메뉴 건너뛰기




Volumn 11, Issue , 2010, Pages

Non-coding RNA detection methods combined to improve usability, reproducibility and precision

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL PREDICTIONS; DETECTION METHODS; EXTENSIBLE FRAMEWORK; GNU GENERAL PUBLIC LICENSE; GUIDING EXPERIMENT; LISTERIA MONOCYTOGENES; NATURAL APPROACHES; STREPTOCOCCUS PYOGENES;

EID: 77957129677     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-491     Document Type: Article
Times cited : (19)

References (36)
  • 1
    • 0037146606 scopus 로고    scopus 로고
    • Breakthrough of the year. Small RNAs make big splash
    • 10.1126/science.298.5602.2296, 12493875
    • Couzin J. Breakthrough of the year. Small RNAs make big splash. Science 2002, 298:2296-2297. 10.1126/science.298.5602.2296, 12493875.
    • (2002) Science , vol.298 , pp. 2296-2297
    • Couzin, J.1
  • 2
    • 20644449571 scopus 로고    scopus 로고
    • An abundance of RNA regulators
    • 10.1146/annurev.biochem.74.082803.133136, 15952886
    • Storz G, Altuvia S, Wassarman KM. An abundance of RNA regulators. Annu Rev Biochem 2005, 74:199-217. 10.1146/annurev.biochem.74.082803.133136, 15952886.
    • (2005) Annu Rev Biochem , vol.74 , pp. 199-217
    • Storz, G.1    Altuvia, S.2    Wassarman, K.M.3
  • 3
    • 0035656688 scopus 로고    scopus 로고
    • Non-coding RNA genes and the modern RNA world
    • 10.1038/35103511, 11733745
    • Eddy SR. Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2001, 2:919-929. 10.1038/35103511, 11733745.
    • (2001) Nat Rev Genet , vol.2 , pp. 919-929
    • Eddy, S.R.1
  • 5
    • 60349120914 scopus 로고    scopus 로고
    • Long non-coding RNAs: insights into functions
    • 10.1038/nrg2521, 19188922
    • Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet 2009, 10:155-159. 10.1038/nrg2521, 19188922.
    • (2009) Nat Rev Genet , vol.10 , pp. 155-159
    • Mercer, T.R.1    Dinger, M.E.2    Mattick, J.S.3
  • 6
    • 36448997409 scopus 로고    scopus 로고
    • Computational methods in noncoding RNA research
    • 10.1007/s00285-007-0122-6, 17786447
    • Machado-Lima A, Portillo HAD, Durham AM. Computational methods in noncoding RNA research. J Math Biol 2008, 56:15-49. 10.1007/s00285-007-0122-6, 17786447.
    • (2008) J Math Biol , vol.56 , pp. 15-49
    • Machado-Lima, A.1    Portillo, H.A.D.2    Durham, A.M.3
  • 7
    • 37749047490 scopus 로고    scopus 로고
    • Sequence census methods for functional genomics
    • Wold B, Myers RM. Sequence census methods for functional genomics. Nat Meth 2008, 5:19-21.
    • (2008) Nat Meth , vol.5 , pp. 19-21
    • Wold, B.1    Myers, R.M.2
  • 8
    • 36549059781 scopus 로고    scopus 로고
    • A practical guide to the art of RNA gene prediction
    • 10.1093/bib/bbm011, 17483123
    • Meyer IM. A practical guide to the art of RNA gene prediction. Brief Bioinform 2007, 8:396-414. 10.1093/bib/bbm011, 17483123.
    • (2007) Brief Bioinform , vol.8 , pp. 396-414
    • Meyer, I.M.1
  • 9
    • 0037188546 scopus 로고    scopus 로고
    • Noncoding RNA genes identified in AT-rich hyperthermophiles
    • 10.1073/pnas.112063799, 124278, 12032319
    • Klein RJ, Misulovin Z, Eddy SR. Noncoding RNA genes identified in AT-rich hyperthermophiles. Proc Natl Acad Sci USA 2002, 99:7542-7547. 10.1073/pnas.112063799, 124278, 12032319.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 7542-7547
    • Klein, R.J.1    Misulovin, Z.2    Eddy, S.R.3
  • 10
    • 0035477134 scopus 로고    scopus 로고
    • A computational approach to identify genes for functional RNAs in genomic sequences
    • 60242, 11574674
    • Carter RJ, Dubchak I, Holbrook SR. A computational approach to identify genes for functional RNAs in genomic sequences. Nucleic Acids Res 2001, 29:3928-3938. 60242, 11574674.
