network Analysis

Bairong Shen, Zhandong Sun, Yuxin Lin, 2014, BioMed research international.

The topology and dynamics of protein complexes: insights from intra- molecular network theory.

Bairong Shen, Wenying Yan, Guang Hu, 2013, Current protein & peptide science.

Knowledge-Guided Bioinformatics Model for Identifying Autism Spectrum Disorder Diagnostic MicroRNA Biomarkers

Bairong Shen, Zhandong Sun, Yuxin Lin, 2016, Scientific Reports.

Understanding Amino Acid Mutations in Hepatitis B Virus Proteins for Rational Design of Vaccines and Drugs.

Bairong Shen, Jing Wang, Zhi Jiang, 2015, Advances in protein chemistry and structural biology.

Effects of Time Point Measurement on the Reconstruction of Gene Regulatory Networks

Bairong Shen, Yang Yang, Wenying Yan, 2010, Molecules.

Megafiller: A Retrofitted Protein Function Predictor for Filling Gaps inMetabolic Networks

Hon Wai Leong, Bairong Shen, Wanwipa Vongsangnak, 2014 .

MicroRNA biomarker identification for pediatric acute myeloid leukemia based on a novel bioinformatics model

Jiajia Chen, Bairong Shen, Zhandong Sun, 2015, Oncotarget.

Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression

Bairong Shen, Wanwipa Vongsangnak, Luonan Chen, 2014, BMC Medical Genomics.

Segmentation of Neuronal Structures Using SARSA (λ)-Based Boundary Amendment with Reinforced Gradient-Descent Curve Shape Fitting

Quan Liu, Yuchen Fu, Bairong Shen, 2014, PloS one.

Identification of biomarker microRNAs for predicting the response of colorectal cancer to neoadjuvant chemoradiotherapy based on microRNA regulatory network

Jiajia Chen, Bairong Shen, Yuxin Lin, 2016, Oncotarget.

Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data

Jiajia Chen, Zhongming Zhao, Bairong Shen, 2015, BMC Genomics.

Amino acid network for prediction of catalytic residues in enzymes: a comparison survey.

Bairong Shen, Wenying Yan, Guang Hu, 2016, Current protein & peptide science.

Biomarker microRNAs for prostate cancer metastasis: screened with a network vulnerability analysis model

Jiajia Chen, Bairong Shen, Zhandong Sun, 2018, Journal of Translational Medicine.

Screening key microRNAs for castration-resistant prostate cancer based on miRNA/mRNA functional synergistic network

Bairong Shen, Bairong Shen, Dong-rong Yang, 2015, Oncotarget.

Informatics for Precision Medicine and Healthcare.

Jiajia Chen, Bairong Shen, Yuxin Lin, 2017, Advances in experimental medicine and biology.

SVR_CAF: An integrated score function for detecting native protein structures among decoys

Bairong Shen, Wenying Yan, Guang Hu, 2014, Proteins.