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Volumn 334, Issue 8-9, 2011, Pages 671-678

Identification and annotation of noncoding RNAs in Saccharomycotina

Author keywords

Genome sequencing; Noncoding RNAs; Saccharomycotina

Indexed keywords

UNTRANSLATED RNA;

EID: 79961165912     PISSN: 16310691     EISSN: 17683238     Source Type: Journal    
DOI: 10.1016/j.crvi.2011.05.016     Document Type: Article
Times cited : (9)

References (48)
  • 1
    • 41349118107 scopus 로고    scopus 로고
    • Complex riboswitches
    • DOI 10.1126/science.1152621
    • R.R. Breaker Complex riboswitches Science (New York N. Y.) 319 2008 1795 1797 (Pubitemid 351451558)
    • (2008) Science , vol.319 , Issue.5871 , pp. 1795-1797
    • Breaker, R.R.1
  • 2
    • 60149089144 scopus 로고    scopus 로고
    • Regulatory RNAs in bacteria
    • L.S. Waters, and G. Storz Regulatory RNAs in bacteria Cell 136 2009 615 628
    • (2009) Cell , vol.136 , pp. 615-628
    • Waters, L.S.1    Storz, G.2
  • 3
    • 60149099385 scopus 로고    scopus 로고
    • Evolution and functions of long noncoding RNAs
    • C.P. Ponting, P.L. Oliver, and W. Reik Evolution and functions of long noncoding RNAs Cell 136 2009 629 641
    • (2009) Cell , vol.136 , pp. 629-641
    • Ponting, C.P.1    Oliver, P.L.2    Reik, W.3
  • 5
    • 0035010211 scopus 로고    scopus 로고
    • Geometric nomenclature and classification of RNA base pairs
    • DOI 10.1017/S1355838201002515
    • N.B. Leontis, and E. Westhof Geometric nomenclature and classification of RNA base pairs RNA (New York, N. Y.) 7 2001 499 512 (Pubitemid 32416808)
    • (2001) RNA , vol.7 , Issue.4 , pp. 499-512
    • Leontis, N.B.1    Westhof, E.2
  • 6
    • 77954985549 scopus 로고    scopus 로고
    • Base pairing constraints drive structural epistasis in ribosomal RNA sequences
    • J.Y. Dutheil, F. Jossinet, and E. Westhof Base pairing constraints drive structural epistasis in ribosomal RNA sequences Mol. Biol. Evol. 27 2010 1868 1876
    • (2010) Mol. Biol. Evol. , vol.27 , pp. 1868-1876
    • Dutheil, J.Y.1    Jossinet, F.2    Westhof, E.3
  • 9
    • 72049104792 scopus 로고    scopus 로고
    • Large telomerase RNA, telomere length heterogeneity and escape from senescence in Candida glabrata
    • R. Kachouri-Lafond, B. Dujon, E. Gilson, E. Westhof, C. Fairhead, and M.T. Teixeira Large telomerase RNA, telomere length heterogeneity and escape from senescence in Candida glabrata FEBS Lett. 583 2009 3605 3610
    • (2009) FEBS Lett. , vol.583 , pp. 3605-3610
    • Kachouri-Lafond, R.1    Dujon, B.2    Gilson, E.3    Westhof, E.4    Fairhead, C.5    Teixeira, M.T.6
  • 11
    • 0242317680 scopus 로고    scopus 로고
    • Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics
    • DOI 10.1093/nar/gkg438
    • J.P. McCutcheon Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics Nucleic Acids Res. 31 2003 4119 4128 (Pubitemid 37442291)
    • (2003) Nucleic Acids Research , vol.31 , Issue.14 , pp. 4119-4128
    • McCutcheon, J.P.1    Eddy, S.R.2
  • 14
    • 62549104232 scopus 로고    scopus 로고
    • Genome-wide evolutionary analysis of the noncoding RNA genes and noncoding DNA of Paramecium tetraurelia
