메뉴 건너뛰기




Volumn 5, Issue 8, 2009, Pages

Evolutionary triplet models of structured RNA

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; CONTEXT FREE GRAMMARS; DECODING; DYNAMIC PROGRAMMING; EVOLUTIONARY ALGORITHMS; FORMAL LANGUAGES; INFERENCE ENGINES; MAXIMUM LIKELIHOOD; STOCHASTIC SYSTEMS; TRANSDUCERS; TREES (MATHEMATICS);

EID: 70049104879     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000483     Document Type: Article
Times cited : (6)

References (104)
  • 1
    • 0014378880 scopus 로고
    • The origin of the genetic code
    • Crick FH (1968) The origin of the genetic code. Journal of Molecular Biology 38: 367-379.
    • (1968) Journal of Molecular Biology , vol.38 , pp. 367-379
    • Crick, F.H.1
  • 3
    • 0038049910 scopus 로고    scopus 로고
    • Group II introns: Structure and catalytic versatility of large natural ribozymes
    • Lehmann K, Schmidt U (2003) Group II introns: structure and catalytic versatility of large natural ribozymes. Critical Reviews in Biochemistry and Molecular Biology 38: 249-303. (Pubitemid 36793893)
    • (2003) Critical Reviews in Biochemistry and Molecular Biology , vol.38 , Issue.3 , pp. 249-303
    • Lehmann, K.1    Schmidt, U.2
  • 4
    • 0037082416 scopus 로고    scopus 로고
    • Analysis of the structure of human telomerase RNA in vivo
    • Antal M, Boros E, Solymosy F, Kiss T (2002) Analysis of the structure of human telomerase RNA in vivo. Nucleic Acids Research 30: 912-920. (Pubitemid 34679659)
    • (2002) Nucleic Acids Research , vol.30 , Issue.4 , pp. 912-920
    • Antal, M.1    Boros, E.2    Solymosy, F.3    Kiss, T.4
  • 6
    • 0024039669 scopus 로고
    • Evolution of the secondary structures and compensatory mutations of the ribosomal RNAs of Drosophila melanogaster
    • Hancock JM, Tautz D, Dover GA (1988) Evolution of the secondary structures and compensatory mutations of the ribosomal RNAs of Drosophila melanogaster. Molecular Biology and Evolution 5: 393-414.
    • (1988) Molecular Biology and Evolution , vol.5 , pp. 393-414
    • Hancock, J.M.1    Tautz, D.2    Dover, G.A.3
  • 7
    • 0036760665 scopus 로고    scopus 로고
    • Motif prediction in ribosomal RNAs: Lessons and prospects for automated motif prediction in homologous RNA molecules
    • DOI 10.1016/S0300-9084(02)01463-3, PII S0300908402014633
    • Leontis NB, Stombaugh J, Westhof E (2002) Motif prediction in ribosomal RNAs: Lessons and prospects for automated motif prediction in homologous RNA molecules. Biochimie 84: 961-973. (Pubitemid 35422922)
    • (2002) Biochimie , vol.84 , Issue.9 , pp. 961-973
    • Leontis, N.B.1    Stombaugh, J.2    Westhof, E.3
  • 8
    • 46349111792 scopus 로고    scopus 로고
    • Ribosomal RNAs are tolerant toward genetic insertions: Evolutionary origin of the expansion segments
    • DOI 10.1093/nar/gkn224
    • Yokoyama T, Suzuki T (2008) Ribosomal RNAs are tolerant toward genetic insertions: evolutionary origin of the expansion segments. Nucleic Acids Research 36: 3539-3551. (Pubitemid 351917519)
    • (2008) Nucleic Acids Research , vol.36 , Issue.11 , pp. 3539-3551
    • Yokoyama, T.1    Suzuki, T.2
  • 9
    • 0025167302 scopus 로고
    • 'compensatory slippage' in the evolution of ribosomal RNA genes
    • Hancock JM, Dover GA (1990) 'compensatory slippage' in the evolution of ribosomal RNA genes. Nucleic Acids Research 18: 5949-5954.