    • (2001) Nucleic Acids Res , vol.29 , pp. 3928-3938
    • Carter, R.J.1    Dubchak, I.2    Holbrook, S.R.3
  • 11
    • 58949092587 scopus 로고    scopus 로고
    • Non-coding RNA prediction and verification in Saccharomyces cerevisiae
    • 10.1371/journal.pgen.1000321, 2603021, 19119416
    • Kavanaugh LA, Dietrich FS. Non-coding RNA prediction and verification in Saccharomyces cerevisiae. PLoS Genet 2009, 5:e1000321. 10.1371/journal.pgen.1000321, 2603021, 19119416.
    • (2009) PLoS Genet , vol.5
    • Kavanaugh, L.A.1    Dietrich, F.S.2
  • 12
    • 27644542383 scopus 로고    scopus 로고
    • A comparison of RNA folding measures
    • 10.1186/1471-2105-6-241, 1274297, 16202126
    • Freyhult E, Gardner PP, Moulton V. A comparison of RNA folding measures. BMC Bioinformatics 2005, 6:241. 10.1186/1471-2105-6-241, 1274297, 16202126.
    • (2005) BMC Bioinformatics , vol.6 , pp. 241
    • Freyhult, E.1    Gardner, P.P.2    Moulton, V.3
  • 14
    • 0003157183 scopus 로고    scopus 로고
    • Noncoding RNA gene detection using comparative sequence analysis
    • 10.1186/1471-2105-2-8, 64605, 11801179
    • Rivas E, Eddy SR. Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2001, 2:8. 10.1186/1471-2105-2-8, 64605, 11801179.
    • (2001) BMC Bioinformatics , vol.2 , pp. 8
    • Rivas, E.1    Eddy, S.R.2
  • 17
    • 19544374354 scopus 로고    scopus 로고
    • Predicting a set of minimal free energy RNA secondary structures common to two sequences
    • 10.1093/bioinformatics/bti349, 15731207
    • Mathews DH. Predicting a set of minimal free energy RNA secondary structures common to two sequences. Bioinformatics 2005, 21:2246-2253. 10.1093/bioinformatics/bti349, 15731207.
    • (2005) Bioinformatics , vol.21 , pp. 2246-2253
    • Mathews, D.H.1
  • 18
    • 59449089754 scopus 로고    scopus 로고
    • Identification of small noncoding RNAs in Helicobacter pylori by a bioinformatics-based approach
    • 10.1007/s00284-008-9318-2, 19123032
    • Xiao B, Li W, Guo G, Li B, Liu Z, Jia K, Guo Y, Mao X, Zou Q. Identification of small noncoding RNAs in Helicobacter pylori by a bioinformatics-based approach. Curr Microbiol 2009, 58:258-263. 10.1007/s00284-008-9318-2, 19123032.
    • (2009) Curr Microbiol , vol.58 , pp. 258-263
    • Xiao, B.1    Li, W.2    Guo, G.3    Li, B.4    Liu, Z.5    Jia, K.6    Guo, Y.7    Mao, X.8    Zou, Q.9
  • 19
    • 57249116905 scopus 로고    scopus 로고
    • Small RNA gene identification and mRNA target predictions in bacteria
    • 10.1093/bioinformatics/btn560, 18974076
    • Pichon C, Felden B. Small RNA gene identification and mRNA target predictions in bacteria. Bioinformatics 2008, 24:2807-2813. 10.1093/bioinformatics/btn560, 18974076.
    • (2008) Bioinformatics , vol.24 , pp. 2807-2813
    • Pichon, C.1    Felden, B.2
  • 20
    • 69249110138 scopus 로고    scopus 로고
    • An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes
    • 10.1093/bib/bbp022, 19383843
    • Solda G, Makunin IV, Sezerman OU, Corradin A, Corti G, Guffanti A. An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes. Brief Bioinform 2009, 10:475-489. 10.1093/bib/bbp022, 19383843.
    • (2009) Brief Bioinform , vol.10 , pp. 475-489
    • Solda, G.1    Makunin, I.V.2    Sezerman, O.U.3    Corradin, A.4    Corti, G.5    Guffanti, A.6
  • 21
    • 2442626706 scopus 로고    scopus 로고
    • Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
    • 10.1073/pnas.0401799101, 409911, 15123812
    • Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci USA 2004, 101:7287-7292. 10.1073/pnas.0401799101, 409911, 15123812.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 7287-7292
    • Mathews, D.H.1    Disney, M.D.2    Childs, J.L.3    Schroeder, S.J.4    Zuker, M.5    Turner, D.H.6
