W Long, Y Yang*, HB Shen, ImPLoc: A multi-instance deep learning model for the prediction of protein subcellular localization based on immunohistochemistry images. Bioinformatics, 2019 (in press).
Y Yang, Q Fang, HB Shen, Predicting gene regulatory interactions based on spatial gene expression data and deep learning, PLOS Computational Biology, 15(9), 2019.
K Zhang, X Pan, Y Yang*, HB Shen, CRIP: predicting circRNA-RBP interaction sites using a codon-based encoding and hybrid deep neural networks. RNA, 2019, 25:1604-1615.
W Long, T Li, Y Yang*, HB Shen, FlyIT: Drosophila Embryogenesis Image Annotation based on Image Tiling and Convolutional Neural Networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2019 (in press).
Y Yang, M Zhou, Q Fang, Hong-Bin Shen. (2019). Annofly: Annotating drosophila embryonic images based on an attention-enhanced RNN model. Bioinformatics, Volume 35, Issue 16, 15 August 2019, Pages 2834–2842.
X Pan#, Y Yang#, C Xia, AH Mirza, HB Shen, Recent Methodology and Progress of Deep learning for RNA-protein interaction prediction. WIREs RNA, 2019:e1544. (# equal contribution)
D Wang, L Geng, Y Zhao, Y Yang, Y Huang, Y Zhang, HB Shen，Artificial intelligence-based multi-objective optimization protocol for protein structure refinement. Bioinformatics, 2019, btz544.
Y Yang, X Fu, W Qu, Y Xiao, HB Shen, MiRGOFS: A GO-based functional similarity measure for miRNAs, with applications to the prediction of miRNA subcellular localization and miRNA-disease association, Bioinformatics, Volume 34, Issue 20, 15 October 2018, Pages 3547–3556.
H Zhang#, Y Yang#, HB Shen, “Detection of Curvilinear Structure in Images by a Multi-Centered Hough Forest Method,” IEEE Access, 2018, vol 6
Z Cao#, X Pan#, Y Yang#, Y Huang, HB Shen, “The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier, Bioinformatics, Volume 34, Issue 13, 1 July 2018, Pages 2185–2194.
K Liu, Y Yang, Incorporating Link Information in Feature Selection for Identifying Tumor Biomarkers by Using miRNA-mRNA Paired Expression Data, Current Proteomics 15 (2), 165-171
Y Yang, Z Wu, W Kong. “Improving clustering of microRNA microarray data by incorporating functional similarity”. Current bioinformatics, 13(1),34-41, 2018
Y Xiao, J Cai, Y Yang*, H Zhao, HB Shen, Prediction of MicroRNA Subcellular Localization by Using a Sequence-to-Sequence Model, in Proceedings of the 2018 IEEE International Conference on Data Mining (ICDM’18), Singapore.
G Ji, Y Yang*, HB Shen, "IterVM: An Iterative Model for Single-Particle Cryo-EM Image Clustering Based on Variational Autoencoder and Multi-Reference Alignment”, The IEEE International Conference on Bioinformatics and Biomedicine (BIBM’18), Madrid, Spain
T Li, Y Yang*, HB Shen,“HMIML: Hierarchical Multi-Instance Multi-Label Learning of Drosophila Embryogenesis Images Using Convolutional Neural Networks” The IEEE International Conference on Bioinformatics and Biomedicine (BIBM’18), Madrid, Spain
Y Yang, Y Xiao, T Cao, W Kong, “MiRFFS: a functional group-based feature selection method for the identification of microRNA biomarkers”, Int. J. Data Mining and Bioinformatics, vol. 18(1), 2017
Y Yang, N Huang, L Hao, W Kong, “A clustering-based approach for the identification of microRNA combinatorial biomarkers”, BMC Genomics, 18 (2), 210, 2017
H Zhou#, Y Yang#, HB Shen, “Hum-mPLoc 3.0: Prediction enhancement of human protein subcellular localization through modeling the hidden correlations of gene ontology and functional domain features,” Bioinformatics, 33(6), 843-853, 2016
Y Yang*, Z. Xu, D Song, “Missing value imputation for microRNA expression data by using a GO-based similarity measure”, BMC bioinformatics, 2016,17(1):10
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