    • (1990) Nucleic Acids Research , vol.18 , pp. 5949-5954
    • Hancock, J.M.1    Dover, G.A.2
  • 10
    • 0028272315 scopus 로고
    • RNA sequence analysis using covariance models
    • Eddy SR, Durbin R (1994) RNA sequence analysis using covariance models. Nucleic Acids Research 22: 2079-2088. (Pubitemid 24192908)
    • (1994) Nucleic Acids Research , vol.22 , Issue.11 , pp. 2079-2088
    • Eddy, S.R.1    Durbin, R.2
  • 12
    • 25444466845 scopus 로고    scopus 로고
    • Noncoding RNA gene detection using comparative sequence analysis
    • Klein R, Eddy SR (2003) Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 4.
    • (2003) BMC Bioinformatics , vol.4
    • Klein, R.1    Eddy, S.R.2
  • 13
    • 34047240607 scopus 로고    scopus 로고
    • Query-dependent banding (QDB) for faster RNA similarity searches
    • DOI 10.1371/journal.pcbi.0030056
    • Nawrocki E, Eddy S (2007) Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Computational Biology 3: e56. (Pubitemid 46535746)
    • (2007) PLoS Computational Biology , vol.3 , Issue.3 , pp. 540-554
    • Nawrocki, E.P.1    Eddy, S.R.2
  • 14
    • 0033524952 scopus 로고    scopus 로고
    • A dynamic programming algorithm for RNA structure prediction including pseudoknots
    • DOI 10.1006/jmbi.1998.2436
    • Rivas E, Eddy SR (1999) A dynamic programming algorithm for RNA structure prediction including pseudoknots. Journal of Molecular Biology 285: 2053-2068. (Pubitemid 29078170)
    • (1999) Journal of Molecular Biology , vol.285 , Issue.5 , pp. 2053-2068
    • Rivas, E.1    Eddy, S.R.2
  • 16
    • 0043123155 scopus 로고    scopus 로고
    • Pfold: RNA secondary structure prediction using stochastic context-free grammars
    • DOI 10.1093/nar/gkg614
    • Knudsen B, Hein J (2003) Pfold: RNA secondary structure prediction using stochastic contextfree grammars. Nucleic Acids Research 31: 3423-3428. (Pubitemid 37442171)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3423-3428
    • Knudsen, B.1    Hein, J.2
  • 17
    • 13244260785 scopus 로고    scopus 로고
    • Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction
    • Dowell RD, Eddy SR (2004) Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics 5.
    • (2004) BMC Bioinformatics , vol.5
    • Dowell, R.D.1    Eddy, S.R.2
  • 18
    • 25444433586 scopus 로고    scopus 로고
    • Accelerated probabilistic inference of RNA structure evolution
    • Holmes I (2005) Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics 6.
    • (2005) BMC Bioinformatics , vol.6
    • Holmes, I.1
  • 19
    • 33749412683 scopus 로고    scopus 로고
    • Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints
    • Dowell RD, Eddy SR (2006) Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics 7.
    • (2006) BMC Bioinformatics , vol.7
    • Dowell, R.D.1    Eddy, S.R.2
  • 20
    • 56649119162 scopus 로고    scopus 로고
    • Specific alignment of structured RNA: Stochastic grammars and sequence annealing
    • DOI 10.1093/bioinformatics/btn495
    • Bradley RK, Pachter L, Holmes I (2008) Specific alignment of structured RNA: Stochastic grammars and sequence annealing. Bioinformatics 24: 2677-2683. (Pubitemid 352722608)
    • (2008) Bioinformatics , vol.24 , Issue.23 , pp. 2677-2683
    • Bradley, R.K.1    Pachter, L.2    Holmes, I.3
  • 21
  • 22
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17: 368-376.
    • (1981) Journal of Molecular Evolution , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 23
    • 0015183542 scopus 로고
    • A general model for the genetic analysis of pedigree data
    • Elston RC, Stewart J (1971) A general model for the genetic analysis of pedigree data. Human Heredity 21: 523-542.
    • (1971) Human Heredity , vol.21 , pp. 523-542
    • Elston, R.C.1    Stewart, J.2
  • 24
    • 0036298990 scopus 로고    scopus 로고
    • An Expectation Maximization algorithm for training hidden substitution models
    • Holmes I, Rubin GM (2002) An Expectation Maximization algorithm for training hidden substitution models. Journal of Molecular Biology 317: 757-768.
