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Volumn 24, Issue 1, 2007, Pages 64-74

Computational Identification and Analysis of Noncoding RNAs

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EID: 85032752374     PISSN: 10535888     EISSN: None     Source Type: Journal    
DOI: 10.1109/MSP.2007.273058     Document Type: Article
Times cited : (24)

References (54)
  • 2
    • 85032750863 scopus 로고    scopus 로고
    • Genomic signal processing
    • July
    • D. Anastassiou, “Genomic signal processing,” IEEE Signal Process. Mag., vol. 18, no. 4, pp. 8–20, July 2001.
    • (2001) IEEE Signal Process. Mag. , vol.18 , Issue.4 , pp. 8-20
    • Anastassiou, D.1
  • 3
    • 0028111863 scopus 로고
    • PROSITE: Recent developments
    • A. Bairoch and P. Bucher, “PROSITE: Recent developments,” Nucleic Acids Research, vol. 22, no. 17, pp. 3583-3589,1994.
    • (1994) Nucleic Acids Research , vol.22 , Issue.17 , pp. 3583-3589
    • Bairoch, A.1    Bucher, P.2
  • 4
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • D.P. Bartel, “MicroRNAs: Genomics, biogenesis, mechanism, and function,” Cell, vol. 116, no. 2, pp. 281–297, 2004.
    • (2004) Cell , vol.116 , Issue.2 , pp. 281-297
    • Bartel, D.P.1
  • 5
    • 0037827862 scopus 로고    scopus 로고
    • Genomes
    • New York: Wiley
    • T.A. Brown, Genomes. New York: Wiley, 2002.
    • (2002)
    • Brown, T.A.1
  • 6
    • 49749213366 scopus 로고
    • On certain formal properties of grammars
    • N. Chomsky, “On certain formal properties of grammars,” Inform. Control, vol. 2, no. 2, pp. 137-167,1959.
    • (1959) Inform. Control , vol.2 , Issue.2 , pp. 137-167
    • Chomsky, N.1
  • 7
    • 4344584927 scopus 로고    scopus 로고
    • MSARI: Multiple sequence alignments for statistical detection of RNA secondary structure
    • A. Coventri, D.J. Kleitman, and B. Berger, “MSARI: Multiple sequence alignments for statistical detection of RNA secondary structure,” Proc. Natl. Acad. Sci., vol. 101, no. 33, pp. 12102–12107, 2004.
    • (2004) Proc. Natl. Acad. Sci. , vol.101 , Issue.33 , pp. 12102-12107
    • Coventri, A.1    Kleitman, D.J.2    Berger, B.3
  • 8
    • 0141515775 scopus 로고    scopus 로고
    • ddbRNA: Detection of conserved secondary structures in multiple alignments
    • D. di Bernardo, T. Down, and T. Hubbard, “ddbRNA: Detection of conserved secondary structures in multiple alignments,” Bioinformatics, vol. 19, no. 13, pp. 1606-1611,2003.
    • (2003) Bioinformatics , vol.19 , Issue.13 , pp. 1606-1611
    • di Bernardo, D.1    Down, T.2    Hubbard, T.3
  • 9
    • 0003516147 scopus 로고    scopus 로고
    • Biological Sequence Analysis
    • Cambridge, UK: Cambridge Univ. Press
    • R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, Biological Sequence Analysis. Cambridge, UK: Cambridge Univ. Press, 1998.
    • (1998)
    • Durbin, R.1    Eddy, S.2    Krogh, A.3    Mitchison, G.4
  • 10
    • 0028272315 scopus 로고
    • RNA sequence analysis using covariance models
    • S.R. Eddy and R. Durbin, “RNA sequence analysis using covariance models,” Nucleic Acids Res., vol. 22, no. 11, pp. 2079-2088,1994.
    • (1994) Nucleic Acids Res. , vol.22 , Issue.11 , pp. 2079-2088
    • Eddy, S.R.1    Durbin, R.2
  • 11
    • 0035656688 scopus 로고    scopus 로고
    • Non-coding RNA genes and the modern RNA world
    • S.R. Eddy, “Non-coding RNA genes and the modern RNA world,” Nature Rev. Genetics, vol. 2, no. 12, pp. 919–929, 2001.
