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Volumn 11, Issue , 2010, Pages

Finding sRNA generative locales from high-throughput sequencing data with NiBLS

Author keywords

[No Author keywords available]

Indexed keywords

CLUSTERING COEFFICIENT; HIGH-THROUGHPUT; HIGH-THROUGHPUT SEQUENCING; NEXT-GENERATION SEQUENCING; REGULATORY RNAS; SENSITIVE METHOD; SENSITIVITY AND SPECIFICITY; SEQUENCE DATA;

EID: 77949441724     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-93     Document Type: Article
Times cited : (9)

References (30)
  • 1
    • 63249121217 scopus 로고    scopus 로고
    • Application of 'Next Generation' sequencing technologies to microbial genetics
    • MacLean D, Jones JDG, Studholme DJ. Application of 'Next Generation' sequencing technologies to microbial genetics. Nat Revs Microbiol 2009, 7(4):287-296.
    • (2009) Nat Revs Microbiol , vol.7 , Issue.4 , pp. 287-296
    • MacLean, D.1    Jones, J.D.G.2    Studholme, D.J.3
  • 2
    • 4644242349 scopus 로고    scopus 로고
    • RNA silencing in plants
    • 10.1038/nature02874, 15372043
    • Baulcombe DC. RNA silencing in plants. Nature 2004, 431:356-363. 10.1038/nature02874, 15372043.
    • (2004) Nature , vol.431 , pp. 356-363
    • Baulcombe, D.C.1
  • 3
    • 33646137364 scopus 로고    scopus 로고
    • The diversity of RNA silencing pathways in plants
    • 10.1016/j.tig.2006.03.003, 16567016
    • Brodersen P, Voinnet O. The diversity of RNA silencing pathways in plants. Trends Genet 2006, 22:268-280. 10.1016/j.tig.2006.03.003, 16567016.
    • (2006) Trends Genet , vol.22 , pp. 268-280
    • Brodersen, P.1    Voinnet, O.2
  • 4
    • 4644312235 scopus 로고    scopus 로고
    • The role of RNA interference in heterochromatic silencing
    • 10.1038/nature02875, 15372044
    • Lippman Z, Martienssen R. The role of RNA interference in heterochromatic silencing. Nature 2004, 431:364-370. 10.1038/nature02875, 15372044.
    • (2004) Nature , vol.431 , pp. 364-370
    • Lippman, Z.1    Martienssen, R.2
  • 5
    • 0034764307 scopus 로고    scopus 로고
    • SSAHA: a fast search method for large DNA databases
    • 10.1101/gr.194201, 311141, 11591649
    • Ning Z, Cox AJ, Mullikin JC. SSAHA: a fast search method for large DNA databases. Genome Res 2001, 11:1725-1729. 10.1101/gr.194201, 311141, 11591649.
    • (2001) Genome Res , vol.11 , pp. 1725-1729
    • Ning, Z.1    Cox, A.J.2    Mullikin, J.C.3
  • 6
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • 10.1101/gr.078212.108, 2577856, 18714091
    • Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008, 18(11):1851-1858. 10.1101/gr.078212.108, 2577856, 18714091.
    • (2008) Genome Res , vol.18 , Issue.11 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 7
    • 40049104732 scopus 로고    scopus 로고
    • SOAP: short oligonucleotide alignment program
    • 10.1093/bioinformatics/btn025, 18227114
    • Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24(5):713-714. 10.1093/bioinformatics/btn025, 18227114.
    • (2008) Bioinformatics , vol.24 , Issue.5 , pp. 713-714
    • Li, R.1    Li, Y.2    Kristiansen, K.3    Wang, J.4
  • 8
    • 33845688601 scopus 로고    scopus 로고
    • A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana
    • 10.1101/gad.1476406, 1698448, 17182867
    • Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 2006, 20:3407-3425. 10.1101/gad.1476406, 1698448, 17182867.
    • (2006) Genes Dev , vol.20 , pp. 3407-3425
    • Rajagopalan, R.1    Vaucheret, H.2    Trejo, J.3    Bartel, D.P.4
  • 9
    • 34347355440 scopus 로고    scopus 로고
    • MiRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii
    • 10.1038/nature05903, 17538623
    • Molnar A, Schwach F, Studholme DJ, Thuenemann EC, Baulcombe DC. miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature 2007, 447:1126-1129. 10.1038/nature05903, 17538623.
    • (2007) Nature , vol.447 , pp. 1126-1129
    • Molnar, A.1    Schwach, F.2    Studholme, D.J.3    Thuenemann, E.C.4    Baulcombe, D.C.5
  • 10
    • 42549096814 scopus 로고    scopus 로고
    • PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis
    • 10.1073/pnas.0709632105, 2268599, 18287047
    • Mosher RA, Schwach F, Studholme D, Baulcombe DC. PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc Nat Acad Sci USA 2008, 105:3145-3150. 10.1073/pnas.0709632105, 2268599, 18287047.
    • (2008) Proc Nat Acad Sci USA , vol.105 , pp. 3145-3150
    • Mosher, R.A.1    Schwach, F.2    Studholme, D.3    Baulcombe, D.C.4
