Topology and prediction of RNA pseudoknots

M. Reidys C, W. D. Huang F, E. Andersen J, C. Penner R, F. Stadler P, Nebel M (2011)
Bioinformatics 27(8): 1076--1085.

Zeitschriftenaufsatz | Englisch
 
Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Autor*in
M. Reidys, Christian; W. D. Huang, Fenix; E. Andersen, Jorgen; C. Penner, Robert; F. Stadler, Peter; Nebel, MarkusUniBi
Erscheinungsjahr
2011
Zeitschriftentitel
Bioinformatics
Band
27
Ausgabe
8
Seite(n)
1076--1085
ISSN
1367-4803
Page URI
https://pub.uni-bielefeld.de/record/2910018

Zitieren

M. Reidys C, W. D. Huang F, E. Andersen J, C. Penner R, F. Stadler P, Nebel M. Topology and prediction of RNA pseudoknots. Bioinformatics. 2011;27(8):1076--1085.
M. Reidys, C., W. D. Huang, F., E. Andersen, J., C. Penner, R., F. Stadler, P., & Nebel, M. (2011). Topology and prediction of RNA pseudoknots. Bioinformatics, 27(8), 1076--1085. doi:10.1093/bioinformatics/btr090
M. Reidys, C., W. D. Huang, F., E. Andersen, J., C. Penner, R., F. Stadler, P., and Nebel, M. (2011). Topology and prediction of RNA pseudoknots. Bioinformatics 27, 1076--1085.
M. Reidys, C., et al., 2011. Topology and prediction of RNA pseudoknots. Bioinformatics, 27(8), p 1076--1085.
C. M. Reidys, et al., “Topology and prediction of RNA pseudoknots”, Bioinformatics, vol. 27, 2011, pp. 1076--1085.
M. Reidys, C., W. D. Huang, F., E. Andersen, J., C. Penner, R., F. Stadler, P., Nebel, M.: Topology and prediction of RNA pseudoknots. Bioinformatics. 27, 1076--1085 (2011).
M. Reidys, Christian, W. D. Huang, Fenix, E. Andersen, Jorgen, C. Penner, Robert, F. Stadler, Peter, and Nebel, Markus. “Topology and prediction of RNA pseudoknots”. Bioinformatics 27.8 (2011): 1076--1085.