    • (2001) Nature Rev. Genetics , vol.2 , Issue.12 , pp. 919-929
    • Eddy, S.R.1
  • 12
    • 0037133945 scopus 로고    scopus 로고
    • Computational genomics of noncoding RNA genes
    • S.R. Eddy, “Computational genomics of noncoding RNA genes,” Cell, vol. 109, no. 2, pp. 137-40, 2002.
    • (2002) Cell , vol.109 , Issue.2 , pp. 137-140
    • Eddy, S.R.1
  • 13
    • 8344234215 scopus 로고    scopus 로고
    • How do RNA folding algorithms work?
    • S.R. Eddy, “How do RNA folding algorithms work?,” Nature Biotechnol., vol. 22, no. 11, pp. 1457–1458, 2004.
    • (2004) Nature Biotechnol. , vol.22 , Issue.11 , pp. 1457-1458
    • Eddy, S.R.1
  • 15
    • 0030194206 scopus 로고    scopus 로고
    • Partially hidden Markov models
    • S. Forchhammer and J. Rissanen, “Partially hidden Markov models,” IEEE Trans. Inform. Theory, vol. 42, no. 4, pp. 1253-1256,1996.
    • (1996) IEEE Trans. Inform. Theory , vol.42 , Issue.4 , pp. 1253-1256
    • Forchhammer, S.1    Rissanen, J.2
  • 16
    • 0003603813 scopus 로고
    • Computers and Intractability: A Guide to the Theory of NP-Completeness
    • New York: W. H. Freeman
    • M.R. Garey and D.S. Johnson, Computers and Intractability: A Guide to the Theory of NP-Completeness. New York: W. H. Freeman, 1979.
    • (1979)
    • Garey, M.R.1    Johnson, D.S.2
  • 17
    • 0037112006 scopus 로고    scopus 로고
    • Stealth regulation: Biological circuits with small RNA switches
    • S. Gottesman, “Stealth regulation: Biological circuits with small RNA switches,” Genes Develop., vol. 16, no. 22, pp. 2829–2842, 2002.
    • (2002) Genes Develop. , vol.16 , Issue.22 , pp. 2829-2842
    • Gottesman, S.1
  • 19
    • 0003626841 scopus 로고
    • Introduction to Formal Language Theory
    • Reading, MA: Addison-Wesley
    • M.A. Harrison, Introduction to Formal Language Theory. Reading, MA: Addison-Wesley, 1978.
    • (1978)
    • Harrison, M.A.1
  • 20
    • 3042767202 scopus 로고    scopus 로고
    • MicroRNAs: Small RNAs with a big role in gene regulation
    • L. He and J. Hannon, “MicroRNAs: Small RNAs with a big role in gene regulation,” Nature Rev. Genetics, vol. 5, no. 7, pp. 522-531,2004.
    • (2004) Nature Rev. Genetics , vol.5 , Issue.7 , pp. 522-531
    • He, L.1    Hannon, J.2
  • 21
    • 2942544566 scopus 로고    scopus 로고
    • RSEARCH: Finding homologs of single structured RNA sequences
    • R.J. Klein and S.R. Eddy, “RSEARCH: Finding homologs of single structured RNA sequences,” BMC Bioinformatics, vol. 4, p. 44, 2003.
    • (2003) BMC Bioinformatics , vol.4 , pp. 44
    • Klein, R.J.1    Eddy, S.R.2
  • 22
    • 0028181441 scopus 로고
    • Hidden Markov models in computational biology: Applications to protein modeling
    • A. Krogh, M. Brown, I.S. Mian, K. Sjölander, and D. Haussler, “Hidden Markov models in computational biology: Applications to protein modeling,” J. Mol. Biol., vol. 235, no. 5, pp. 1501-1531, 1994.
    • (1994) J. Mol. Biol. , vol.235 , Issue.5 , pp. 1501-1531
    • Krogh, A.1    Brown, M.2    Mian, I.S.3    Sjölander, K.4    Haussler, D.5
  • 23
    • 0027944605 scopus 로고
    • A hidden Markov model that finds genes in E. coli DNA
    • A. Krogh, I.S. Mian, and D. Haussler, “A hidden Markov model that finds genes in E. coli DNA,” Nucleic Acids Res., vol. 22, no. 22, pp. 4768-4778, 1994.
