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Cited by 3,042

miRBase: integrating microRNA annotation and deep-sequencing data

Kozomara, A., Griffiths-Jones, S.·2011·Nucleic Acids Research
DOI 10.1093/nar/gkq1027PMC PMC3013655
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Crossref · 10.1093/nar/gkq1027

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  • In total, ∼9 billion of the ∼20 billion trimmed reads of the 2,406 runs mapped to guide and passenger miRNAs covering 89.8% of miRNAs in miRBase and 99.5% of all miRNAs in MirGeneDB2.1.

    “In total, ∼9 billion of the ∼20 billion trimmed reads of the 2,406 runs mapped to guide and passenger miRNAs covering 89.8% of miRNAs in miRBase [15] and 99.5% of all miRNAs in MirGeneDB2.1 (99.8% of mature strands) (Supplementary Table S3) [16].”

    From A curated human cellular microRNAome based on 196 primary cell types (2022) · cites this paper as [15]

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Research works printed but not linked: 21

  1. [1]Griffiths-Jones S The microRNA Registry Nucleic Acids Res. 2004 32 D109 D111 14681370 PMC308757
  2. [2]Griffiths-Jones S Grocock RJ van Dongen S Bateman A Enright AJ miRBase: microRNA sequences, targets and gene nomenclature Nucleic Acids Res. 2006 34 D140 D144 16381832 PMC1347474
  3. [3]Griffiths-Jones S Saini HK van Dongen S Enright AJ miRBase: tools for microRNA genomics Nucleic Acids Res. 2008 36 D154 D158 17991681 PMC2238936
  4. [4]Jensen LJ Saric J Bork P Literature mining for the biologist: from information retrieval to biological discovery Nat. Rev. Genet. 2006 7 119 129 16418747
  5. [7]Celniker SE Dillon LA Gerstein MB Gunsalus KC Henikoff S Karpen GH Kellis M Lai EC Lieb JD MacAlpine DM Unlocking the secrets of the genome Nature 2009 459 927 930 19536255 PMC2843545
  6. [8]Ambros V Bartel B Bartel DP Burge CB Carrington JC Chen X Dreyfuss G Eddy SR Griffiths-Jones S Marshall M A uniform system for microRNA annotation RNA 2003 9 277 279 12592000 PMC1370393
  7. [9]Meyers BC Axtell MJ Bartel B Bartel DP Baulcombe D Bowman JL Cao X Carrington JC Chen X Green PJ Criteria for annotation of plant MicroRNAs Plant Cell 2008 20 3186 3190 19074682 PMC2630443
  8. [10]Chiang HR Schoenfeld LW Ruby JG Auyeung VC Spies N Baek D Johnston WK Russ C Luo S Babiarz JE Mammalian microRNAs: experimental evaluation of novel and previously annotated genes Genes Dev. 2010 24 992 1009 20413612 PMC2867214
  9. [11]Berezikov E Liu N Flynt AS Hodges E Rooks M Hannon GJ Lai EC Evolutionary flux of canonical microRNAs and mirtrons in Drosophila Nat. Genet. 2010 42 6 9 20037610 PMC4136759
  10. [12]Marco A Hui JH Ronshaugen M Griffiths-Jones S Functional shifts in insect microRNA evolution Genome Biol. Evol. 2010 2 686 696 20817720 PMC2956262
  11. [13]Friedlander MR Chen W Adamidi C Maaskola J Einspanier R Knespel S Rajewsky N Discovering microRNAs from deep sequencing data using miRDeep Nat. Biotechnol. 2008 26 407 415 18392026
  12. [14]Hendrix D Levine M Shi W miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data Genome Biol. 2010 11 R39 20370911 PMC2884542
  13. [15]Chung WJ Okamura K Martin R Lai EC Endogenous RNA interference provides a somatic defense against Drosophila transposons Curr. Biol. 2008 18 795 802 18501606 PMC2812477
  14. [16]Mi S Cai T Hu Y Chen Y Hodges E Ni F Wu L Li S Zhou H Long C Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide Cell 2008 133 116 127 18342361 PMC2981139
  15. [17]Gardner PP Daub J Tate JG Nawrocki EP Kolbe DL Lindgreen S Wilkinson AC Finn RD Griffiths-Jones S Eddy SR Rfam: updates to the RNA families database Nucleic Acids Res. 2009 37 D136 D140 18953034 PMC2686503
  16. [18]Daub J Gardner PP Tate J Ramskold D Manske M Scott WG Weinberg Z Griffiths-Jones S Bateman A The RNA WikiProject: community annotation of RNA families RNA 2008 14 2462 2464 18945806 PMC2590952
  17. [20]Krek A Grun D Poy MN Wolf R Rosenberg L Epstein EJ MacMenamin P da Piedade I Gunsalus KC Stoffel M Combinatorial microRNA target predictions Nat. Genet. 2005 37 495 500 15806104
  18. [21]Maragkakis M Reczko M Simossis VA Alexiou P Papadopoulos GL Dalamagas T Giannopoulos G Goumas G Koukis E Kourtis K DIANA-microT web server: elucidating microRNA functions through target prediction Nucleic Acids Res. 2009 37 W273 W276 19406924 PMC2703977
  19. [22]Betel D Wilson M Gabow A Marks DS Sander C The microRNA.org resource: targets and expression Nucleic Acids Res. 2008 36 D149 D153 18158296 PMC2238905
  20. [23]Papadopoulos GL Reczko M Simossis VA Sethupathy P Hatzigeorgiou AG The database of experimentally supported targets: a functional update of TarBase Nucleic Acids Res. 2009 37 D155 D158 18957447 PMC2686456
  21. [24]Xiao F Zuo Z Cai G Kang S Gao X Li T miRecords: an integrated resource for microRNA-target interactions Nucleic Acids Res. 2009 37 D105 D110 18996891 PMC2686554

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Authors
Kozomara, A., & Griffiths-Jones, S.
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2010-10-30
Volume
39
Issue
Database
Pages
D152-D157
ISSN
  • 0305-1048
  • 1362-4962
DOI
10.1093/nar/gkq1027
PMC
PMC3013655
Cited by
3,042
References
3
Language
en
Licence
creativecommons.org/licenses/by-nc/2.5 (vor, 2207 d)

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