    • (2002) Journal of Molecular Biology , vol.317 , pp. 757-768
    • Holmes, I.1    Rubin, G.M.2
  • 25
    • 0034804321 scopus 로고    scopus 로고
    • Mutations as missing data: Inferences on the ages and distributions of nonsynonymous and synonymous mutations
    • Nielsen R (2001) Mutations as missing data: inferences on the ages and distributions of nonsynonymous and synonymous mutations. Genetics 159: 401-411.
    • (2001) Genetics , vol.159 , pp. 401-411
    • Nielsen, R.1
  • 27
    • 0028214103 scopus 로고
    • Estimating the pattern of nucleotide substitution
    • Yang Z (1994) Estimating the pattern of nucleotide substitution. Journal of Molecular Evolution 39: 105-111.
    • (1994) Journal of Molecular Evolution , vol.39 , pp. 105-111
    • Yang, Z.1
  • 28
    • 0035031966 scopus 로고    scopus 로고
    • A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    • Whelan S, Goldman N (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Molecular Biology and Evolution 18: 691-699. (Pubitemid 32372940)
    • (2001) Molecular Biology and Evolution , vol.18 , Issue.5 , pp. 691-699
    • Whelan, S.1    Goldman, N.2
  • 29
    • 13244253776 scopus 로고    scopus 로고
    • A probabilistic model for the evolution of RNA structure
    • Holmes I (2004) A probabilistic model for the evolution of RNA structure. BMC Bioinformatics 5.
    • (2004) BMC Bioinformatics , vol.5
    • Holmes, I.1
  • 30
    • 0034791551 scopus 로고    scopus 로고
    • Evolutionary HMMs: A Bayesian approach to multiple alignment
    • Holmes I, Bruno WJ (2001) Evolutionary HMMs: a Bayesian approach to multiple alignment. Bioinformatics 17: 803-820. (Pubitemid 32970479)
    • (2001) Bioinformatics , vol.17 , Issue.9 , pp. 803-820
    • Holmes, I.1    Bruno, W.J.2
  • 31
    • 0345442505 scopus 로고    scopus 로고
    • Aarhus, Denmark: Dept. of Theoretical Statistics, University of Aarhus, Technical Report No. 429
    • Jensen J, Hein J (2002) Gibbs sampler for statistical multiple alignment. Aarhus, Denmark: Dept. of Theoretical Statistics, University of Aarhus, Technical Report No. 429.
    • (2002) Gibbs Sampler for Statistical Multiple Alignment
    • Jensen, J.1    Hein, J.2
  • 32
    • 22844450838 scopus 로고    scopus 로고
    • Joint bayesian estimation of alignment and phylogeny
    • DOI 10.1080/10635150590947041
    • Redelings BD, Suchard MA (2005) Joint bayesian estimation of alignment and phylogeny. Systematic Biology 54: 401-418. (Pubitemid 41040440)
    • (2005) Systematic Biology , vol.54 , Issue.3 , pp. 401-418
    • Redelings, B.D.1    Suchard, M.A.2
  • 33
  • 34
    • 0003157183 scopus 로고    scopus 로고
    • Noncoding RNA gene detection using comparative sequence analysis
    • DOI 10.1186/1471-2105-2-8
    • Rivas E, Eddy SR (2001) Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2. (Pubitemid 38751156)
    • (2001) BMC Bioinformatics , vol.2 , pp. 8
    • Rivas, E.1    Eddy, S.R.2
  • 35
    • 36549075072 scopus 로고    scopus 로고
    • Transducers: An emerging probabilistic framework for modeling indels on trees
    • Bradley RK, Holmes I (2007) Transducers: an emerging probabilistic framework for modeling indels on trees. Bioinformatics 23: 3258-3262.
    • (2007) Bioinformatics , vol.23 , pp. 3258-3262
    • Bradley, R.K.1    Holmes, I.2
  • 38
    • 52949150097 scopus 로고    scopus 로고
    • Probabilistic phylogenetic inference with insertions and deletions
    • Rivas E, Eddy S (2008) Probabilistic phylogenetic inference with insertions and deletions. PLoS Computational Biology 4: e1000172.
