메뉴 건너뛰기




Volumn 106, Issue 52, 2009, Pages 22061-22066

Random k-noncrossing RNA structures

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO CALCULATION; ALGORITHM; ARTICLE; ENERGY; PRIORITY JOURNAL; PROBABILITY; RNA STRUCTURE; SAMPLING; STATISTICS;

EID: 76049085900     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0907269106     Document Type: Article
Times cited : (22)

References (38)
  • 2
    • 0029949699 scopus 로고    scopus 로고
    • Domain structure of the ribozyme from eubacterial ribonuclease P
    • Loria A, Pan T (1996) Domain structure of the ribozyme from eubacterial ribonuclease P. RNA 2:551-563.
    • (1996) RNA , vol.2 , pp. 551-563
    • Loria, A.1    Pan, T.2
  • 3
    • 22744455135 scopus 로고    scopus 로고
    • Pseudoknots: RNA structures with diverse functions
    • Staple DW, Butcher SE (2005) Pseudoknots: RNA structures with diverse functions. PLoS Biol 3:956-959.
    • (2005) PLoS Biol , vol.3 , pp. 956-959
    • Staple, D.W.1    Butcher, S.E.2
  • 4
    • 0029348884 scopus 로고
    • A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs
    • Konings DAM, Gutell RR (1995) A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs. RNA 1:559-574.
    • (1995) RNA , vol.1 , pp. 559-574
    • Konings, D.A.M.1    Gutell, R.R.2
  • 5
    • 0026651981 scopus 로고
    • RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase
    • Tuerk C, MacDougal S, Gold L (1992) RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc Natl Acad Sci USA 89:6988-6992.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 6988-6992
    • Tuerk, C.1    MacDougal, S.2    Gold, L.3
  • 6
    • 0026598965 scopus 로고
    • An RNA pseudoknot and an optimal heptameric shift site are required for highly efficient ribosomal frameshifting on a retroviral messenger RNA
    • Chamorro M, Parkin N, Varmus HE (1991) An RNA pseudoknot and an optimal heptameric shift site are required for highly efficient ribosomal frameshifting on a retroviral messenger RNA J. Proc Natl Acad Sci USA 89:713-717.
    • (1991) J. Proc Natl Acad Sci USA , vol.89 , pp. 713-717
    • Chamorro, M.1    Parkin, N.2    Varmus, H.E.3
  • 7
    • 0033524952 scopus 로고    scopus 로고
    • A dynamic programming algorithm for RNA structure prediction including pseudoknots
    • Rivas E, Eddy SR (1999) A dynamic programming algorithm for RNA structure prediction including pseudoknots. J Mol Biol 285:2053-2068.
    • (1999) J Mol Biol , vol.285 , pp. 2053-2068
    • Rivas, E.1    Eddy, S.R.2
  • 8
    • 0033709625 scopus 로고    scopus 로고
    • RNA pseudoknot prediction in energy-based models
    • Lyngso RB, Pedersen CNS (2000) RNA pseudoknot prediction in energy-based models. J Comput Biol 7:409-427.
    • (2000) J Comput Biol , vol.7 , pp. 409-427
    • Lyngso, R.B.1    Pedersen, C.N.S.2
  • 9
    • 0001947129 scopus 로고
    • Combinatorics of RNA hairpins and cloverleafs
    • Waterman MS (1979) Combinatorics of RNA hairpins and cloverleafs. Stud Appl Math 60:91-96.
    • (1979) Stud Appl Math , vol.60 , pp. 91-96
    • Waterman, M.S.1
  • 11
    • 0038284450 scopus 로고
    • Proportions of irreducible diagrams
    • Kleitman D (1970) Proportions of irreducible diagrams. Stud Appl Math 49:297-299.
    • (1970) Stud Appl Math , vol.49 , pp. 297-299
    • Kleitman, D.1
  • 12
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31:3429-3431.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 13
    • 6344263491 scopus 로고    scopus 로고
