Softwares

1.microDoR:

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.  

2.miRRecog:

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.  

3.SProtP:

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.  

4.ProtCC:

Protein Convex-Concave Feature Analyzer  

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).

5.mUbiSiDa:

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.  

6.UROBORUS:

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.  

7.lncScore:

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)  

8.GFsuion:

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)  

9.circRNADb:

circRNADb is a comprehensive human exonic circRNA database.

Reference:

(1) Xiaoping Chen, Ping Han, Xuejiang Guo, Xiaofeng Song. circRNADb: A comprehensive database for human circular RNAs with protein-coding annotations.Scientific Reports.(accepted)