    • (2008) PLoS Computational Biology , vol.4
    • Rivas, E.1    Eddy, S.2
  • 39
    • 0345457233 scopus 로고    scopus 로고
    • Using guide trees to construct multiple-sequence evolutionary HMMs
    • Holmes I (2003) Using guide trees to construct multiple-sequence evolutionary HMMs. Bioinformatics 19 Suppl. 1: i147-157.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Holmes, I.1
  • 40
    • 36549003090 scopus 로고    scopus 로고
    • Phylocomposer and Phylodirector: Analysis and Visualization of Transducer Indel Models
    • Holmes I (2007) Phylocomposer and Phylodirector: Analysis and Visualization of Transducer Indel Models. Bioinformatics 23: 3263-3264.
    • (2007) Bioinformatics , vol.23 , pp. 3263-3264
    • Holmes, I.1
  • 41
    • 34548727998 scopus 로고    scopus 로고
    • HMMoC - A compiler for hidden Markov models
    • DOI 10.1093/bioinformatics/btm350
    • Lunter G (2007) HMMoC-a compiler for hidden Markov models. Bioinformatics 23: 2485-2487. (Pubitemid 47423848)
    • (2007) Bioinformatics , vol.23 , Issue.18 , pp. 2485-2487
    • Lunter, G.1
  • 42
    • 0022146059 scopus 로고
    • Simultaneous solution of the RNA folding, alignment, and protosequence problems
    • Sankoff D (1985) Simultaneous solution of the RNA folding, alignment, and protosequence problems. SIAM Journal of Applied Mathematics 45: 810-825.
    • (1985) SIAM Journal of Applied Mathematics , vol.45 , pp. 810-825
    • Sankoff, D.1
  • 43
    • 13244251724 scopus 로고    scopus 로고
    • Pairwise RNA structure comparison using stochastic context-free grammars
    • 2002
    • Holmes I, Rubin GM (2002) Pairwise RNA structure comparison using stochastic context-free grammars. Pacific Symposium on Biocomputing, 2002.
    • (2002) Pacific Symposium on Biocomputing
    • Holmes, I.1    Rubin, G.M.2
  • 44
  • 45
  • 49
    • 0031864548 scopus 로고    scopus 로고
    • Database on the structure of large ribosomal subunit RNA
    • DOI 10.1093/nar/26.1.183
    • Rijk PD, Caers A, Peer YVd, Wachter RD (1998) Database on the structure of large ribosomal subunit RNA. Nucleic Acids Research 26: 183-186 (Pubitemid 28291529)
    • (1998) Nucleic Acids Research , vol.26 , Issue.1 , pp. 183-186
    • De Rijk, P.1    Caers, A.2    Van De Peer, Y.3    De Wachter, R.4
  • 50
    • 0027265356 scopus 로고
    • Collection of small subunit (16S- And 16S-like) ribosomal RNA structures
    • Gutell RR (1993) Collection of small subunit (16S and 16S-like) ribosomal RNA structures. Nucleic Acids Research 21: 3051-3054. (Pubitemid 23223604)
    • (1993) Nucleic Acids Research , vol.21 , Issue.13 , pp. 3051-3054
    • Gutell, R.R.1
  • 52
    • 33846659941 scopus 로고    scopus 로고
    • Multiple alignment by sequence annealing
    • Schwartz AS, Pachter L (2007) Multiple alignment by sequence annealing. Bioinformatics 23: e24-9.
    • (2007) Bioinformatics , vol.23
    • Schwartz, A.S.1    Pachter, L.2
  • 55
    • 17844386108 scopus 로고    scopus 로고
    • A benchmark of multiple sequence alignment programs upon structural RNAs
    • DOI 10.1093/nar/gki541
    • Gardner PP, Wilm A, Washietl S (2005) A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Research 33: 2433-2439. (Pubitemid 41511262)
    • (2005) Nucleic Acids Research , vol.33 , Issue.8 , pp. 2433-2439
    • Gardner, P.P.1    Wilm, A.2    Washietl, S.3
  • 56
    • 34248374330 scopus 로고    scopus 로고
    • An enhanced RNA alignment benchmark for sequence alignment programs
    • DOI 10.1186/1748-7188-1-19
    • Wilm A, Mainz I, Steger G (2006) An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms for Molecular Biology 1: 19. (Pubitemid 46736701)
    • (2006) Algorithms for Molecular Biology , vol.1 , Issue.1 , pp. 19
    • Wilm, A.1    Mainz, I.2    Steger, G.3
  • 57
    • 0002725360 scopus 로고
    • Chemical paleogenetics, molecular "restoration studies" of extinct forms of life
    • Pauling L, Zuckerkandl E (1963) Chemical paleogenetics, molecular "restoration studies" of extinct forms of life. Acta Chemica Scandinavica 17: S9-S16.
