Predicting miRNA-Mediated Gene Silencing, mRNA degradation or translational repression This web server was developed by our Lab collaborated with Nanjing Medical University.
Reference:(1) 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.
This is a powerful miRNA recognizer in diverse species. If you use miRRecog, please cite following Journal.
Reference:(1) 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.
Recognition of short-lived protein in eukaryotic cell. This software was developed by our Lab collaborated with Nanjing Medical University.
Reference:(1) 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.
Reference:(1) CCI, a new molecular surface structure parameter that identifies convex and concave regions in proteins. International Journal of Computational Biology and Drug Design. (accepted).
Database of mammalian protein ubiquitination site. This database was developed by our Lab collaborated with Nanjing Medical University.
Reference:(1) Chen T, Zhou T, He B, Yu H, Guo X, et al. (2014) mUbiSiDa: A Comprehensive Database for Protein Ubiquitination Sites in Mammals. PLoS ONE 9(1): e85744. doi:10.1371/journal.pone.0085744.
UROBORUS is a computational pipeline to detect circular RNA supported by junction reads from back spliced exons.
Reference:(1) 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.2016,1.doi: 10.1093/nar/gkw075.
lncScore is an alignment-free tool to detect lncRNAs from assembled transcripts, and it also can be used to calculate the coding potential.
Reference:(1) 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)
GFusion is a software package to detect fusion genes using RNA-Seq data.
Reference:(1) Jiang 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)
circRNADb is a comprehensive human exonic circRNA database.