  • 22
    • 36448976216 scopus 로고    scopus 로고
    • Prediction of small, noncoding RNAs in bacteria using heterogeneous data
    • 10.1007/s00285-007-0079-5, 17354017
    • Tjaden B. Prediction of small, noncoding RNAs in bacteria using heterogeneous data. J Math Biol 2008, 56:183-200. 10.1007/s00285-007-0079-5, 17354017.
    • (2008) J Math Biol , vol.56 , pp. 183-200
    • Tjaden, B.1
  • 23
    • 44449162237 scopus 로고    scopus 로고
    • The genome browser at UCSC for locating genes, and much more!
    • 10.1007/s12033-007-9019-2, 18058261
    • Bina M. The genome browser at UCSC for locating genes, and much more!. Mol Biotechnol 2008, 38:269-275. 10.1007/s12033-007-9019-2, 18058261.
    • (2008) Mol Biotechnol , vol.38 , pp. 269-275
    • Bina, M.1
  • 25
  • 26
    • 39149086705 scopus 로고    scopus 로고
    • LeARN: a platform for detecting, clustering and annotating non-coding RNAs
    • 10.1186/1471-2105-9-21, 2241582, 18194551
    • Noirot C, Gaspin C, Schiex T, Gouzy J. LeARN: a platform for detecting, clustering and annotating non-coding RNAs. BMC Bioinformatics 9:21-21. 10.1186/1471-2105-9-21, 2241582, 18194551.
    • BMC Bioinformatics , vol.9 , pp. 21-21
    • Noirot, C.1    Gaspin, C.2    Schiex, T.3    Gouzy, J.4
  • 31
    • 39049168212 scopus 로고    scopus 로고
    • Generic eukaryotic core promoter prediction using structural features of DNA
    • 10.1101/gr.6991408, 2203629, 18096745
    • Abeel T, Saeys Y, Bonnet E, Rouzé P, Van de Peer Y. Generic eukaryotic core promoter prediction using structural features of DNA. Genome Research 2008, 18:310-323. 10.1101/gr.6991408, 2203629, 18096745.
    • (2008) Genome Research , vol.18 , pp. 310-323
    • Abeel, T.1    Saeys, Y.2    Bonnet, E.3    Rouzé, P.4    Van de Peer, Y.5
  • 32
    • 34447499141 scopus 로고    scopus 로고
    • Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
    • 10.1186/gb-2007-8-2-r22, 1852404, 17313685
    • Kingsford CL, Ayanbule K, Salzberg SL. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol 2007, 8:R22. 10.1186/gb-2007-8-2-r22, 1852404, 17313685.
    • (2007) Genome Biol , vol.8
    • Kingsford, C.L.1    Ayanbule, K.2    Salzberg, S.L.3
  • 33
    • 0022360113 scopus 로고
    • Significance of nucleotide sequence alignments: a method for random sequence permutation that preserves dinucleotide and codon usage
    • Altschul SF, Erickson BW. Significance of nucleotide sequence alignments: a method for random sequence permutation that preserves dinucleotide and codon usage. Mol Biol Evol 1985, 2:526-538.
    • (1985) Mol Biol Evol , vol.2 , pp. 526-538
    • Altschul, S.F.1    Erickson, B.W.2
  • 34
    • 70449435697 scopus 로고    scopus 로고
    • A Genome-Wide Analysis of Small Regulatory RNAs in the Human Pathogen Group A Streptococcus
    • 10.1371/journal.pone.0007668, 2765633, 19888332
    • Perez N, Treviño J, Liu Z, Ho SCM, Babitzke P, Sumby P. A Genome-Wide Analysis of Small Regulatory RNAs in the Human Pathogen Group A Streptococcus. PLoS ONE 2009, 4:e7668. 10.1371/journal.pone.0007668, 2765633, 19888332.
    • (2009) PLoS ONE , vol.4
    • Perez, N.1    Treviño, J.2    Liu, Z.3    Ho, S.C.M.4    Babitzke, P.5    Sumby, P.6
  • 35
    • 33750416896 scopus 로고    scopus 로고
    • PSoL: a positive sample only learning algorithm for finding non-coding RNA genes
    • 10.1093/bioinformatics/btl441, 16945945
    • Wang C, Ding C, Meraz RF, Holbrook SR. PSoL: a positive sample only learning algorithm for finding non-coding RNA genes. Bioinformatics 2006, 22:2590-2596. 10.1093/bioinformatics/btl441, 16945945.
    • (2006) Bioinformatics , vol.22 , pp. 2590-2596
    • Wang, C.1    Ding, C.2    Meraz, R.F.3    Holbrook, S.R.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.