26 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Statistics of topological RNA structures.
Li TJX, Reidys CM., J Math Biol 74(7), 2017
PMID: 27853818
The Ecological Role of Volatile and Soluble Secondary Metabolites Produced by Soil Bacteria.
Tyc O, Song C, Dickschat JS, Vos M, Garbeva P., Trends Microbiol 25(4), 2017
PMID: 28038926
Pseudoknots in RNA folding landscapes.
Kucharík M, Hofacker IL, Stadler PF, Qin J., Bioinformatics 32(2), 2016
PMID: 26428288
URS DataBase: universe of RNA structures and their motifs.
Baulin E, Yacovlev V, Khachko D, Spirin S, Roytberg M., Database (Oxford) 2016(), 2016
PMID: 27242032
Topological language for RNA.
Huang FW, Reidys CM., Math Biosci 282(), 2016
PMID: 27773681
On RNA-RNA interaction structures of fixed topological genus.
Fu BM, Han HS, Reidys CM., Math Biosci 262(), 2015
PMID: 25640867
Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores.
Song Y, Hua L, Shapiro BA, Wang JT., BMC Bioinformatics 16(), 2015
PMID: 25727492
Product Grammars for Alignment and Folding.
Höner Zu Siederdissen C, Hofacker IL, Stadler PF., IEEE/ACM Trans Comput Biol Bioinform 12(3), 2015
PMID: 26357262
Algebraic Dynamic Programming over general data structures.
zu Siederdissen CH, Prohaska SJ, Stadler PF., BMC Bioinformatics 16 Suppl 19(), 2015
PMID: 26695390
Combinatorics of γ-structures.
Han HS, Li TJ, Reidys CM., J Comput Biol 21(8), 2014
PMID: 24689708
Shapes of interacting RNA complexes.
Fu BM, Reidys CM., J Comput Biol 21(9), 2014
PMID: 25075750
Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures.
Qin J, Fricke M, Marz M, Stadler PF, Backofen R., Algorithms Mol Biol 9(), 2014
PMID: 25285153
Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture.
Penner RC, Andersen ES, Jensen JL, Kantcheva AK, Bublitz M, Nissen P, Rasmussen AM, Svane KL, Hammer B, Rezazadegan R, Nielsen NC, Nielsen JT, Andersen JE., Nat Commun 5(), 2014
PMID: 25517704
Topological classification and enumeration of RNA structures by genus.
Andersen JE, Penner RC, Reidys CM, Waterman MS., J Math Biol 67(5), 2013
PMID: 23053535
McGenus: a Monte Carlo algorithm to predict RNA secondary structures with pseudoknots.
Bon M, Micheletti C, Orland H., Nucleic Acids Res 41(3), 2013
PMID: 23248008
Enumeration of RNA complexes via random matrix theory.
Andersen JE, Chekhov LO, Penner RC, Reidys CM, Sułkowski P., Biochem Soc Trans 41(2), 2013
PMID: 23514171
On topological RNA interaction structures.
Qin J, Reidys CM., J Comput Biol 20(7), 2013
PMID: 23829651
Generation of RNA pseudoknot structures with topological genus filtration.
Huang FW, Nebel ME, Reidys CM., Math Biosci 245(2), 2013
PMID: 23900061
Addendum: topology and prediction of RNA pseudoknots.
Reidys CM, Huang FW, Andersen JE, Penner RC, Stadler PF, Nebel ME., Bioinformatics 28(2), 2012
PMID: 22106334
On the page number of RNA secondary structures with pseudoknots.
Clote P, Dobrev S, Dotu I, Kranakis E, Krizanc D, Urrutia J., J Math Biol 65(6-7), 2012
PMID: 22159642
Topology of RNA-RNA interaction structures.
Andersen JE, Huang FW, Penner RC, Reidys CM., J Comput Biol 19(7), 2012
PMID: 22731621
On the combinatorics of sparsification.
Huang FW, Reidys CM., Algorithms Mol Biol 7(1), 2012
PMID: 23088372

58 References

Daten bereitgestellt von Europe PubMed Central.

Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
Akutsu, Discr. Appl. Math. 104(), 2000
Enumeration of linear chord diagrams
Andersen, J. Alg. Comb. (), 2010
Topology links RNA secondary structure with global conformation, dynamics, and adaptation.
Bailor MH, Sun X, Al-Hashimi HM., Science 327(5962), 2010
PMID: 20056889
Topological classification of RNA structures.
Bon M, Vernizzi G, Orland H, Zee A., J. Mol. Biol. 379(4), 2008
PMID: 18485361
Stochastic modeling of RNA pseudoknotted structures: a grammatical approach.
Cai L, Malmberg RL, Wu Y., Bioinformatics 19 Suppl 1(), 2003
PMID: 12855439
An O(n(5)) algorithm for MFE prediction of kissing hairpins and 4-chains in nucleic acids.
Chen HL, Condon A, Jabbari H., J. Comput. Biol. 16(6), 2009
PMID: 19522664
Classifying RNA pseudoknotted structures
Condon, Theor. Comput. Sci. 320(), 2004
RNA secondary structure prediction with simple pseudoknots
Deogun, 2004
A statistical sampling algorithm for RNA secondary structure prediction.
Ding Y, Lawrence CE., Nucleic Acids Res. 31(24), 2003
PMID: 14654704
The chemical repertoire of natural ribozymes.
Doudna JA, Cech TR., Nature 418(6894), 2002
PMID: 12110898
Crystal structure of a hepatitis delta virus ribozyme.
Ferre-D'Amare AR, Zhou K, Doudna JA., Nature 395(6702), 1998
PMID: 9783582
Frameshifting RNA pseudoknots: structure and mechanism.
Giedroc DP, Cornish PV., Virus Res. 139(2), 2008
PMID: 18621088
Abstract shapes of RNA.
Giegerich R, Voss B, Rehmsmeier M., Nucleic Acids Res. 32(16), 2004
PMID: 15371549
Fast folding and comparison of RNA secondary structures
Hofacker, Monatsh. Chem. 125(), 1994
Folding 3-noncrossing RNA pseudoknot structures.
Huang FW, Peng WW, Reidys CM., J. Comput. Biol. 16(11), 2009
PMID: 19958083
Target prediction and a statistical sampling algorithm for RNA-RNA interaction.
Huang FW, Qin J, Reidys CM, Stadler PF., Bioinformatics 26(2), 2009
PMID: 19910305
Combinatorics of RNA structures with pseudoknots.
Jin EY, Qin J, Reidys CM., Bull. Math. Biol. 70(1), 2007
PMID: 17896159
tRNAdb 2009: compilation of tRNA sequences and tRNA genes.
Juhling F, Morl M, Hartmann RK, Sprinzl M, Stadler PF, Putz J., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18957446
RNA pseudoknotted structure prediction using stochastic multiple context-free grammar
Kato, IPSJ Digit. Cour. 2(), 2006
Proportions of irreducible diagrams
Kleitman, Stud. Appl. Math. 49(), 1970
A new pseudoknots folding algorithm for RNA structure prediction
Li, 2005
The chromatic polynomial of fatgraphs and its categorification
Loebl, Adv. Math. 217(), 2008
RNA pseudoknot prediction in energy-based models.
Lyngso RB, Pedersen CN., J. Comput. Biol. 7(3-4), 2000
PMID: 11108471

