MiRNA-dis: MicroRNA precursor identification based on distance structure status pairs

Molecular BioSystems

Volumn 11, Issue 4, 2015, Pages 1194-1204

  Liu, Bin ^a   Fang, Longyun ^a   Chen, Junjie ^a   Liu, Fule ^a   Wang, Xiaolong ^a  

^a HARBIN INSTITUTE OF TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA;

MICRORNA; PLANT RNA; VIRUS RNA;

ANIMAL; BIOLOGY; CHEMISTRY; COMPUTER INTERFACE; GENETIC DATABASE; GENETICS; HUMAN; INTERNET; PROCEDURES;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; HUMANS; INTERNET; MICRORNAS; RNA, PLANT; RNA, VIRAL; USER-COMPUTER INTERFACE;

EID: 84924975850     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/c5mb00050e     Document Type: Article

References (43)

1. K. Chen N. Rajewsky The evolution of gene regulation by transcription factors and microRNAs Nat. Rev. Genet. 2007 8 93 103
2. P. Fasanaro S. Greco M. Ivan M. C. Capogrossi F. Martelli microRNA: emerging therapeutic targets in acute ischemic diseases Pharmacol. Ther. 2010 125 92 104
3. P. Trang J. B. Weidhaas F. J. Slack MicroRNAs as potential cancer therapeutics Oncogene 2008 27 Suppl 2 S52 S57
4. C. Li Y. Feng G. Coukos L. Zhang Therapeutic microRNA strategies in human cancer AAPS J. 2009 11 747 757
5. M. R. Friedlander W. Chen C. Adamidi J. Maaskola R. Einspanier S. Knespel N. Rajewsky Discovering microRNAs from deep sequencing data using miRDeep Nat. Biotechnol. 2008 26 407 415
6. C. Xue F. Li T. He G. P. Liu Y. Li X. Zhang Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine BMC Bioinf. 2005 6 310
7. J. W. Nam K. R. Shin J. Han Y. Lee V. N. Kim B. T. Zhang Human microRNA prediction through a probabilistic co-learning model of sequence and structure Nucleic Acids Res. 2005 33 3570 3581
8. T. H. Huang B. Fan M. F. Rothschild Z. L. Hu K. Li S. H. Zhao MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans BMC Bioinf. 2007 8 341
9. Y. Wu B. Wei H. Liu T. Li S. Rayner MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences BMC Bioinf. 2011 12 107
10. Y. Wang X. Chen W. Jiang L. Li W. Li L. Yang M. Liao B. Lian Y. Lv S. Wang et al., Predicting human microRNA precursors based on an optimized feature subset generated by GA-SVM Genomics 2011 98 73 78
11. S. A. Helvik O. Snove Jr. P. Saetrom Reliable prediction of Drosha processing sites improves microRNA gene prediction Bioinformatics 2007 23 142 149
12. P. Jiang H. Wu W. Wang W. Ma X. Sun Z. Lu MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features Nucleic Acids Res. 2007 35 W339 W344
13. S. Agarwal C. Vaz A. Bhattacharya A. Srinivasan Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM) BMC Bioinf. 2010 11 Suppl 1 S29
14. M. Yousef M. Nebozhyn H. Shatkay S. Kanterakis L. C. Showe M. K. Showe Combining multi-species genomic data for microRNA identification using a Naive Bayes classifier Bioinformatics 2006 22 1325 1334
15. M. Brameier C. Wiuf Ab initio identification of human microRNAs based on structure motifs BMC Bioinf. 2007 8 478
16. L. Li J. Xu D. Yang X. Tan H. Wang Computational approaches for microRNA studies: a review Mamm. Genome 2010 21 1 12
17. L. Y. Wei M. H. Liao Y. Gao R. R. Ji Z. Y. He Q. Zou Improved and Promising Identification of Human MicroRNAs by Incorporating a High-quality Negative Set IEEE/ACM Trans. Comput. Biol. Bioinf. 2014 11 192 201
18. K. C. Chou Prediction of protein cellular attributes using pseudo amino acid composition Proteins: Struct., Funct., Genet. 2001 43 246 255
19. B. Liu X. Wang Q. Chen Q. Dong X. Lan Using amino acid physicochemical distance transformation for fast protein remote homology detection PLoS One 2012 7 e46633
