Statistical and Bayesian approaches to RNA secondary structure prediction.

PubWeight™: 1.04‹?› | Rank: Top 15%

🔗 View Article (PMC 1383571)

Published in RNA on March 01, 2006

Authors

Ye Ding1

Author Affiliations

1: Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY 12208, USA. yding@wadsworth.org

Articles citing this

RNA folding: conformational statistics, folding kinetics, and ion electrostatics. Annu Rev Biophys (2008) 2.00

Predicting structures and stabilities for H-type pseudoknots with interhelix loops. RNA (2009) 1.51

Computational approaches for RNA energy parameter estimation. RNA (2010) 1.33

Hitting bacteria at the heart of the central dogma: sequence-specific inhibition. Microb Cell Fact (2007) 1.22

Computational methods in noncoding RNA research. J Math Biol (2007) 1.08

Predicting RNA secondary structures with pseudoknots by MCMC sampling. J Math Biol (2007) 1.08

Putative cis-acting stem-loops in the 5' untranslated region of the severe acute respiratory syndrome coronavirus can substitute for their mouse hepatitis virus counterparts. J Virol (2006) 1.06

Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity. J Mol Biol (2007) 0.99

Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions. Nucleic Acids Res (2013) 0.99

Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation. Nucleic Acids Res (2006) 0.94

Analysis of riboswitch structure and function by an energy landscape framework. J Mol Biol (2009) 0.93

Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy: the boustrophedon method. J Math Biol (2007) 0.88

RNA localization signals: deciphering the message with bioinformatics. Semin Cell Dev Biol (2007) 0.86

RNA structure prediction from evolutionary patterns of nucleotide composition. Nucleic Acids Res (2009) 0.86

In silico generation of alternative hypotheses using causal mapping (CMAP). PLoS One (2009) 0.83

Boltzmann ensemble features of RNA secondary structures: a comparative analysis of biological RNA sequences and random shuffles. J Math Biol (2007) 0.80

Basis for ligand discrimination between ON and OFF state riboswitch conformations: the case of the SAM-I riboswitch. RNA (2012) 0.79

Bioinformatics of prokaryotic RNAs. RNA Biol (2014) 0.77

Structural dynamics control the MicroRNA maturation pathway. Nucleic Acids Res (2016) 0.75

Novel Approach to Analyzing MFE of Noncoding RNA Sequences. Genomics Insights (2016) 0.75

Effect of 3'UTR RET Variants on RET mRNA Secondary Structure and Disease Presentation in Medullary Thyroid Carcinoma. PLoS One (2016) 0.75

Statistical mechanical modeling of RNA folding: from free energy landscape to tertiary structural prediction. Nucleic Acids Mol Biol (2012) 0.75

ptRNApred: computational identification and classification of post-transcriptional RNA. Nucleic Acids Res (2014) 0.75

Articles cited by this

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res (1981) 61.59

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol (1999) 41.48

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science (1993) 36.84

Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput Appl Biosci (1994) 31.96

The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics (2002) 29.41

Position-based sequence weights. J Mol Biol (1994) 24.41

Principles that govern the folding of protein chains. Science (1973) 23.40

Estimation of secondary structure in ribonucleic acids. Nature (1971) 20.52

On finding all suboptimal foldings of an RNA molecule. Science (1989) 20.36

Vienna RNA secondary structure server. Nucleic Acids Res (2003) 19.69

Weighting in sequence space: a comparison of methods in terms of generalized sequences. Proc Natl Acad Sci U S A (1993) 17.71

Improving the sensitivity of the sequence profile method. Protein Sci (1994) 13.54

The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers (1990) 10.92

Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc Natl Acad Sci U S A (1980) 10.48

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci U S A (2004) 10.35

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry (1998) 9.75

Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers (1999) 7.80

A dynamic programming algorithm for RNA structure prediction including pseudoknots. J Mol Biol (1999) 6.19

The Ribonuclease P Database. Nucleic Acids Res (1999) 5.91

Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res (2005) 5.28

Prediction of hybridization and melting for double-stranded nucleic acids. Biophys J (2004) 5.11

The RNA Modification Database: 1999 update. Nucleic Acids Res (1999) 4.97

SRP-RNA sequence alignment and secondary structure. Nucleic Acids Res (1991) 4.88

A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res (2003) 4.62

The Bayesian revolution in genetics. Nat Rev Genet (2004) 4.50

Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res (2004) 3.81

RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA (2005) 3.80

Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Res (2003) 3.53

A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics (2004) 3.20

Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. RNA (2004) 2.86

Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics (2004) 2.73

Calculating nucleic acid secondary structure. Curr Opin Struct Biol (2000) 2.71

A partition function algorithm for nucleic acid secondary structure including pseudoknots. J Comput Chem (2003) 2.58

Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinformatics (2004) 2.57

SRPDB: Signal Recognition Particle Database. Nucleic Acids Res (2003) 2.16

Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. Nucleic Acids Res (2001) 2.09

Bayesian inference on biopolymer models. Bioinformatics (1999) 2.02

Abstract shapes of RNA. Nucleic Acids Res (2004) 1.90

Secondary structure prediction of interacting RNA molecules. J Mol Biol (2004) 1.85

tmRDB (tmRNA database). Nucleic Acids Res (2003) 1.77

A potential smoothing algorithm accurately predicts transmembrane helix packing. Nat Struct Biol (1999) 1.68

An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. J Comput Chem (2004) 1.66

What is Bayesian statistics? Nat Biotechnol (2004) 1.40

A bayesian statistical algorithm for RNA secondary structure prediction. Comput Chem (1999) 1.33

BayesFold: rational 2 degrees folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences. RNA (2004) 1.24

Bayesian adaptive sequence alignment algorithms. Bioinformatics (1998) 1.22

Extracting stacking interaction parameters for RNA from the data set of native structures. J Mol Biol (2005) 1.22

A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation. Nucleic Acids Res (2005) 1.04

An efficient algorithm to compute the landscape of locally optimal RNA secondary structures with respect to the Nussinov-Jacobson energy model. J Comput Biol (2005) 1.00

Density of states, metastable states, and saddle points exploring the energy landscape of an RNA molecule. Proc Int Conf Intell Syst Mol Biol (1997) 0.96

Structure clustering features on the Sfold Web server. Bioinformatics (2005) 0.96

Moments of the Boltzmann distribution for RNA secondary structures. Bull Math Biol (2005) 0.93

Towards protein folding by global energy optimization. FEBS Lett (1993) 0.91

Energy landscape of k-point mutants of an RNA molecule. Bioinformatics (2005) 0.89

Articles by these authors

Clustering of RNA secondary structures with application to messenger RNAs. J Mol Biol (2006) 1.27