Computational classification of microRNAs in next-generation sequencing data

Theoretical Chemistry Accounts

Volumn 125, Issue 3-6, 2010, Pages 637-642

  Riback, Joshua ^a   Hatzigeorgiou, Artemis G ^a,b   Reczko, Martin ^a,c  

^a Biomedical Sciences Research Center Alexander Fleming Institute of Molecular Oncology   (Greece)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c Synaptic Ltd   (Greece)

Author keywords

Deep sequencing; Gene finding; MicroRNA; Next generation sequencing; Non coding RNA

Indexed keywords

EID: 77949271531     PISSN: 1432881X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00214-009-0684-z     Document Type: Article

References (17)

1. Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, Daub CO, Kai C, Kawai J, Yasuda J, Carninci P, Hayashizaki Y (2008) Hidden layers of human small RNAs. BMC Genomics 9: 57-58.
2. Kawaji H, Hayashizaki Y (2008) Exploration of small RNAs. PLOS Genet 4: e22.
3. Enright AJ, Jogn B, Gaul U, Tuschl T, Sander S, Marks DS (2003) MicroRNA targets in Drosophila. Genome Biol 5: R1.
4. Wang Y, Stricker HM, Gou D, Liu L (2007) MicroRNA: past and present. Front Biosci 12: 2316-2329.
5. Maziere P, Enright A (2007) Prediction of microRNA targets. Drug Discov Today 12(11-12): 452-458.
6. Brennecke J, Stark A, Russell RB, Cohen SM (2005) Principles of microRNA-target recognition. PLoS Biol 3(3): e85.
7. Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N (2008) Discovering microRNAs from deep-sequencing data using miRDeep. Nat Biotechnol 26: 407-415.
8. Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M (2007) Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res 17: 1865-1879.
9. Holt RA, Jones SJ (2008) The new paradigm of flow cell sequencing. Genome Res 18: 839-846.
10. Sheng Y, Engström PG, Lenhard B (2007) Mammalian microRNA prediction through a support vector machine model of sequence and structure. PLoS One 2: e946.
11. Szafranski K, Megraw M, Reczko M, Hatzigeorgiou GH (2006) Support vector machine for predicting microRNA hairpins. In: Proceedings of the 2006 international conference on bioinformatics and computational biology, pp 270-276.
12. Jiang P, Wu H, Wang W, Ma W, Sun X, Lu Z (2007) MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res 35(Web Server issue): W339-W344.
13. Burnside J, Ouyang M, Anderson A, Bernberg E, Lu C, Meyers B, Green P, Markis M, Isaacs G, Huang E, Morgan R (2008) Deep sequencing of chicken microRNAs. BMC Genomics 9: 185.
14. Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31(13): 3429-3431.
15. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154-D158.
16. Hubbard JP, Aken BL, Beall K, Ballesterl B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Overduin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney E (2007) Ensembl 2007. Nucleic Acids Res 33 (Database issue): D447-D453.
17. Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, Schäffer AA (2008) Database indexing for production MegaBLAST searches. Bioinformatics 15: 1757-1764.