    • (1963) Acta Chemica Scandinavica , vol.17
    • Pauling, L.1    Zuckerkandl, E.2
  • 58
    • 0025270813 scopus 로고
    • Ancestral lysozymes reconstructed, neutrality testes, and thermostability linked to hydrocarbon packing
    • DOI 10.1038/345086a0
    • Malcolm BA, Wilson KP, Matthews BW, Kirsch JF, Wilson AC (1990) Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing. Nature 345: 86-89. (Pubitemid 20152459)
    • (1990) Nature , vol.345 , Issue.6270 , pp. 86-89
    • Malcolm, B.A.1    Wilson, K.P.2    Matthews, B.W.3    Kirsch, J.F.4    Wilson, A.C.5
  • 60
    • 0037117541 scopus 로고    scopus 로고
    • Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates
    • DOI 10.1073/pnas.072626199
    • Zhang J, Rosenberg HF (2002) Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates. Proceedings of the National Academy of Sciences of the United States of America 99: 5486-5491. (Pubitemid 34411575)
    • (2002) Proceedings of the National Academy of Sciences of the United States of America , vol.99 , Issue.8 , pp. 5486-5491
    • Zhang, J.1    Rosenberg, H.F.2
  • 61
    • 0141828152 scopus 로고    scopus 로고
    • Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins
    • Gaucher EA, Thomson JM, Burgan MF, Benner SA (2003) Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425: 285-288.
    • (2003) Nature , vol.425 , pp. 285-288
    • Gaucher, E.A.1    Thomson, J.M.2    Burgan, M.F.3    Benner, S.A.4
  • 64
    • 0036726406 scopus 로고    scopus 로고
    • Identification of essential amino acid changes in paired domain evolution using a novel combination of evolutionary analysis and in vitro and in vivo studies
    • Sun H, Merugu S, Gu X, Kang YY, Dickinson DP, et al. (2002) Identification of essential amino acid changes in paired domain evolution using a novel combination of evolutionary analysis and in vitro and in vivo studies. Molecular Biology and Evolution 19: 1490-1500. (Pubitemid 36752774)
    • (2002) Molecular Biology and Evolution , vol.19 , Issue.9 , pp. 1490-1500
    • Sun, H.1    Merugu, S.2    Gu, X.3    Kang, Y.Y.4    Dickinson, D.P.5    Callaerts, P.6    Li, W.-H.7
  • 65
    • 34548040966 scopus 로고    scopus 로고
    • Crystal structure of an ancient protein: Evolution by conformational epistasis
    • Ortlund EA, Bridgham JT, Redinbo MR, Thornton JW (2007) Crystal structure of an ancient protein: evolution by conformational epistasis. Science 317: 1544-1548
    • (2007) Science , vol.317 , pp. 1544-1548
    • Ortlund, E.A.1    Bridgham, J.T.2    Redinbo, M.R.3    Thornton, J.W.4
  • 66
    • 0030662074 scopus 로고    scopus 로고
    • Molecular reconstruction of sleeping beauty, a Tc1-like transposon from fish, and its transposition in human cells
    • Ivics Z, Hackett PB, Plasterk RH, Izsvak Z (1997) Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells. Cell 91: 501-510 (Pubitemid 27508239)
    • (1997) Cell , vol.91 , Issue.4 , pp. 501-510
    • Ivics, Z.1    Hackett, P.B.2    Plasterk, R.H.3    Izsvak, Z.4
  • 68
    • 10944228197 scopus 로고    scopus 로고
    • Reconstructing large regions of an ancestral mammalian genome in silico
    • DOI 10.1101/gr.2800104
    • Blanchette M, Green ED, Miller W, Haussler D (2004) Reconstructing large regions of an ancestral mammalian genome in silico. Genome Research 14: 2412-2423. (Pubitemid 40012224)
    • (2004) Genome Research , vol.14 , Issue.12 , pp. 2412-2423
    • Blanchette, M.1    Green, E.D.2    Miller, W.3    Haussler, D.4
  • 70
    • 38949105667 scopus 로고    scopus 로고
    • Ancestral sequence reconstruction as a tool to understand natural history and guide synthetic biology: Realizing and extending the vision of Zuckerkandl and Pauling
    • chapter 2
    • Gaucher EA (2007) Ancestral sequence reconstruction as a tool to understand natural history and guide synthetic biology: realizing and extending the vision of Zuckerkandl and Pauling. In: Liberles [83], chapter 2. pp 20-33.
