- Yang Yang, Abhishek Niroula, Bairong Shen and Mauno Vihinen，PON-Sol: prediction of effects of amino acid substitutions on protein solubility. Bioinformatics, 2016
- Tao M, Liu L, Shen M, Zhi Q, Gong FR, Zhou BP, Wu Y, Liu H, Chen K, Shen B, Wu MY, Shou LM, Li W. Inflammatory stimuli promote growth and invasion of pancreatic cancer cells through NF-κB pathway dependent repression of PP2Ac. Cell Cycle. 2016 Feb;15(3):381-93.
- Yan W, Qian L, Chen J, Chen W, Shen B. Comparison of Prognostic MicroRNA Biomarkers in Blood and Tissues for Gastric Cancer. J Cancer. 2016 Jan 1;7(1):95-106.
- Yan W, Xu L, Sun Z, Lin Y, Zhang W, Chen J, Hu S, Shen B.MicroRNA biomarker identification for pediatric acute myeloid leukemia based on a novel bioinformatics model. Oncotarget. 2015 Sep 22;6(28):26424-36.
- Lu J, Zeng H, Liang Z, Chen L, Zhang L, Zhang H, Liu H, Jiang H, Shen B, Huang M, Geng M, Spiegel S, Luo C. Network modelling reveals the mechanism underlying colitis-associated colon cancer and identifies novel combinatorial anti-cancer targets. Sci Rep. 2015 Oct 8;5:14739.
- Zhang W, Landback P, Gschwend AR, Shen B, Long M. New genes drive the evolution of gene interaction networks in the human and mouse genomes. Genome Biol. 2015 Oct 1;16(1):202.
- Zhu F, Liu Q, Zhang X, Shen B. Protein interaction network constructing based on text mining and reinforcement learning with application to prostate cancer. IET Syst Biol. 2015 Aug;9(4):106-12.
- Cui W, Qian Y, Zhou X, Lin Y, Jiang J, Chen J, Zhao Z, Shen B. Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data. BMC Genomics. 2015;16 Suppl 7:S3.
- Shen K, Shen L, Wang J, Jiang Z, Shen B. Understanding Amino Acid Mutations in Hepatitis B Virus Proteins for Rational Design of Vaccines and Drugs. Adv Protein Chem Struct Biol. 2015;99:131-53.
- Naillat F, Yan W, Karjalainen R, Liakhovitskaia A, Samoylenko A, Xu Q, Sun Z, Shen B, Medvinsky A, Quaggin S, Vainio SJ. Identification of the genes regulated by Wnt-4, a critical signal for commitment of the ovary. Exp Cell Res. 2015 Mar 15;332(2):163-78.
- Chen J, Sun M, Shen B. Deciphering oncogenic drivers: from single genes to integrated pathways. Brief Bioinform. 2015 May;16(3):413-28.
- Zhu F, Liu Q, Fu Y and Shen B. Segmentation of Neuronal Structures Using SARSA (lambda)-Based Boundary Amendment with Reinforced Gradient-Descent Curve Shape Fitting. Plos One. 2014; 9(3).
- Zhou J, Yan W, Hu G and Shen B. Amino Acid Network for the Discrimination of Native Protein Structures from Decoys. Current Protein & Peptide Science. 2014; 15(6):522-528.
- Zhou J, Yan W, Hu G and Shen B. SVR_CAF: An integrated score function for detecting native protein structures among decoys. Proteins-Structure Function and Bioinformatics. 2014; 82(4):556-564.
- Zhang W, Zang J, Jing X, Sun Z, Yan W, Yang D, Guo F and Shen B. Identification of candidate miRNA biomarkers from miRNA regulatory network with application to prostate cancer. Journal of Translational Medicine. 2014; 12.
- Yan W, Zhou J, Sun M, Chen J, Hu G and Shen B. The construction of an amino acid network for understanding protein structure and function. Amino Acids. 2014; 46(6):1419-1439.
- Yan W, Sun M, Hu G, Zhou J, Zhang W, Chen J, Chen B and Shen B. Amino acid contact energy networks impact protein structure and evolution. Journal of Theoretical Biology. 2014; 355:95-104.