Massey, 1967
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
Mathews DH, Sabina J, Zuker M, Turner DH., J. Mol. Biol. 288(5), 1999
PMID: 10329189
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.
Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH., Proc. Natl. Acad. Sci. U.S.A. 101(19), 2004
PMID: 15123812
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

Nebel, An algebraic approach to rna pseudoknotted structures. (), 2011
Algorithms for loop matching
Nussinov, SIAM J. Appl. Math. 35(), 1978
Fatgraph models of proteins
Penner, Comm. Pure Appl. Math. 63(), 2010
Shapes of RNA pseudoknot structures.
Reidys CM, Wang RR., J. Comput. Biol. 17(11), 2010
PMID: 20868269
The language of RNA: a formal grammar that includes pseudoknots.
Rivas E, Eddy SR., Bioinformatics 16(4), 2000
PMID: 10869031
On multiple context free grammars
Seki, Theor. Comput. Sci. 88(), 1991
Pseudoknots: RNA structures with diverse functions.
Staple DW, Butcher SE., PLoS Biol. 3(6), 2005
PMID: 15941360
Versatile and declarative dynamic programming using pair algebras.
Steffen P, Giegerich R., BMC Bioinformatics 6(), 2005
PMID: 16156887
An RNA folding method capable of identifying pseudoknots and base triples.
Tabaska JE, Cary RB, Gabow HN, Stormo GD., Bioinformatics 14(8), 1998
PMID: 9789095
Algorithm independent properties of RNA structure prediction
Tacker, Eur. Biophy. J. 25(), 1996
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
Prediction of rna secondary structure including kissing hairpin motifs
Theis, Algorithms Bioinformatics 6293(), 2010
Tree adjoining grammars for RNA structure prediction
Uemura, Theor. Comput. Sci. 210(), 1999
PseudoBase: structural information on RNA pseudoknots.
van Batenburg FH, Gultyaev AP, Pleij CW., Nucleic Acids Res. 29(1), 2001
PMID: 11125088
Large-N random matrices for RNA folding
Vernizzi, Acta Phys. Polon. 36(), 2005
Complete probabilistic analysis of RNA shapes.
Voss B, Giegerich R, Rehmsmeier M., BMC Biol. 4(), 2006
PMID: 16480488
Secondary structure of single-stranded nucleic acids
Waterman, Adv. Math. 1(), 1978
On finding all suboptimal foldings of an RNA molecule.
Zuker M., Science 244(4900), 1989
PMID: 2468181

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 21335320
PubMed | Europe PMC

Suchen in

Google Scholar