    • (2007) Liberles , vol.83 , pp. 20-33
    • Gaucher, E.A.1
  • 71
    • 34248184703 scopus 로고    scopus 로고
    • Reconstruction of ancestral genomic sequences using likelihood
    • DOI 10.1089/cmb.2006.0101
    • Elias I, Tuller T (2007) Reconstruction of ancestral genomic sequences using likelihood. Journal of Computational Biology 14: 216-237 (Pubitemid 46709355)
    • (2007) Journal of Computational Biology , vol.14 , Issue.2 , pp. 216-237
    • Elias, I.1    Tuller, T.2
  • 72
    • 25644436944 scopus 로고    scopus 로고
    • Translation initiation: Structures, mechanisms and evolution
    • DOI 10.1017/S0033583505004026, PII S0033583505004026
    • Marintchev A, Wagner G (2004) Translation initiation: structures, mechanisms and evolution. Quarterly reviews of biophysics 37: 197-284. (Pubitemid 41379756)
    • (2004) Quarterly Reviews of Biophysics , vol.37 , Issue.3-4 , pp. 197-284
    • Marintchev, A.1    Wagner, G.2
  • 73
    • 24644439590 scopus 로고    scopus 로고
    • Thermosynthesis as energy source for the RNA world: A model for the bioenergetics of the origin of life
    • Muller AWJ (2005) Thermosynthesis as energy source for the RNA world: a model for the bioenergetics of the origin of life. Bio Systems 82: 93-102.
    • (2005) Bio Systems , vol.82 , pp. 93-102
    • Muller, A.W.J.1
  • 74
    • 33846349924 scopus 로고    scopus 로고
    • Rooting the tree of life by transition analyses
    • Cavalier-Smith T (2006) Rooting the tree of life by transition analyses. Biology Direct 1: 19.
    • (2006) Biology Direct , vol.1 , pp. 19
    • Cavalier-Smith, T.1
  • 75
    • 33644783626 scopus 로고    scopus 로고
    • Introns and the origin of nucleus-cytosol compartmentalization
    • Martin W, Koonin EV (2006) Introns and the origin of nucleus-cytosol compartmentalization. Nature 440: 41-45.
    • (2006) Nature , vol.440 , pp. 41-45
    • Martin, W.1    Koonin, E.V.2
  • 76
    • 33644859575 scopus 로고    scopus 로고
    • Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain
    • Forterre P (2006) Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain. Proceedings of the National Academy of Sciences of the USA 103: 3669-3674.
    • (2006) Proceedings of the National Academy of Sciences of the USA , vol.103 , pp. 3669-3674
    • Forterre, P.1
  • 77
    • 36448988935 scopus 로고    scopus 로고
    • A model for the origin of protein synthesis as coreplicational scanning of nascent RNA. Origins of life and evolution of the biosphere
    • Yakhnin AV (2007) A model for the origin of protein synthesis as coreplicational scanning of nascent RNA. Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life 37: 523-536.