- Xie Y, Zhou R, Lian F, Liu Y, Chen L, Shi Z, Zhang N, Zheng M, Shen B, Jiang H, Liang Z and Luo C. Virtual screening and biological evaluation of novel small molecular inhibitors against protein arginine methyltransferase 1 (PRMT1). Organic & Biomolecular Chemistry. 2014; 12(47):9665-9673.
- Prunskaite-Hyyrylainen R, Shan J, Railo A, Heinonen KM, Miinalainen I, Yan W, Shen B, Perreault C and Vainio SJ. Wnt4, a pleiotropic signal for controlling cell polarity, basement membrane integrity, and antimullerian hormone expression during oocyte maturation in the female follicle. Faseb Journal. 2014; 28(4):1568-1581.
- Li Y, Vongsangnak W, Chen L and Shen B. Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression. Bmc Medical Genomics. 2014; 7.
- Jiang J, Jia P, Zhao Z and Shen B. Key regulators in prostate cancer identified by co-expression module analysis. Bmc Genomics. 2014; 15.
- Jiang J, Jia P, Shen B and Zhao Z. Top associated SNPs in prostate cancer are significantly enriched in cis-expression quantitative trait loci and at transcription factor binding sites. Oncotarget. 2014; 5(15):6168-6177.
- Hu G, Yan W, Zhou J and Shen B. Residue interaction network analysis of Dronpa and a DNA clamp. Journal of Theoretical Biology. 2014; 348:55-64.
- Yang Y, Chen B, Tan G, Vihinen M and Shen B. Structure-based prediction of the effects of a missense variant on protein stability. Amino Acids. 2013; 44(3):847-855.
- Vongsangnak W, Ruenwai R, Tang X, Hu X, Zhang H, Shen B, Song Y and Laoteng K. Genome-scale analysis of the metabolic networks of oleaginous Zygomycete fungi. Gene. 2013; 521(1):180-190.
- Tang Y, Yan W, Chen J, Luo C, Kaipia A and Shen B. Identification of novel microRNA regulatory pathways associated with heterogeneous prostate cancer. Bmc Systems Biology. 2013; 7.
- Schoenbach C, Shen B, Tan TW and Ranganathan S. InCoB2013 introduces Systems Biology as a major conference theme INTRODUCTION. Bmc Systems Biology. 2013; 7.
- Jiang J, Cui W, Vongsangnak W, Hu G and Shen B. Post genome-wide association studies functional characterization of prostate cancer risk loci. Bmc Genomics. 2013; 14.
- Hu Y, Li J, Yan W, Chen J, Li Y, Hu G and Shen B. Identifying novel glioma associated pathways based on systems biology level meta-analysis. Bmc Systems Biology. 2013; 7.
- Hu G, Zhou J, Yan W, Chen J and Shen B. The Topology and Dynamics of Protein Complexes: Insights from Intra-Molecular Network Theory. Current Protein & Peptide Science. 2013; 14(2):121-132.
- Chen J, Zhang D, Zhang W, Tang Y, Yan W, Guo L and Shen B. Clear cell renal cell carcinoma associated microRNA expression signatures identified by an integrated bioinformatics analysis. Journal of Translational Medicine. 2013; 11.
- Zhu F and Shen B. Combined SVM-CRFs for Biological Named Entity Recognition with Maximal Bidirectional Squeezing. Plos One. 2012; 7(6).
- Xu C, Chen J and Shen B. The preservation of bidirectional promoter architecture in eukaryotes: what is the driving force? BMC systems biology. 2012; 6 Suppl 1:S21-S21.
- Li Y, Zhang Z, Liu F, Vongsangnak W, Jing Q and Shen B. Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis. Nucleic Acids Research. 2012; 40(10):4298-4305.
- Jiang J, Lu J, Lu D, Liang Z, Li L, Ouyang S, Kong X, Jiang H, Shen B and Luo C. Investigation of the Acetylation Mechanism by GCN5 Histone Acetyltransferase. Plos One. 2012; 7(5).
- Chen J, Wang Y, Guo D and Shen B. A Systems Biology Perspective on Rational Design of Peptide Vaccine Against Virus Infections. Current Topics in Medicinal Chemistry. 2012; 12(12):1310-1319.