    • (1994) Nucleic Acids Res. , vol.22 , Issue.22 , pp. 4768-4778
    • Krogh, A.1    Mian, I.S.2    Haussler, D.3
  • 24
    • 0002532056 scopus 로고
    • The estimation of stochastic context-free grammars using the inside-outside algorithm
    • K. Lari and S.J. Young, “The estimation of stochastic context-free grammars using the inside-outside algorithm,” Comp. Speech Lang., vol. 4, no. 1, pp. 35-56, 1990.
    • (1990) Comp. Speech Lang. , vol.4 , Issue.1 , pp. 35-56
    • Lari, K.1    Young, S.J.2
  • 25
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • T.M. Lowe and S.R. Eddy, “tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence,” Nucleic Acids Res., vol. 25, no. 5, pp. 955-964, 1997.
    • (1997) Nucleic Acids Res. , vol.25 , Issue.5 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 26
    • 2942560804 scopus 로고    scopus 로고
    • Gene regulation by riboswitches
    • M. Mandal and R.R. Breaker, “Gene regulation by riboswitches,” Nature Rev. Mol. Cell Biol., vol. 5, no. 6, pp. 451-463, 2004.
    • (2004) Nature Rev. Mol. Cell Biol. , vol.5 , Issue.6 , pp. 451-463
    • Mandal, M.1    Breaker, R.R.2
  • 27
    • 0141867857 scopus 로고    scopus 로고
    • Challenging the dogma: The hidden layer of non-protein-coding RNAs in complex organisms
    • J.S. Mattick, “Challenging the dogma: The hidden layer of non-protein-coding RNAs in complex organisms,” BioEssays, vol. 25, no. 10, pp. 930-939, 2003.
    • (2003) BioEssays , vol.25 , Issue.10 , pp. 930-939
    • Mattick, J.S.1
  • 28
    • 20744449966 scopus 로고    scopus 로고
    • Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures
    • H. Matsui, K. Sato, and Y. Sakakibara, “Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures,” Bioinformatics, vol. 21, no. 11, pp. 2611-2617, 2005.
    • (2005) Bioinformatics , vol.21 , Issue.11 , pp. 2611-2617
    • Matsui, H.1    Sato, K.2    Sakakibara, Y.3
  • 29
    • 10644237968 scopus 로고    scopus 로고
    • RNAi-mediated pathways in the nucleus
    • M.A. Matzke and J.A. Birchler, “RNAi-mediated pathways in the nucleus,” Nature Rev. Genetics, vol. 6, no. 1, 2005.
    • (2005) Nature Rev. Genetics , vol.6 , Issue.1
    • Matzke, M.A.1    Birchler, J.A.2
  • 30
    • 0036788304 scopus 로고    scopus 로고
    • Gene silencing in mammals by small interfering RNAs
    • M.T. McManus and P.A. Sharp, “Gene silencing in mammals by small interfering RNAs,” Nature Rev. Genetics, vol. 3, no. 10, 2002.
    • (2002) Nature Rev. Genetics , vol.3 , Issue.10
    • McManus, M.T.1    Sharp, P.A.2
  • 31
    • 14044273097 scopus 로고    scopus 로고
    • Tracking down noncoding RNAs
    • V. Moulton, “Tracking down noncoding RNAs,” Proc. Natl. Acad. Sci., vol. 102, no. 7, pp. 2269-2270, 2005.
    • (2005) Proc. Natl. Acad. Sci. , vol.102 , Issue.7 , pp. 2269-2270
    • Moulton, V.1
  • 33
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • W.R. Pearson and D.J. Lipman, “Improved tools for biological sequence comparison,” Proc. Natl. Acad. Sci., vol. 85, no. 8, pp. 2444-2448, 1988.
    • (1988) Proc. Natl. Acad. Sci. , vol.85 , Issue.8 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 34
    • 0034046133 scopus 로고    scopus 로고
    • The language of RNA: A formal grammar that includes pseudoknots
    • E. Rivas and S.R. Eddy, “The language of RNA: A formal grammar that includes pseudoknots,” Bioinformatics, vol. 16, no. 4, pp. 334-340, 2000.
    • (2000) Bioinformatics , vol.16 , Issue.4 , pp. 334-340
    • Rivas, E.1    Eddy, S.R.2
  • 35
    • 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, vol. 16, no. 7, pp. 583-605, 2000.