    • (2007) The Journal of the International Society for the Study of the Origin of Life , vol.37 , pp. 523-536
    • Yakhnin, A.V.1
  • 78
    • 33947725697 scopus 로고    scopus 로고
    • The extant core bacterial proteome is an archive of the origin of life
    • DOI 10.1002/pmic.200600442
    • Danchin A, Fang G, Noria S (2007) The extant core bacterial proteome is an archive of the origin of life. Proteomics 7: 875-889. (Pubitemid 46506735)
    • (2007) Proteomics , vol.7 , Issue.6 , pp. 875-889
    • Danchin, A.1    Fang, G.2    Noria, S.3
  • 79
    • 0027751663 scopus 로고
    • The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    • DOI 10.1016/0092-8674(93)90529-Y
    • Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854. (Pubitemid 24014542)
    • (1993) Cell , vol.75 , Issue.5 , pp. 843-854
    • Lee, R.C.1    Feinbaum, R.L.2    Ambros, V.3
  • 80
    • 0033582628 scopus 로고    scopus 로고
    • A computational screen for methylation guide snoRNAs in yeast
    • Lowe TM, Eddy SR (1999) A computational screen for methylation guide snoRNAs in yeast. Science 283: 1168-1171. (Pubitemid 129504120)
    • (1999) Science , vol.283 , Issue.5405 , pp. 1168-1171
    • Lowe, T.M.1    Eddy, S.R.2
  • 81
    • 0035656688 scopus 로고    scopus 로고
    • Non-coding RNA genes and the modern RNA world
    • DOI 10.1038/35103511
    • Eddy SR (2001) Non-coding RNA genes and the modern RNA world. Nature Reviews Genetics 2: 919-929. (Pubitemid 33691089)
    • (2001) Nature Reviews Genetics , vol.2 , Issue.12 , pp. 919-929
    • Eddy, S.R.1
  • 82
    • 0038210214 scopus 로고    scopus 로고
    • Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria
    • DOI 10.1016/S0092-8674(03)00391-X
    • Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR (2003) Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113: 577-586. (Pubitemid 36694183)
    • (2003) Cell , vol.113 , Issue.5 , pp. 577-586
    • Mandal, M.1    Boese, B.2    Barrick, J.E.3    Winkler, W.C.4    Breaker, R.R.5
  • 83
    • 84870718483 scopus 로고    scopus 로고
    • Liberles DA, ed Oxford University Press
    • Liberles DA, ed (2007) Ancestral Sequence Reconstruction. Oxford University Press.
    • (2007) Ancestral Sequence Reconstruction
  • 85
    • 0020286044 scopus 로고
    • Branch and bound algorithms to determine minimal evolutionary trees
    • Hendy MD, Penny D (1982) Branch and bound algorithms to determine minimal evolutionary trees. Mathematical Biosciences 59: 277-290.
    • (1982) Mathematical Biosciences , vol.59 , pp. 277-290
    • Hendy, M.D.1    Penny, D.2
  • 86
    • 0034623015 scopus 로고    scopus 로고
    • Statistical alignment: Computational properties, homology testing and goodness-of-fit
    • DOI 10.1006/jmbi.2000.4061
    • Hein J, Wiuf C, Knudsen B, Moller MB, Wibling G (2000) Statistical alignment: computational properties, homology testing and goodness-of-fit. Journal of Molecular Biology 302: 265-279. (Pubitemid 30694435)
    • (2000) Journal of Molecular Biology , vol.302 , Issue.1 , pp. 265-279
    • Hein, J.1    Wiuf, C.2    Knudsen, B.3    Moller, M.B.4    Wibling, G.5
  • 87
    • 0035228391 scopus 로고    scopus 로고
    • An algorithm for statistical alignment of sequences related by a binary tree
    • Altman RB, Dunker AK, Hunter L, Lauderdale K, Klein TE, eds. Singapore: World Scientific
    • Hein J (2001) An algorithm for statistical alignment of sequences related by a binary tree. In: Altman RB, Dunker AK, Hunter L, Lauderdale K, Klein TE, eds. Pacific Symposium on Biocomputing. Singapore: World Scientific. pp 179-190.
