Algebraic and Combinatorial Properties of Common RNA Pseudoknot Classes with Applications

Nebel M, Weinberg F (2012)
Journal of Computational Biology 19(10): 1134--1150.

Zeitschriftenaufsatz | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
DOI
Autor*in
Nebel, MarkusUniBi; Weinberg, Frank
Einrichtung
Technische Fakultät
Erscheinungsjahr
2012
Zeitschriftentitel
Journal of Computational Biology
Band
19
Ausgabe
10
Seite(n)
1134--1150
ISSN
1066-5277
Page URI
https://pub.uni-bielefeld.de/record/2910012

Zitieren

Nebel M, Weinberg F. Algebraic and Combinatorial Properties of Common RNA Pseudoknot Classes with Applications. Journal of Computational Biology. 2012;19(10):1134--1150.
Nebel, M., & Weinberg, F. (2012). Algebraic and Combinatorial Properties of Common RNA Pseudoknot Classes with Applications. Journal of Computational Biology, 19(10), 1134--1150. doi:10.1089/cmb.2011.0094
Nebel, Markus, and Weinberg, Frank. 2012. “Algebraic and Combinatorial Properties of Common RNA Pseudoknot Classes with Applications”. Journal of Computational Biology 19 (10): 1134--1150.
Nebel, M., and Weinberg, F. (2012). Algebraic and Combinatorial Properties of Common RNA Pseudoknot Classes with Applications. Journal of Computational Biology 19, 1134--1150.
Nebel, M., & Weinberg, F., 2012. Algebraic and Combinatorial Properties of Common RNA Pseudoknot Classes with Applications. Journal of Computational Biology, 19(10), p 1134--1150.
M. Nebel and F. Weinberg, “Algebraic and Combinatorial Properties of Common RNA Pseudoknot Classes with Applications”, Journal of Computational Biology, vol. 19, 2012, pp. 1134--1150.
Nebel, M., Weinberg, F.: Algebraic and Combinatorial Properties of Common RNA Pseudoknot Classes with Applications. Journal of Computational Biology. 19, 1134--1150 (2012).
Nebel, Markus, and Weinberg, Frank. “Algebraic and Combinatorial Properties of Common RNA Pseudoknot Classes with Applications”. Journal of Computational Biology 19.10 (2012): 1134--1150.

6 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

RCPred: RNA complex prediction as a constrained maximum weight clique problem.
Legendre A, Angel E, Tahi F., BMC Bioinformatics 20(suppl 3), 2019
PMID: 30925864
An algebraic language for RNA pseudoknots comparison.
Quadrini M, Tesei L, Merelli E., BMC Bioinformatics 20(suppl 4), 2019
PMID: 30999864
Statistics of topological RNA structures.
Li TJX, Reidys CM., J Math Biol 74(7), 2017
PMID: 27853818
Pseudoknots in RNA folding landscapes.
Kucharík M, Hofacker IL, Stadler PF, Qin J., Bioinformatics 32(2), 2016
PMID: 26428288
Combinatorics of γ-structures.
Han HS, Li TJ, Reidys CM., J Comput Biol 21(8), 2014
PMID: 24689708
Generation of RNA pseudoknot structures with topological genus filtration.
Huang FW, Nebel ME, Reidys CM., Math Biosci 245(2), 2013
PMID: 23900061

31 References

Daten bereitgestellt von Europe PubMed Central.

Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
Akutsu T.., 2000
The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs: Correction.
Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Muller KM, Pande N, Shang Z, Yu N, Gutell RR., BMC Bioinformatics 3(), 2002
PMID: PMC116672
Predicting structures and stabilities for H-type pseudoknots with interhelix loops.
Cao S, Chen SJ., RNA 15(4), 2009
PMID: 19237463
An O(n) algorithm for MFE prediction of kissing hairpins and 4-chains in nucleic acids
Jabbari H.., 2009
RNA folding: conformational statistics, folding kinetics, and ion electrostatics.
Chen SJ., Annu Rev Biophys 37(), 2008
PMID: 18573079
Classifying RNA pseudoknotted structures
Rastegari B.., 2004
A partition function algorithm for nucleic acid secondary structure including pseudoknots.
Dirks RM, Pierce NA., J Comput Chem 24(13), 2003
PMID: 12926009
The chemical repertoire of natural ribozymes.
Doudna JA, Cech TR., Nature 418(6894), 2002
PMID: 12110898
Singularity analysis of generating functions
Odlyzko A.., 1990
Frameshifting RNA pseudoknots: structure and mechanism.
Giedroc DP, Cornish PV., Virus Res. 139(2), 2008
PMID: 18621088

Harrison M.A.., 1978

Hille E.., 1962
RNA pseudoknotted structure prediction using stochastic multiple context-free grammar
Kasami T.., 2006

Salomaa A.., 1986
Pseudoknots in RNA secondary structures
Pedersen C.N.., 2000
RNA pseudoknot prediction in energy-based models
Pedersen C.N.., 2000
Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.
Matsui H, Sato K, Sakakibara Y., Bioinformatics 21(11), 2005
PMID: 15784748
Predicting RNA secondary structures with pseudoknots by MCMC sampling.
Metzler D, Nebel ME., J Math Biol 56(1-2), 2007
PMID: 17589847
A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting.
Namy O, Moran SJ, Stuart DI, Gilbert RJ, Brierley I., Nature 441(7090), 2006
PMID: 16688178
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics.
Reeder J, Giegerich R., BMC Bioinformatics 5(), 2004
PMID: 15294028
Topology and prediction of RNA pseudoknots.
Reidys CM, Huang FW, Andersen JE, Penner RC, Stadler PF, Nebel ME., Bioinformatics 27(8), 2011
PMID: 21335320
A dynamic programming algorithm for RNA structure prediction including pseudoknots.
Rivas E, Eddy SR., J. Mol. Biol. 285(5), 1999
PMID: 9925784
Pseudoknots in RNA secondary structures: Representation, enumeration, and prevalence
Rødland E.A.., 2006
Counting RNA pseudoknotted structures.
Saule C, Regnier M, Steyaert JM, Denise A., J. Comput. Biol. 18(10), 2011
PMID: 21548808
On multiple context free grammars
Fujii M.., 1991
Pseudoknots: RNA structures with diverse functions.
Staple DW, Butcher SE., PLoS Biol. 3(6), 2005
PMID: 15941360
PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots.
Taufer M, Licon A, Araiza R, Mireles D, van Batenburg FH, Gultyaev AP, Leung MY., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18988624
Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function.
Theimer CA, Blois CA, Feigon J., Mol. Cell 17(5), 2005
PMID: 15749017
Tree adjoining grammars for RNA structure prediction
Kobayashi S.., 1999
An earley-style parser for solving the rna-rna interaction problem [Bachelor thesis]
Wild S.., 2010
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information.
Zuker M, Stiegler P., Nucleic Acids Res. 9(1), 1981
PMID: 6163133
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 23057823
PubMed | Europe PMC

Suchen in

Google Scholar