    • C.-L. Chen, H. Zhou, J.-Y. Liao, L.-H. Qu, and L. Amar Genome-wide evolutionary analysis of the noncoding RNA genes and noncoding DNA of Paramecium tetraurelia Rna 15 2009 503 514
    • (2009) Rna , vol.15 , pp. 503-514
    • Chen, C.-L.1    Zhou, H.2    Liao, J.-Y.3    Qu, L.-H.4    Amar, L.5
  • 16
    • 58949092587 scopus 로고    scopus 로고
    • Non-coding RNA prediction and verification in Saccharomyces cerevisiae
    • L.A. Kavanaugh, and F.S. Dietrich Non-coding RNA prediction and verification in Saccharomyces cerevisiae PLoS Genet. 5 2009 e1000321
    • (2009) PLoS Genet. , vol.5 , pp. 1000321
    • Kavanaugh, L.A.1    Dietrich, F.S.2
  • 17
    • 79961168914 scopus 로고    scopus 로고
    • LeARN: A platform for detecting, clustering and annotating
    • C. Noirot, C. Gaspin, T. Schiex, and J. Gouzy LeARN: a platform for detecting, clustering and annotating BMC Bioinformatics 11 2008 1 11
    • (2008) BMC Bioinformatics , vol.11 , pp. 1-11
    • Noirot, C.1    Gaspin, C.2    Schiex, T.3    Gouzy, J.4
  • 18
    • 71849109186 scopus 로고    scopus 로고
    • The tedious task of finding homologous noncoding RNA genes
    • P. Menzel, J. Gorodkin, and P.F. Stadler The tedious task of finding homologous noncoding RNA genes RNA (New York N. Y.) 15 2009 2075 2082
    • (2009) RNA (New York N. Y.) , vol.15 , pp. 2075-2082
    • Menzel, P.1    Gorodkin, J.2    Stadler, P.F.3
  • 19
    • 77955110979 scopus 로고    scopus 로고
    • Genome-wide computational identification and manual annotation of human long noncoding RNA genes
    • Jia, H., Osak, M., Bogu, G.K., Stanton, L.W., Johnson, R., Lipovich, L., Genome-wide computational identification and manual annotation of human long noncoding RNA genes, RNA 16 (2010) 1478-1487.
    • (2010) RNA , vol.16 , pp. 1478-1487
    • Jia, H.1    Osak, M.2    Bogu, K.G.3    Stanton, W.L.4    Johnson, R.5    Lipovich, L.6
  • 20
    • 65349153630 scopus 로고    scopus 로고
    • Discovering cis-regulatory RNAs in Shewanella genomes by support vector machines
    • X. Xu, Y. Ji, and G.D. Stormo Discovering cis-regulatory RNAs in Shewanella genomes by support vector machines PLoS Comput. Biol. 5 2009 e1000338
    • (2009) PLoS Comput. Biol. , vol.5 , pp. 1000338
    • Xu, X.1    Ji, Y.2    Stormo, G.D.3
  • 21
    • 71049154451 scopus 로고    scopus 로고
    • Systematic identification and characterization of chicken (Gallus gallus) ncRNAs
    • Y. Zhang, J. Wang, S. Huang, X. Zhu, J. Liu, and N. Yang Systematic identification and characterization of chicken (Gallus gallus) ncRNAs Nucleic Acids Res. 37 2009 6562 6574
    • (2009) Nucleic Acids Res. , vol.37 , pp. 6562-6574
    • Zhang, Y.1    Wang, J.2    Huang, S.3    Zhu, X.4    Liu, J.5    Yang, N.6
  • 22
    • 0347090332 scopus 로고    scopus 로고
    • Génolevures: Comparative genomics and molecular evolution of hemiascomycetous yeasts
    • D. Sherman, P. Durrens, E. Beyne, and M. Nikolski Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts Nucleic Acids Res. 32 2004 D315 D318
    • (2004) Nucleic Acids Res. , vol.32
    • Sherman, D.1    Durrens, P.2    Beyne, E.3    Nikolski, M.4
  • 25
    • 0037062949 scopus 로고    scopus 로고
    • The chemical repertoire of natural ribozymes
    • DOI 10.1038/418222a
    • J.A. Doudna, and T.R. Cech The chemical repertoire of natural ribozymes Nature 418 2002 222 228 (Pubitemid 34773781)
