Publications


    1. Jian Zhao, Bing He, Xiaofeng Song. Predicting the ubiquitination site of the protein in human cells. (under review) (corresponding author)

    2. Xiao Wang, Jian Zhao, Yujiao Yan, Jingye Qian, Ping Han,Xiaofeng Song.CCI, a new molecular surface structure parameter that identifies convex and concave regions in proteins. International Journal of Computational Biology and Drug Design. (accepted).(corresponding author)

    3. Jian Zhao, Qi Chen, Jing Wu, Ping Han, Xiaofeng Song. GFusion: a Novel Algorithm to Identify Fusion Genes from Cancer RNA-Seq Data. Scientific Reports. (accepted).(corresponding author) (SCI,IF# 5.2)

    4. Tianyi Xu, Jing Wu, Ping Han, Zhongming Zhao, Xiaofeng Song. Circular RNA expression profiles and features in human tissues: A study using RNA-seq data. BMC Genomics.(accepted).(corresponding author) (SCI,IF#3.86)

    5. Jian Zhao, Xiaofeng Song, Kai Wang. lncScore: alignment-free identification of long noncoding RNA from assembled novel transcripts. Scientific Reports.2016,6:34838.(corresponding author) (SCI,IF# 5.2)

    6. Xiaoping Chen, Ping Han, Xuejiang Guo, Xiaofeng Song, Yan Li. circRNADb: A comprehensive database for human circular RNAs with protein-coding annotations. Scientific Reports.2016,6:34985. (corresponding author) (SCI,IF# 5.2)

    7. Xiaofeng Song, Naibo Zhang, Ping Han, Rose K. Lai, Kai Wang, Wange Lu. Circular RNA Profile in Gliomas Revealed by Identification Tool UROBORUS. Nucleic Acids Research.2016,,44(9):e87. (SCI,IF# 9.2)

    8. Xiaofeng Song, Lizhen Hu, Ping Han, Xuejiang Guo, Jiahao Sha. In silico identification and functional annotation of yeast E3 ubiquitin ligase Rsp5 substrates. Int. J. Data Min. Bioinform. 2015,13(4):321-337. (corresponding author) (SCI, IF#1.22)

    9. Xiaofeng Song,Yan Jing, Ping Han. The Relationship between Experimentally Validated Intracellular Human Protein Stability and the Features of its Solvent Accessible Surface.Int. J. Data Min. Bioinform. 2015;11(1):84-101. (corresponding author) (SCI, IF#1.22)

    10. Tong Chen, Tao Zhou, Bing He, Xuejiang Guo, Xiaofeng Song, Jiahao Sha. mUbiSiDa: a comprehensive database for protein ubiquitination site in mammals.PLoS ONE,2014,9(1): e85744. doi:10.1371/journal.pone.0085744. (corresponding author) (SCI, IF#4.78)

    11. Hui Yi, Cuimei Bo, Xiaofeng Song, Yuan, Yuhao. Initial points selection for clustering gene expression data: A spatial contiguity analysis-based approach. Bio-medical Materials and Engineering, 2014,24(6):3709-3717. (SCI, IF#1.28)

    12. Hui Yi; Xiaofeng Song; Bin Jiang; Yufang Liu; Zhihua Zhou. Flexible Support Vector Regression and Its Application to Fault Detection. Acta Automatica Sinica. 2013, 39(3):272-284.(corresponding author)

    13. Kun Sun, Xiaona Chen, Peiyong Jiang, Xiaofeng Song, Huating Wang, and Hao Sun. iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data. BMC Genomics. 2013,14(Suppl 2):S7.(corresponding author) (SCI, IF#4.3)

    14. Xiaofeng Song; Minghao Wang; Yi-Ping Phoebe Chen; Ping Han; Hao Sun. Prediction of pre-miRNA with multiple stem-loops using pruning algorithm. Comput. Biol. Med. 2013 Jun 1;43(5):409-416.(corresponding author) (SCI, IF#1.485)