- Zou J, Li W-Q, Li Q, Li X-Q, Zhang J-T, Liu G-Q, Chen J, Qiu X-X, Tian F-J, Wang Z-Z, Zhu N, Qin Y-W, Shen B, Liu TX and Jing Q. Two Functional MicroRNA-126s Repress a Novel Target Gene p21-Activated Kinase 1 to Regulate Vascular Integrity in Zebrafish. Circulation Research. 2011; 108(2):201-U105.
- Zhang W, Chen J, Yang Y, Tang Y, Shang J and Shen B. A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies. Plos One. 2011; 6(3).
- Wang Y, Chen J, Li Q, Wang H, Liu G, Jing Q and Shen B. Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. Computational Biology and Chemistry. 2011; 35(3):151-158.
- Sun J, Fu F, Gu W, Yan R, Zhang G, Shen Z, Zhou Y, Wang H, Shen B and Zhang X. Origination of New Immunological Functions in the Costimulatory Molecule B7-H3: The Role of Exon Duplication in Evolution of the Immune System. Plos One. 2011; 6(9).
- Liu B, Chen J and Shen B. Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs. Bmc Systems Biology. 2011; 5.
- Kong X, Ouyang S, Liang Z, Lu J, Chen L, Shen B, Li D, Zheng M, Li KK, Luo C and Jiang H. Catalytic Mechanism Investigation of Lysine-Specific Demethylase 1 (LSD1): A Computational Study. Plos One. 2011; 6(9).
- Concu R, Podda G, Gonzalez-Diaz H and Shen B. Review of Computer-Aided Models for Predicting Collagen Stability. Current Computer-Aided Drug Design. 2011; 7(4):287-303.
- Chis O, Dumitru O, Concu R and Shen B. Yeast Network and Report of New Stochastic-Credibility Cell Cycle Models. Current Bioinformatics. 2011; 6(1):35-43.
- Zou J, Li W, Liu T, Shen B, Qin Y-W and Jing Q. The Endothelial Cell-Specific MicroRNA-126a/b Functionally Regulates Vasculogenesis and Angiogenesis in Zebrafish. Arteriosclerosis Thrombosis and Vascular Biology. 2010; 30(11):E190-E190.
- Yan W, Zhu H, Yang Y, Chen J, Zhang Y and Shen B. Effects of Time Point Measurement on the Reconstruction of Gene Regulatory Networks. Molecules. 2010; 15(8):5354-5368.
- Wang H, Wang Q, Pape UJ, Shen B, Huang J, Wu B and Li X. Systematic investigation of global coordination among mRNA and protein in cellular society. Bmc Genomics. 2010; 11.
- Tang B, Wu X, Tan G, Chen S-S, Jing Q and Shen B. Computational inference and analysis of genetic regulatory networks via a supervised combinatorial-optimization pattern. Bmc Systems Biology. 2010; 4.
- Liu G, Ding M, Chen J, Huang J, Wang H, Jing Q and Shen B. Computational analysis of microRNA function in heart development. Acta Biochimica Et Biophysica Sinica. 2010; 42(9):662-670.
- Gonzalez-Diaz H, Duardo-Sanchez A, Ubeira FM, Prado-Prado F, Perez-Montoto LG, Concu R, Podda G and Shen B. Review of MARCH-INSIDE & Complex Networks Prediction of Drugs: ADMET, Anti-parasite Activity, Metabolizing Enzymes and Cardiotoxicity Proteome Biomarkers. Current Drug Metabolism. 2010; 11(4):379-406.
- Zanotto E, Hakkinen A, Teku G, Shen B, Ribeiro AS and Jacobs HT. NF-Y influences directionality of transcription from the bidirectional Mrps12/Sarsm promoter in both mouse and human cells. Biochimica Et Biophysica Acta-Gene Regulatory Mechanisms. 2009; 1789(5):432-442.
- Tang B, He L, Jing Q and Shen B. Model-Based Identification And Adaptive Control Of The Core Module In A Typical Cell Cycle Pathway Via Network And System Control Theories. Advances in Complex Systems. 2009; 12(1):21-43.
- Qi C-J, Zheng L, Ma H-B, Fei M, Qian K-Q, Shen B, Wu C-P, Vihinen M and Zhang X-G. A Novel Mutation in CD40 and Its Functional Characterization. Human Mutation. 2009; 30(6):985-994.
- Chen J and Shen B. Computational Analysis of Amino Acid Mutation: A Proteome Wide Perspective. Current Proteomics. 2009; 6(4):228-234.