    • Boltzmann samplers for the random generation of combinatorial structures
    • Duchon P, Flajolet P, Louchard G, Schaeffer G (2004) Boltzmann samplers for the random generation of combinatorial structures. Combin Probab Comput 13:577-625.
    • (2004) Combin Probab Comput , vol.13 , pp. 577-625
    • Duchon, P.1    Flajolet, P.2    Louchard, G.3    Schaeffer, G.4
  • 14
    • 38049010529 scopus 로고    scopus 로고
    • Combinatorics of RNA structures with pseudoknots
    • Jin EY, Qin J, Reidys CM (2008) Combinatorics of RNA structures with pseudoknots. Bull Math Biol 70:45-67.
    • (2008) Bull Math Biol , vol.70 , pp. 45-67
    • Jin, E.Y.1    Qin, J.2    Reidys, C.M.3
  • 15
    • 58549116688 scopus 로고    scopus 로고
    • Combinatorial design of pseudoknot RNA
    • Jin EY, Reidys CM (2008) Combinatorial design of pseudoknot RNA. Adv Appl Math 42:135-151.
    • (2008) Adv Appl Math , vol.42 , pp. 135-151
    • Jin, E.Y.1    Reidys, C.M.2
  • 16
    • 0033032887 scopus 로고    scopus 로고
    • RNA structures with pseudo-knots: Graph-theoretical, combinatorial, and statistical properties
    • Haslinger C, Stadler PF (1999) RNA structures with pseudo-knots: Graph-theoretical, combinatorial, and statistical properties. Bull Math Bio 61:437-467.
    • (1999) Bull Math Bio , vol.61 , pp. 437-467
    • Haslinger, C.1    Stadler, P.F.2
  • 17
    • 38049046550 scopus 로고    scopus 로고
    • Central and local limit theorems for RNA structures
    • Jin EY, Reidys CM (2007) Central and local limit theorems for RNA structures. J Theor Biol 250:547-559.
    • (2007) J Theor Biol , vol.250 , pp. 547-559
    • Jin, E.Y.1    Reidys, C.M.2
  • 19
    • 38249043088 scopus 로고
    • Random generation of combinatorial structures from a uniform distribution
    • Jerrum MR, Valiant LG, Vazirant VV (1986) Random generation of combinatorial structures from a uniform distribution. Theor Comput Sci 43:169-188.
    • (1986) Theor Comput Sci , vol.43 , pp. 169-188
    • Jerrum, M.R.1    Valiant, L.G.2    Vazirant, V.V.3
  • 20
    • 0025703080 scopus 로고
    • Fast uniform generation of regular graphs
    • Jerrum M, Sinclair A (1990) Fast uniform generation of regular graphs. Theor Comput Sci 73:91-100.
    • (1990) Theor Comput Sci , vol.73 , pp. 91-100
    • Jerrum, M.1    Sinclair, A.2
  • 21
    • 0000569649 scopus 로고
    • Random walks on finite groups and rapidly mixing Markov chains
    • Séminaire de Probabilités XVII, Springer, Berlin
    • Aldous D (1982) Random walks on finite groups and rapidly mixing Markov chains. Séminaire de Probabilités XVII. Lecture Notes in Mathematics (Springer, Berlin) Vol. 986, pp 243-297.
    • (1982) Lecture Notes in Mathematics , vol.986 , pp. 243-297
    • Aldous, D.1
  • 22
    • 0041026073 scopus 로고
    • A unified setting for sequencing, ranking, and selection algorithms for combinatorial objects
    • Wilf HS (1977) A unified setting for sequencing, ranking, and selection algorithms for combinatorial objects, Adv Math 24:281-291.
    • (1977) Adv Math , vol.24 , pp. 281-291
    • Wilf, H.S.1
  • 24
    • 0000410641 scopus 로고
    • Differentiably finite power series
    • Stanley RP (1980) Differentiably finite power series. Eur J Combin 1:175-188.
    • (1980) Eur J Combin , vol.1 , pp. 175-188
    • Stanley, R.P.1
  • 27
    • 42549100782 scopus 로고    scopus 로고
    • Lost (and found) in translation: André's actual method and its application to the generalized Ballot problem
