Cpss: A computational platform for the analysis of small rna deep sequencing data

Bioinformatics

Volumn 28, Issue 14, 2012, Pages 1925-1927

  Zhang, Yuanwei ^a   Xu, Bo ^a   Yang, Yifan ^b   Ban, Rongjun ^c   Zhang, Huan ^a   Jiang, Xiaohua ^a   Cooke, Howard J ^a,d   Xue, Yu ^e   Shi, Qinghua ^a  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^b UNIVERSITY OF KENTUCKY   (United States)

^c NANJING UNIVERSITY   (China)

^d UNIVERSITY OF EDINBURGH   (United Kingdom)

^e HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; TRANSCRIPTOME;

ANIMAL; ARTICLE; BIOLOGY; CHROMOSOME MAP; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; INTERNET; METHODOLOGY; MOUSE; SEQUENCE ANALYSIS;

ANIMALS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INTERNET; MICE; MICRORNAS; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84864153006     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts282     Document Type: Article

References (14)

1. Ashburner, M. et al. (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat. Genet., 25, 25-29.
2. Carthew, R. W. and Sontheimer, E. J. (2009) Origins and mechanisms of miRNAs and siRNAs. Cell, 136, 642-655.
3. Fasold, M. et al. (2011) DARIO: a ncRNAdetection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res., 39, 112-117.
4. Friedlander, M. R. et al. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat. Biotechnol., 26, 407-415.
5. Hackenberg, M. et al. (2009) miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res., 37, W68-W76.
6. Jensen, L. J. et al. (2009) STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res., 37, D412-D416.
7. Kanehisa, M. et al. (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res., 38, D355-D360.
8. Moazed, D. (2009) Small RNAs in transcriptional gene silencing and genome defence. Nature, 457, 413-420.
9. Pantano, L. et al. (2010) SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNAmodifications in human embryonic cells. Nucleic Acids Res., 38, e34.
10. Wang, W. C. et al. (2009) miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics, 10, 328.
11. Zhang, Y. W. et al. (2011) Prediction of novel pre-microRNAs with high accuracy through boosting and SVM. Bioinformatics, 27, 1436-1437.
12. Zhao, W. et al. (2011) wapRNA: a web-based application for the processing of RNA sequences. Bioinformatics, 27, 3076-3077.
13. Zhou, L. et al. (2011) Small RNA transcriptome investigation based on next-generation sequencing technology. J. Genet. Genomics, 38, 505-513.
14. Zhu, E. et al. (2010) mirTools: microRNA profiling and discovery based on highthroughput sequencing. Nucleic Acids Res., 38, W392-W397.