    • (2002) Nature , vol.418 , Issue.6894 , pp. 222-228
    • Doudna, J.A.1    Cech, T.R.2
  • 26
    • 0028272315 scopus 로고
    • RNA sequence analysis using covariance models
    • S.R. Eddy, and R. Durbin RNA analysis using covariance models Nucleic Acids Res. 22 1994 2079 2088 (Pubitemid 24192908)
    • (1994) Nucleic Acids Research , vol.22 , Issue.11 , pp. 2079-2088
    • Eddy, S.R.1    Durbin, R.2
  • 27
    • 33845362968 scopus 로고    scopus 로고
    • Measuring covariation in RNA alignments: Physical realism improves information measures
    • DOI 10.1093/bioinformatics/btl514
    • S. Lindgreen, P.P. Gardner, and A. Krogh Measuring covariation in RNA alignments: physical realism improves information measures Bioinformatics (Oxford, England) 22 2006 2988 2995 (Pubitemid 44884072)
    • (2006) Bioinformatics , vol.22 , Issue.24 , pp. 2988-2995
    • Lindgreen, S.1    Gardner, P.P.2    Krogh, A.3
  • 30
    • 30144440914 scopus 로고    scopus 로고
    • Receiver operating characteristics curves and related decision measures: A tutorial
    • DOI 10.1016/j.chemolab.2005.05.004, PII S0169743905000766
    • C. Brown, and H. Davis Receiver operating characteristics curves and related decision measures: A tutorial Chemom. and Intell. Lab. Syst. 80 2006 24 38 (Pubitemid 43052337)
    • (2006) Chemometrics and Intelligent Laboratory Systems , vol.80 , Issue.1 , pp. 24-38
    • Brown, C.D.1    Davis, H.T.2
  • 31
    • 0346366823 scopus 로고    scopus 로고
    • Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5′-UTR
    • DOI 10.1016/S0014-5793(03)01335-8
    • T. Kubodera, M. Watanabe, K. Yoshiuchi, N. Yamashita, A. Nishimura, and S. Nakai Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5′-UTR FEBS Lett. 555 2003 516 520 (Pubitemid 37532603)
    • (2003) FEBS Letters , vol.555 , Issue.3 , pp. 516-520
    • Kubodera, T.1    Watanabe, M.2    Yoshiuchi, K.3    Yamashita, N.4    Nishimura, A.5    Nakai, S.6    Gomi, K.7    Hanamoto, H.8
  • 32
    • 34249278470 scopus 로고    scopus 로고
    • Control of alternative RNA splicing and gene expression by eukaryotic riboswitches
    • DOI 10.1038/nature05769, PII NATURE05769
    • M.T. Cheah, A. Wachter, N. Sudarsan, and R.R. Breaker Control of alternative RNA splicing and gene expression by eukaryotic riboswitches Nature. 447 2007 497 500 (Pubitemid 46816734)
    • (2007) Nature , vol.447 , Issue.7143 , pp. 497-500
    • Cheah, M.T.1    Wachter, A.2    Sudarsan, N.3    Breaker, R.R.4
  • 33
    • 33748300801 scopus 로고    scopus 로고
    • Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule Recognition
    • DOI 10.1016/j.str.2006.07.008, PII S0969212606003303
    • T.E. Edwards, and A.R. Ferré-D'Amaré Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition Structure (London, England: 1993) 14 2006 1459 1468 (Pubitemid 44331619)
    • (2006) Structure , vol.14 , Issue.9 , pp. 1459-1468
    • Edwards, T.E.1    Ferre-D'Amare, A.R.2
  • 34
    • 33744469562 scopus 로고    scopus 로고
    • Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand
    • DOI 10.1126/science.1128451
    • S. Thore, M. Leibundgut, and N. Ban Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand Science 312 2006 1208 1211 (Pubitemid 43801145)