    • Renault M (2008) Lost (and found) in translation: André's actual method and its application to the generalized Ballot problem. Am Math Monthly 115: 358-363.
    • (2008) Am Math Monthly , vol.115 , pp. 358-363
    • Renault, M.1
  • 29
    • 33845907500 scopus 로고
    • On the vector representation of induced matroids
    • Lindström B (1973) On the vector representation of induced matroids. Bull London Math Soc 5:85-90.
    • (1973) Bull London Math Soc , vol.5 , pp. 85-90
    • Lindström, B.1
  • 30
    • 0000557786 scopus 로고
    • Random walks inWeyl chambers and the decomposition of Tensor Powers
    • Grabiner DJ, Magyar P (1993) Random walks inWeyl chambers and the decomposition of Tensor Powers. J Algebr Combin 2:239-260.
    • (1993) J Algebr Combin , vol.2 , pp. 239-260
    • Grabiner, D.J.1    Magyar, P.2
  • 31
    • 0001601404 scopus 로고
    • A holonomic systems approach to special functions identities
    • Zeilberger D (1990) A holonomic systems approach to special functions identities. J Comput Appl Math 32:321-368.
    • (1990) J Comput Appl Math , vol.32 , pp. 321-368
    • Zeilberger, D.1
  • 32
    • 0028443687 scopus 로고
    • GFUN: A Maple package for the manipulation of generating and holonomic functions in one variable
    • Salvy B, Zimmerman P (1994) GFUN: A Maple package for the manipulation of generating and holonomic functions in one variable. ACM Trans Math Software 20:163-177.
    • (1994) ACM Trans Math Software , vol.20 , pp. 163-177
    • Salvy, B.1    Zimmerman, P.2
  • 33
    • 0004093999 scopus 로고
    • Determinants, paths, and plane partitions
    • preprint
    • Gessel IM, Viennot XG (1989) Determinants, paths, and plane partitions, preprint.
    • (1989)
    • Gessel, I.M.1    Viennot, X.G.2
  • 34
    • 0039480031 scopus 로고
    • Standard Young tableaux of height 4 and 5
    • Gouyou-Beauschamps D (1989) Standard Young tableaux of height 4 and 5. Eur J Combin 10:69-82.
    • (1989) Eur J Combin , vol.10 , pp. 69-82
    • Gouyou-Beauschamps, D.1
  • 35
    • 10944232068 scopus 로고    scopus 로고
    • Witwer C, Hofacker IL, Stadler PF (2004) Prediction of consensus RNA secondary structures including pseudoknots. IEEE/ACM Trans Comput Biol Bioinform 1:66-77.
    • Witwer C, Hofacker IL, Stadler PF (2004) Prediction of consensus RNA secondary structures including pseudoknots. IEEE/ACM Trans Comput Biol Bioinform 1:66-77.
  • 36
    • 0032796501 scopus 로고    scopus 로고
    • RNA secondary structure prediction using stochastic context-free grammars and evolutionary history
    • Knudsen B, Hein J (1999) RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics 15:446-454.
    • (1999) Bioinformatics , vol.15 , pp. 446-454
    • Knudsen, B.1    Hein, J.2
  • 37
    • 36448984918 scopus 로고    scopus 로고
    • Predicting RNA secondary structures with pseudoknots by MCMC sampling
    • Metzler D, Nebel ME (2008) Predicting RNA secondary structures with pseudoknots by MCMC sampling. J Math Biol 56:161-181.
    • (2008) J Math Biol , vol.56 , pp. 161-181
    • Metzler, D.1    Nebel, M.E.2
  • 38
    • 71749113510 scopus 로고    scopus 로고
    • Maximum likelihood analysis of algorithms and data structures
    • doi: 10.1016/j.tcs.2009.09.025
    • Laube U, Nebel ME (2009) Maximum likelihood analysis of algorithms and data structures. Theor Comp Sci, doi: 10.1016/j.tcs.2009.09.025.
    • (2009) Theor Comp Sci
    • Laube, U.1    Nebel, M.E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.