  • 11
    • 52949088691 scopus 로고    scopus 로고
    • A toolkit for the analysis of large-scale plant small RNA datasets
    • 10.1093/bioinformatics/btn428, 18713789
    • Moxon S, Schwach F, Dalmay T, MacLean D, Studholme DJ, Moulton V. A toolkit for the analysis of large-scale plant small RNA datasets. Bioinformatics 2008, 24(19):2252-2253. 10.1093/bioinformatics/btn428, 18713789.
    • (2008) Bioinformatics , vol.24 , Issue.19 , pp. 2252-2253
    • Moxon, S.1    Schwach, F.2    Dalmay, T.3    MacLean, D.4    Studholme, D.J.5    Moulton, V.6
  • 13
    • 33847652140 scopus 로고    scopus 로고
    • Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis
    • 10.1073/pnas.0611119104, 1805617, 17360645
    • Chen HM, Li YH, Wu SH. Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis. Proc Natl Acad Sci USA 2007, 104:3318-3323. 10.1073/pnas.0611119104, 1805617, 17360645.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 3318-3323
    • Chen, H.M.1    Li, Y.H.2    Wu, S.H.3
  • 16
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small-world' networks
    • 10.1038/30918, 9623993
    • Watts DJ, Strogatz SH. Collective dynamics of 'small-world' networks. Nature 1998, 393:409-410. 10.1038/30918, 9623993.
    • (1998) Nature , vol.393 , pp. 409-410
    • Watts, D.J.1    Strogatz, S.H.2
  • 17
    • 54349104464 scopus 로고    scopus 로고
    • Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs
    • 10.1101/gad.1705308, 2569885, 18923076
    • Babiarz JE, Ruby JG, Wang Y, Bartel DP, Blelloch R. Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev 2008, 22:2773-2785. 10.1101/gad.1705308, 2569885, 18923076.
    • (2008) Genes Dev , vol.22 , pp. 2773-2785
    • Babiarz, J.E.1    Ruby, J.G.2    Wang, Y.3    Bartel, D.P.4    Blelloch, R.5
  • 18
    • 84888278847 scopus 로고    scopus 로고
    • RFAM
    • RFAM. , http://rfam.sanger.ac.uk/
  • 19
    • 33845436047 scopus 로고    scopus 로고
    • Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans
    • 10.1016/j.cell.2006.10.040, 17174894
    • Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 2006, 127(6):1193-1207. 10.1016/j.cell.2006.10.040, 17174894.
    • (2006) Cell , vol.127 , Issue.6 , pp. 1193-1207
    • Ruby, J.G.1    Jan, C.2    Player, C.3    Axtell, M.J.4    Lee, W.5    Nusbaum, C.6    Ge, H.7    Bartel, D.P.8
  • 20
    • 84871636673 scopus 로고    scopus 로고
    • The Perl Directory
    • The Perl Directory. , http://www.perl.org
  • 21
    • 84874659619 scopus 로고    scopus 로고
    • Boost Graph Library
    • Boost Graph Library. , http://www.boost.org/
  • 22
    • 84888278579 scopus 로고    scopus 로고
    • Boost-Graph-1.2 Perl module
    • Boost-Graph-1.2 Perl module. , http://search.cpan.org/~dburdick/Boost-Graph-1.2/Graph.pm
  • 23
    • 84888279362 scopus 로고    scopus 로고
    • The GNU Public License Version 3
    • The GNU Public License Version 3. , http://www.gnu.org/licenses/gpl-3.0.txt
  • 24
    • 84874662675 scopus 로고    scopus 로고
    • GFF file format
    • GFF file format. , http://www.sanger.ac.uk/Software/formats/GFF/
  • 25
    • 84888281922 scopus 로고    scopus 로고
    • The Sainsbury Laboratory ncRNA webserver
    • The Sainsbury Laboratory ncRNA webserver. , http://github.com/danmaclean/NiBLS
  • 26
    • 84870532154 scopus 로고    scopus 로고
    • The Gene Expression Omnibus
    • The Gene Expression Omnibus. , http://www.ncbi.nlm.nih.gov/geo/
  • 27
    • 84871345497 scopus 로고    scopus 로고
    • The Arabidopsis Information Resource
    • The Arabidopsis Information Resource. , http://arabidopsis.org
  • 28
    • 84871628911 scopus 로고    scopus 로고
    • The UCSC Genome Bioinformatics Website
    • The UCSC Genome Bioinformatics Website. , http://hgdownload.cse.ucsc.edu/goldenPath/mm9/chromosomes/
  • 29
    • 84888281432 scopus 로고    scopus 로고
    • CRAN - Comprehensive R Archive Network, akima package
    • CRAN - Comprehensive R Archive Network, akima package. , http://cran.r-project.org/web/packages/akima/index.html
  • 30
    • 0037336331 scopus 로고    scopus 로고
    • Open source software for the analysis of microarray data
    • 12664684
    • Dudoit S, Gentleman RC, Quackenbush J. Open source software for the analysis of microarray data. Biotechniques 2003, (Suppl):45-51. 12664684.
    • (2003) Biotechniques , Issue.SUPPL. , pp. 45-51
    • Dudoit, S.1    Gentleman, R.C.2    Quackenbush, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.