    • (2000) Bioinformatics , vol.16 , Issue.7 , pp. 583-605
    • Rivas, E.1    Eddy, S.R.2
  • 36
    • 0003157183 scopus 로고    scopus 로고
    • Noncoding RNA gene detection using comparative sequence analysis
    • E. Rivas and S.R. Eddy, “Noncoding RNA gene detection using comparative sequence analysis,” BMC Bioinformatics, vol. 2, p. 8, 2001.
    • (2001) BMC Bioinformatics , vol.2 , pp. 8
    • Rivas, E.1    Eddy, S.R.2
  • 37
    • 0347724163 scopus 로고    scopus 로고
    • An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots
    • J. Ruan, G.D. Stormo, and W. Zhang, “An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots,” Bioinformatics, vol. 20, no. 1, pp. 12102-12107, 2004.
    • (2004) Bioinformatics , vol.20 , Issue.1 , pp. 12102-12107
    • Ruan, J.1    Stormo, G.D.2    Zhang, W.3
  • 38
    • 0035955406 scopus 로고    scopus 로고
    • Glimpses of a tiny RNA world
    • G. Ruvkun, “Glimpses of a tiny RNA world,” Science, vol. 294, no. 5543, pp. 797-799, 2001.
    • (2001) Science , vol.294 , Issue.5543 , pp. 797-799
    • Ruvkun, G.1
  • 40
    • 0037123632 scopus 로고    scopus 로고
    • An expanding universe of noncoding RNAs
    • S. Gisela, “An expanding universe of noncoding RNAs,” Science, vol. 296, no. 5571, pp. 1260-1263, 2002.
    • (2002) Science , vol.296 , Issue.5571 , pp. 1260-1263
    • Gisela, S.1
  • 41
    • 0038136962 scopus 로고    scopus 로고
    • Metabolite-binding RNA domains are present in the genes of eukaryotes
    • N. Sudarsan, J.E. Barrick, and R.R. Breaker, “Metabolite-binding RNA domains are present in the genes of eukaryotes,” RNA, vol. 9, no. 6, pp. 644-647, 2003.
    • (2003) RNA , vol.9 , Issue.6 , pp. 644-647
    • Sudarsan, N.1    Barrick, J.E.2    Breaker, R.R.3
  • 42
    • 0026483177 scopus 로고
    • Structural and functional aspects of RNA pseudoknots
    • E.B. ten Dam, C.W.A. Pleij, and D. Draper, “Structural and functional aspects of RNA pseudoknots,” Biochem., vol. 31, no. 47, pp. 11665-11676, 1992.
    • (1992) Biochem. , vol.31 , Issue.47 , pp. 11665-11676
    • ten Dam, E.B.1    Pleij, C.W.A.2    Draper, D.3
  • 44
    • 20444478991 scopus 로고    scopus 로고
    • Riboswitches as versatile gene control elements
    • B.J. Tucker and R.R. Breaker, “Riboswitches as versatile gene control elements,” Current Opinion Structural Biol., vol. 15, no. 3, pp. 342-348, 2005.
    • (2005) Current Opinion Structural Biol. , vol.15 , Issue.3 , pp. 342-348
    • Tucker, B.J.1    Breaker, R.R.2
  • 45
    • 1542742235 scopus 로고    scopus 로고
    • The role of signal-processing concepts in genomics and proteomics
    • P.P. Vaidyanathan and B.-J. Yoon, “The role of signal-processing concepts in genomics and proteomics,” J. Franklin Inst., vol. 341, no. 1-2, pp 111-135, 2003.
    • (2003) J. Franklin Inst. , vol.341 , Issue.1-2 , pp. 111-135
    • Vaidyanathan, P.P.1    Yoon, B.-J.2
  • 46
    • 11444250228 scopus 로고    scopus 로고
    • Genomics and proteomics: A signal processor's tour
    • P.P. Vaidyanathan, “Genomics and proteomics: A signal processor's tour,” IEEE Circuits Syst. Mag., vol. 4, no. 4, pp. 6-29, 2005.