    • (2006) Science , vol.312 , Issue.5777 , pp. 1208-1211
    • Thore, S.1    Leibundgut, M.2    Ban, N.3
  • 36
    • 62549108676 scopus 로고    scopus 로고
    • Identification and comparative analysis of telomerase RNAs from Candida species reveal conservation of functional elements
    • S. Gunisova, E. Elboher, J. Nosek, V. Gorkovoy, Y. Brown, and J.F. Lucier Identification and comparative analysis of telomerase RNAs from Candida species reveal conservation of functional elements RNA (New York, N.Y.) 15 2009 546 559
    • (2009) RNA (New York, N.Y.) , vol.15 , pp. 546-559
    • Gunisova, S.1    Elboher, E.2    Nosek, J.3    Gorkovoy, V.4    Brown, Y.5    Lucier, J.F.6
  • 38
    • 32544452741 scopus 로고    scopus 로고
    • CMfinder - A covariance model based RNA motif finding algorithm
    • DOI 10.1093/bioinformatics/btk008
    • Z. Yao, Z. Weinberg, and W.L. Ruzzo CMfinder - a covariance model based RNA motif finding algorithm Bioinformatics (Oxford, England) 22 2006 445 452 (Pubitemid 43231419)
    • (2006) Bioinformatics , vol.22 , Issue.4 , pp. 445-452
    • Yao, Z.1    Weinberg, Z.2    Ruzzo, W.L.3
  • 39
    • 0033765362 scopus 로고    scopus 로고
    • Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs
    • E. Rivas, and S.R. Eddy Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs Bioinformatics 16 2000 583 605
    • (2000) Bioinformatics , vol.16 , pp. 583-605
    • Rivas, E.1    Eddy, S.R.2
  • 40
    • 17844391015 scopus 로고    scopus 로고
    • Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency
    • DOI 10.1261/rna.7220505
    • P. Clote, F. Ferré, E. Kranakis, and D. Krizanc Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency RNA (New York N. Y.) 11 2005 578 591 (Pubitemid 40594326)
    • (2005) RNA , vol.11 , Issue.5 , pp. 578-591
    • Clote, P.1    Ferre, F.2    Kranakis, E.3    Krizanc, D.4
  • 41
    • 56849104634 scopus 로고    scopus 로고
    • Taxon sampling and the accuracy of phylogenetic analyses
    • S.M. Hedtke, and D.M. Hillis Taxon sampling and the accuracy of phylogenetic analyses Evolution 46 2008 239 257
    • (2008) Evolution , vol.46 , pp. 239-257
    • Hedtke, S.M.1    Hillis, D.M.2
  • 43
    • 24644443227 scopus 로고    scopus 로고
    • The functional genomics of noncoding RNA
    • DOI 10.1126/science.1117806
    • J.S. Mattick The functional genomics of noncoding RNA Science (New York N. Y.) 309 2005 1527 1528 (Pubitemid 41266470)
    • (2005) Science , vol.309 , Issue.5740 , pp. 1527-1528
    • Mattick, J.S.1
  • 45
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • DOI 10.1126/science.1158441
    • U. Nagalakshmi, Z. Wang, K. Waern, C. Shou, D. Raha, and M. Gerstein The transcriptional landscape of the yeast genome defined by RNA sequencing Science (New York N. Y.) 320 2008 1344 1349 (Pubitemid 351929471)
    • (2008) Science , vol.320 , Issue.5881 , pp. 1344-1349
    • Nagalakshmi, U.1    Wang, Z.2    Waern, K.3    Shou, C.4    Raha, D.5    Gerstein, M.6    Snyder, M.7
  • 46
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Z. Wang, M. Gerstein, and M. Snyder RNA-Seq: a revolutionary tool for transcriptomics Nat. Rev. Genet. 10 2009 57 63
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3


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