20. W. Chen P. M. Feng H. Lin K. C. Chou iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition Nucleic Acids Res. 2013 41 e68
21. W. R. Qiu X. Xiao K. C. Chou iRSpot-TNCPseAAC: identify recombination spots with trinucleotide composition and pseudo amino acid components Int. J. Mol. Sci. 2014 15 1746 1766
22. B. Liu F. Liu L. Fang X. Wang K.-C. Chou repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects Bioinformatics 10.1093/bioinformatics/btu1820
23. S. H. Guo E. Z. Deng L. Q. Xu H. Ding H. Lin W. Chen K. C. Chou iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition Bioinformatics 2014 30 1522 1529
24. A. Kozomara S. Griffiths-Jones miRBase: integrating microRNA annotation and deep-sequencing data Nucleic Acids Res. 2011 39 D152 D157
25. V. Ambros A uniform system for microRNA annotation RNA 2003 9 277 279
26. W. Li A. Godzik Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Bioinformatics 2006 22 1658 1659
27. K. C. Chou H. B. Shen Recent progress in protein subcellular location prediction Anal. Biochem. 2007 370 1 16
28. I. L. Hofacker Vienna RNA secondary structure server Nucleic Acids Res. 2003 31 3429 3431
29. C. Cortes V. Vapnik Support-Vector Networks Mach. Learn. 1995 20 273 297
30. C. C. Chang, C. J. Lin, LIBSVM A Library for Support Vector Machines, 2009
31. K. C. Chou H. B. Shen Recent advances in developing web-servers for predicting protein attributes Nat. Sci. 2009 1 63 92
32. X. Xiao J.-L. Min P. Wang K.-C. Chou iCDI-PseFpt: Identify the channel-drug interaction in cellular networking with PseAAC and molecular fingerprints J. Theor. Biol. 2013 337 71 79
33. J. L. Min X. Xiao K. C. Chou iEzy-drug: a web server for identifying the interaction between enzymes and drugs in cellular networking BioMed Res. Int. 2013 2013 701317
34. Y. Xu X. J. Shao L. Y. Wu N. Y. Deng K. C. Chou iSNO-AAPair: incorporating amino acid pairwise coupling into PseAAC for predicting cysteine S-nitrosylation sites in proteins PeerJ 2013 1 e171
35. B. Liu L. Fang F. Liu X. W. J. Chen K.-C. Chou Identification of real microRNA precursors with a pseudo structure status composition approach PLoS One 2015 10.1371/journal.pone.0121501
36. Q. Zou Y. Mao L. Hu Y. Wu Z. Ji miRClassify: An advanced web server for miRNA family classification and annotation Comput. Biol. Med. 2014 45 157 160
37. B. Liu L. Fang F. Liu X. Wang K.-C. Chou iMiRNA-PseDPC: microRNA precursor identification with a pseudo distance-pair composition approach J. Biomol. Struct. Dyn. 2015 10.1080/07391102.07392015.01014422
38. C. Y. Wang L. Y. Wei M. Z. Guo Q. Zou Computational Approaches in Detecting non-coding RNA Curr. Genomics 2013 14 371 377
39. B. Liu D. Zhang R. Xu J. Xu X. Wang Q. Chen Q. Dong K.-C. Chou Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection Bioinformatics 2014 30 472 479
40. B. Liu J. Xu Q. Zou R. Xu X. Wang Q. Chen Using distances between Top-n-gram and residue pairs for protein remote homology detection BMC Bioinf. 2014 15 Suppl 2 S3
41. B. Liu X. Wang Q. Zou Q. Dong Q. Chen Protein Remote Homology Detection by Combining Chou's Pseudo Amino Acid Composition and Profile-Based Protein Representation Mol. Inf. 2013 32 775 782
42. B. Liu J. Xu S. Fan R. Xu J. Zhou X. Wang PseDNA-Pro: DNA-Binding Protein Identification by Combining Chou's PseAAC and Physicochemical Distance Transformation Mol. Inf. 2015 34 8 17
43. B. Liu J. Xu X. Lan R. Xu J. Zhou X. Wang K.-C. Chou iDNA-Protdis: Identifying DNA-Binding Proteins by Incorporating Amino Acid Distance-Pairs and Reduced Alphabet Profile into the General Pseudo Amino Acid Composition PLoS One 2014 9 e106691