    15. Xiaofeng Song,Lei Cheng, Tao Zhou, Xuejiang Guo, Xiaobai Zhang, Ping Han, Yi-ping Phoebe Chen, Jiahao Sha. Predicting miRNA-Mediated Gene Silencing mode based on miRNA-target Duplex Features. Comput. Biol. Med..2012, 42(1):1-6. (SCI, IF#1.485)

    16. Xiao-feng Song,Ping Han,Yi-Ping Phoebe Chen. Genetic variation of the hemagglutinin of avian influenza virus H9N2. J. Med. Virol. 2011,83(5):838-846.(SCI#736BL, IF# 2.572)

    17. Xiaofeng Song, Hao Jia,Tao Zhou, Xuejiang Guo, Ping Han, Xiaobai Zhang and Jiahao Sha. SProtP: a web server to recognize those short-lived proteins based on sequence-derived features in human cells. PLoS ONE.2011, 6(11): e27836. (SCI, IF#4.78)

    18. Xiaofeng Song, Peipei Wang.Flexible Array Self-Organizing Map Neural Network and Its Application in Complex Pattern Recognition. Neural Computing and Application,2011,20(1):9-16. (SCI# 712NZ, IF#1.088)

    19. Hui Yi, Xiaofeng Song, and Bin Jiang. Structure Selection for DAG-SVM based on Misclassification Cost Minimization. Int. J. Innov. Comput. I..2011, 7(9) (co-corresponding author)

    20. Xiaobai Zhang, Juan Cui, Daniel Nilsson; Kapila Gunasekera; Isabel Roditi; Astrid Chanfon; Xiaofeng Song, Huinan Wang, Ying Xu and Torsten Ochsenreiter. The Trypanosoma brucei Mitocarta and its Regulation and Splicing Pattern during Development. Nucleic Acids Research.2010,38(21):7378-7387. (SCI#689TK,  IF# 9.1)

    21. Xiaobai Zhang. Xiaofeng Song, Huinan Wang。Characteristic comparison between two types of miRNA precursors in metazoan species。BioSystems,2010,100(2):144-149. (SCI# 599MX, IF#1.653)(corresponding author)

    22. Minghao Wang, Xiaofeng Song,Ping Han, Wei Li, Bin Jiang. New syntax to describe local continuous structure-sequence information for recognizing new pre-miRNAs. Journal of Theoretical Biology. 2010,264(2):578-584.(SCI# 588GG, IF#2.738)(corresponding author)

    23. Xiao-feng Song,Saman K Halgamuge, CHEN De-zhao, HU Shang-xu, and Bin Jiang. The Optimized Support Vector Machine with Correlative Features for Classification of Natural Spearmint Essence. Int. J. Innov. Comp. Inf. Con., 2010, 6(3): 1089-1099, (SCI# 571PW, IF#2.735) (corresponding author)

    24. Xiao-feng Song, Wei-min Chen, Yi-Ping Phoebe Chen, Bin Jiang. Candidate Working Set Strategy based SMO Algorithm in Support Vector Machine. Inform. Process. & Manag. 2009,45(5): 584-592.(SCI# 481FP, IF# 2.106)(corresponding author)

    25. Zhang huanping, Xiaofeng Song, Huinan Wang, Xiaobai Zhang. MIClique: An Algorithm to Identify Differentially Coexpressed Disease Gene Subset from Microarray Data. J. Biomed. Biotechnol.. 2009, doi:10.1155/2009/642524(SCI#560FT, IF#2.647)(corresponding author)

    26. Xiao-feng Song, Yan Hao. Adaptive Evolution of Rotavirus VP7 & NSP4 Genes in Different Species. Comput. Biol. Chem. 2009, 33(4): 344-349.(SCI# 495BM, IF# 1.733)(corresponding author)