    • (2005) IEEE Circuits Syst. Mag. , vol.4 , Issue.4 , pp. 6-29
    • Vaidyanathan, P.P.1
  • 47
    • 14044272835 scopus 로고    scopus 로고
    • Fast and reliable prediction of noncoding RNAs
    • S. Washietl, I.L. Hofacker, and P.F. Stadler, “Fast and reliable prediction of noncoding RNAs,” Proc. Natl. Acad. Sci., vol. 102, no. 7 pp. 2454-2459, 2005.
    • (2005) Proc. Natl. Acad. Sci. , vol.102 , Issue.7 , pp. 2454-2459
    • Washietl, S.1    Hofacker, I.L.2    Stadler, P.F.3
  • 48
    • 27944464131 scopus 로고    scopus 로고
    • Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome
    • S. Washietl, I.L. Hofacker, M. Lukasser, A. Hüttenhofer and P.F. Stadler, “Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome,” Nature Biotechnol., vol. 23, no. 11, pp. 1383-1390, 2005.
    • (2005) Nature Biotechnol. , vol.23 , Issue.11 , pp. 1383-1390
    • Washietl, S.1    Hofacker, I.L.2    Lukasser, M.3    Hüttenhofer, A.4    Stadler, P.F.5
  • 49
    • 10944232068 scopus 로고    scopus 로고
    • Prediction of consensus RNA secondary structures including pseudoknots
    • C. Witwer, I.L. Hofacker, and P.F. Stadler, “Prediction of consensus RNA secondary structures including pseudoknots,” IEEE Trans. Comp. Biol. Bioinformatics, vol. 1, no. 2, pp. 66-77, 2004.
    • (2004) IEEE Trans. Comp. Biol. Bioinformatics , vol.1 , Issue.2 , pp. 66-77
    • Witwer, C.1    Hofacker, I.L.2    Stadler, P.F.3
  • 50
    • 21644437291 scopus 로고    scopus 로고
    • HMM with auxiliary memory: A new tool for modeling RNA secondary structures
    • Monterey, CA Nov.
    • B.-J. Yoon and P.P. Vaidyanathan, “HMM with auxiliary memory: A new tool for modeling RNA secondary structures,” in Proc. 38th Asilomar Conf. Signals, Systems, Computers, Monterey, CA, vol. 2, pp. 1651-1655, Nov. 2004.
    • (2004) Proc. 38th Asilomar Conf. Signals, Systems, Computers , vol.2 , pp. 1651-1655
    • Yoon, B.-J.1    Vaidyanathan, P.P.2
  • 51
    • 33947114852 scopus 로고    scopus 로고
    • An overview of the role of context-sensitive HMMs in the prediction of ncRNA genes
    • Bordeaux, France July
    • B.J. Yoon and P.P. Vaidyanthan, “An overview of the role of context-sensitive HMMs in the prediction of ncRNA genes,” in Proc. IEEE Workshop Statistical Signal Processing, Bordeaux, France, pp. 1378-1383, July 2005.
    • (2005) Proc. IEEE Workshop Statistical Signal Processing , pp. 1378-1383
    • Yoon, B.J.1    Vaidyanthan, P.P.2
  • 52
    • 85032756182 scopus 로고    scopus 로고
    • Context-sensitive hidden Markov models for modeling long-range dependencies in symbol sequences
    • submitted for publication
    • B.J. Yoon and P.P. Vaidyanathan, “Context-sensitive hidden Markov models for modeling long-range dependencies in symbol sequences,” submitted for publication.
    • Yoon, B.J.1    Vaidyanathan, P.P.2
  • 53
    • 33947635525 scopus 로고    scopus 로고
    • Profile context-sensitive HMMs for probabilistic modeling of sequences with complex correlations
    • Toulouse, France May
    • B.J. Yoon and P.P. Vaidyanathan, “Profile context-sensitive HMMs for probabilistic modeling of sequences with complex correlations,” in Proc. 31st IEEE Int. Conf. Acoustics, Speech, Signal Processing, Toulouse, France, vol. 3, pp. III-317-III-320, May 2006.
    • (2006) Proc. 31st IEEE Int. Conf. Acoustics, Speech, Signal Processing , vol.3 , pp. III-317-III-320
    • Yoon, B.J.1    Vaidyanathan, P.P.2
  • 54
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • M. Zuker and P. Stiegler, “Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information,” Nucleic Acids Res., vol. 9, no. 1, pp. 133-148, 1981.
    • (1981) Nucleic Acids Res. , vol.9 , Issue.1 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2


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