Data Mining and Bioinformatics Lab
School of Software | Central South University
Articles and Proceedings
  • Yuliang Pan, Zixiang Wang, Weihua Zhan and Lei Deng*. Computational identification of binding energy hot spots in protein-RNA complexes using an ensemble approach. Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx822
  • Jingpu Zhang, Zuping Zhang, Zixiang Wang, Yuting Liu and Lei Deng*. Ontological function annotation of long non-coding RNAs through hierarchical multi-label classification. Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx833
  • Jingpu Zhang, Shuai Zou, and Lei Deng*. BiRWLGO: A global network-based strategy for lncRNA function annotation using bi-random walk, The IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017), Kansas City, 2017
  • Junqiang Wang, Yun Xiao, Zixiang Wang, Weihua Zhan, and Lei Deng*. Combining diffusion and HeteSim features across the global heterogeneous network for accurate prediction of protein-lncRNA interactions. The IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017), Kansas City, 2017
  • Yun Xiao, Jingpu Zhang and Lei Deng*, Prediction of lncRNA-protein interactions using HeteSim scores based on heterogeneous networks, Scientific Reports, 2017, 7:3664
  • Lei Deng, Chao Fan and Zhiwen Zeng. A sparse autoencoder-based deep neural network for protein solvent accessibility and contact number prediction. BMC Bioinformatics, 2017, 18(S16):569
  • Yongjun Tang, Diwei Liu, Zixiang Wang, Ting Wen and Lei Deng*. A boosting approach for prediction of protein-RNA binding residues. BMC Bioinformatics, 2017, 18(Suppl 13):465
  • Pan Y, Liu D, Deng L*, Accurate prediction of functional effects for variants by combining gradient tree boosting with optimal neighborhood properties. PLoS One. 2017,12(6):e0179314
  • Jingpu Zhang, Zuping Zhang, Zhigang Chen, and Lei Deng*. Integrating Multiple Heterogeneous Networks for Novel LncRNA-disease Association Inference. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017, DOI: 10.1109/TCBB.2017.2701379
  • Zuping Zhang, Jingpu Zhang, Chao Fan, Yongjun Tang, and Lei Deng*，KATZLGO: Large-scale Prediction of LncRNA Functions by Using the KATZ Measure Based on Multiple Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017, DOI: 10.1109/TCBB.2017.2704587
  • Diwei Liu, Yongjun Tang, Chao Fan, Zhigang Chen, and Lei Deng*, PredRBR: Accurate Prediction of RNA-binding Residues in Proteins Using Gradient Tree Boosting. The IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016), Shenzhen, 􏶌2016.12.15-2016.12.18
  • Garzón J, Deng L, Murray D, Shapira S, Petrey D and Honig B. A computational interactome and functional annotation for the human proteome. Elife. 2016, e18715
  • Yong Gao, Weilin Hao, Jing Gu, Diwei Liu, Chao Fan, Zhigang Chen and Lei Deng(*corresponding author). PredPhos: an ensemble framework for structure-based prediction of phosphorylation sites. Journal of Biological Research-Thessaloniki, 2016,23(Suppl 1):12
  • Chao Fan, Diwei Liu, Rui Huang, Zhigang Chen and Lei Deng(*corresponding author). PredRSA: a gradient boosted regression trees approach for predicting protein solvent accessibility. BMC Bioinformatics, 2016, 17(Suppl 1):8
  • Petrey D, Chen TS, Deng L, Garzon JI, Hwang H, Lasso G, Lee H, Silkov A and Honig B. Template-based prediction of protein function. Current Opinion in Structural Biology. 2015, 32:33–38
  • Deng L(*corresponding author) and Chen Z. An Integrated Framework for Functional Annotation of Protein Structural Domains. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015, 12(4):902-913
  • Deng L, Zhang QC, Chen Z, Meng Y, Guan J, Zhou S. PredHS: a web server for predicting protein-protein interaction hot spots by using structural neighborhood properties. Nucleic Acids Res 2014, 42:W290-5
  • Deng L, Guan J, Wei X, Yi Y and Zhou S. Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties. Journal of Computational Biology. 2013, 20(11):878-91
  • Zhang QC, Petrey D, Garzon J, Deng L and Honig B. PrePPI: A structure informed database of protein-protein interactions. Nucleic Acids Res. 2013, 41(D1):D828-33.
  • Deng L, Guan J􏶌, Wei X􏶌, Yi Y􏶌, Zhou S􏶌. Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties􏶌. 17th annual international conference on research in computational molecular biology (RECOMB 2013)􏶌, Beijing, 􏶌2013.4.7-2013.4.10
  • Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Chan A, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A and Honig B. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature, 2012, 490,556-560
  • Xu B, Wei X, Deng L, Guan JH, Zhou S. A Semi-supervised Boosting SVM for Predicting Hot Spots at Protein-protein Interfaces. BMC Systems Biology. 2012, 6(Suppl 2):S6
  • Zhang QC＃, Deng L＃(＃co-first author), Fisher M, Guan JH, Honig B and Petrey D. PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res. 2011, W283-7.
  • Deng L, Guan JH, Dong QW, Zhou SG. SemiHS: An Iterative Semi-supervised Approach for Predicting Protein-protein Interaction Hot Spots. Protein and Peptide Letters. 2011, 18(9):896-905.
  • Dong Q, Zhou S, Deng L, Guan J. Gene ontology-based protein function prediction by using sequence composition information. Protein and Peptide Letters. 2010, 17(6):789-95.
  • Deng L, Guan JH, Dong QW, Zhou SG. Prediction of protein-protein interaction sites using an ensemble method. BMC Bioinformatics. 2009, 10:426
Talks