    27. Xiaofeng Song, Chen,Weimin, Jiang,bin. Sample reducing method in Support Vector Machine based on K-closed Sub-clusters, Int. J. Innov. Comp. Inf. Con.,2008,4(7):1751-1760 (SCI#326XS, IF#2.735) (corresponding author)

    28. Xiaobai Zhang. Xiaofeng Song, Huinan Wang. Sequential Local Least Squares Imputation Estimating Missing Value of Microarray Data. Comput. Biol. Med., 2008,38(10): 1112-1120. (SCI#368QN, IF#1.485) (corresponding author)

    29. Dominik Slezak, Tughrul Arslan, Wai-Chi Fang, Xiaofeng Song, Tai-hoon Kim. Bio-Science and Bio-Technology. Berlin: Springer-Verlag. 2009.

    30. Zhang huanping, Wang Huinan, Song Xiaofeng. New Hybrid Ai-SVM Algorithm: Combination of Support Vector Machines and Artificial Immune Network. Journal of Nanjing Univ. of Aero. & Astro.2006,23(4):272-277.(EI index)

    31. Xiaofeng Song, Tong Zhou, Huanping Zhang. Support Vector Regression Estimation Based on Non-uniformly Lost Function. Shanghai: Proceedings of IEEE-EMBC05,(ISTP#BER00)(corresponding author)

    32. Hui Yi; Xiaofeng Song. Missing Value Estimation for Gene Expression Data Using GRNN. Progress on Post-genome Technologies: 2006: 375-378,(ISTP#BFQ08) (corresponding author)

    33. Xiao-feng Song,Saman K Halgamuge, CHEN De-zhao, and HU Shang-xu. Support Vector Machine Integrated CCA for Classification of Complex Chemical Patterns. The Proceedings of International Conference on Bio-Science and Bio-Technology (BSBT 2008) (EI# 10439176)(corresponding author)

    34. Huanping Zhang, Xiaofeng Song, Huinan Wang. Identifying Candidate Disease Gene GAD2 for Obesity by Computational Gene Prioritization Tool ENDEAVOUR. The Proceedings of International Conference on Bio-Science and Bio-Technology (BSBT 2009)(corresponding author)

    35. Xiaofeng Song, Yan Hao, Ping Han. Analysis of the positions of amino acid substitution on the VP7 and NSP4 molecules of Rotaviruses circulating in China. Jeju: The Proceedings of International Conference on Bio-Science and Bio-Technology (BSBT 2010)(corresponding author)

    36. Lei Cheng; Tao Zhou; Xuejiang Guo; Xiaofeng Song;et al. microDoR for HUMAN: A web server to predict mode of miRNA-Mediated Gene Silencing. HongKong: Proceedings of IEEE International Conference on Bioinformatics & Biomedicine, 2010. (Co-corresponding author)

    37. 易辉,宋晓峰,姜斌,王定成. 基于结点优化的决策导向非循环图支持向量机。自动化学报, 2010,36(3): 427-432.

    38. 周正荣,宋晓峰,王明浩。使用组合分类器预测蛋白质相互作用。电子学报,2010,38(6). (通讯作者)

    39. 宋晓峰,韩平,邹丽,陈德钊,胡上序。基于支持向量机的足月胎儿体重预测新方法.中国生物医学工程学报, 2004, 23(6):516-522.(EI收录)。(通讯作者)

    40. 宋晓峰,陈德钊,胡上序。结构可调的支持向量回归估计. 控制与决策, 2003, 18(6): 698-702.

    41. 易辉,宋晓峰,姜斌,王定成。基于AdaBoost方法的支持向量机训练样本选择. 仪器仪表学报,2009, 30(10s): 72-74. (通讯作者)

    42. 宋晓峰,俞欢军,陈德钊,胡上序。藉助自适应支持向量机为延迟焦化反应过程建模. 化工学报, 2004, 55(1): 147-150.(EI收录)