    • (2001) Pacific Symposium on Biocomputing , pp. 179-190
    • Hein, J.1
  • 88
    • 0035427291 scopus 로고    scopus 로고
    • Applying the Thorne-Kishino-Felsenstein model to sequence evolution on a star-shaped tree
    • DOI 10.1016/S0893-9659(01)80026-4, PII S0893965901800264
    • Steel M, Hein J (2001) Applying the Thorne-Kishino-Felsenstein model to sequence evolution on a star-shaped tree. Applied Mathematics Letters 14: 679-684. (Pubitemid 33675393)
    • (2001) Applied Mathematics Letters , vol.14 , Issue.6 , pp. 679-684
    • Steel, M.1    Hein, J.2
  • 89
    • 0141869092 scopus 로고    scopus 로고
    • Sequence alignments and pair hidden Markov models using evolutionary history
    • DOI 10.1016/j.jmb.2003.08.015
    • Knudsen B, Miyamoto M (2003) Sequence alignments and pair hidden Markov models using evolutionary history. Journal of Molecular Biology 333: 453-460. (Pubitemid 37188584)
    • (2003) Journal of Molecular Biology , vol.333 , Issue.2 , pp. 453-460
    • Knudsen, B.1    Miyamoto, M.M.2
  • 90
    • 0141492991 scopus 로고    scopus 로고
    • An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees
    • DOI 10.1089/106652703322756122
    • Lunter GA, Miklós I, Song YS, Hein J (2003) An efficient algorithm for statistical multiple alignment on arbitrary phylogenetic trees. Journal of Computational Biology 10: 869-889. (Pubitemid 38156403)
    • (2003) Journal of Computational Biology , vol.10 , Issue.6 , pp. 869-889
    • Lunter, G.A.1    Miklos, I.2    Song, Y.S.3    Hein, J.4
  • 92
    • 43349091196 scopus 로고    scopus 로고
    • Combining statistical alignment and phylogenetic footprinting to detect regulatory elements
    • DOI 10.1093/bioinformatics/btn104
    • Satija R, Pachter L, Hein J (2008) Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. Bioinformatics 24: 1236-1242. (Pubitemid 351659619)
    • (2008) Bioinformatics , vol.24 , Issue.10 , pp. 1236-1242
    • Satija, R.1    Pachter, L.2    Hein, J.3
  • 93
    • 33847257936 scopus 로고    scopus 로고
    • Indelign: A probabilistic framework for annotation of insertions and deletions in a multiple alignment
    • DOI 10.1093/bioinformatics/btl578
    • Kim J, Sinha S (2007) Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment. Bioinformatics 23: 289-297. (Pubitemid 46323150)
    • (2007) Bioinformatics , vol.23 , Issue.3 , pp. 289-297
    • Kim, J.1    Sinha, S.2
  • 94
    • 34250354438 scopus 로고    scopus 로고
    • Exact and heuristic algorithms for the indel maximum likelihood problem
    • DOI 10/1089/cmb.2007.A006
    • Diallo AB, Makarenkov V, Blanchette M (2007) Exact and heuristic algorithms for the indel maximum likelihood problem. Journal of Computational Biology 14: 446-461. (Pubitemid 46911218)
    • (2007) Journal of Computational Biology , vol.14 , Issue.4 , pp. 446-461
    • Diallo, A.B.1    Makarenkov, V.2    Blanchette, M.3
  • 96
  • 97
  • 100
    • 4944232234 scopus 로고    scopus 로고
    • Pair hidden Markov models on tree structures
    • Sakakibara Y (2003) Pair hidden Markov models on tree structures. Bioinformatics 19 Suppl 1: i232-240.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Sakakibara, Y.1
  • 101
    • 34548443728 scopus 로고    scopus 로고
    • SimulFold: Simultaneously inferring rna structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework
    • Meyer IM, Miklós I (2007) SimulFold: simultaneously inferring rna structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework. PLoS Computational Biology 3: e149.
    • (2007) PLoS Computational Biology , vol.3
    • Meyer, I.M.1    Miklós, I.2
  • 102
    • 0036203448 scopus 로고    scopus 로고
    • Multiple sequence alignment using partial order graphs
    • Lee C, Grasso C, Sharlow M (2002) Multiple sequence alignment using partial order graphs. Bioinformatics 18: 452-464. (Pubitemid 34284947)
    • (2002) Bioinformatics , vol.18 , Issue.3 , pp. 452-464
    • Lee, C.1    Grasso, C.2    Sharlow, M.F.3
  • 103
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • DOI 10.1093/nar/27.13.2682
    • Thompson JD, Plewniak F, Poch O (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Research 27: 2682-2690. (Pubitemid 29306566)
    • (1999) Nucleic Acids Research , vol.27 , Issue.13 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.