Computational methods in noncoding RNA research (Q36929494)

17 August 2017

1 reference

title

Computational methods in noncoding RNA research (English)

1 reference

17 August 2017

computational research

1 reference

3

Alan Mitchell Durham

1 reference

17 August 2017

1

Ariane Machado-Lima

1 reference

17 August 2017

Hernando A del Portillo

series ordinal

2

1 reference

17 August 2017

4 September 2007

1 reference

17 August 2017

35

1 reference

Journal of Mathematical Biology

inferred from page(s)

published in

1 reference

17 August 2017

56

1 reference

17 August 2017

1-2

1 reference

17 August 2017

15-49

1 reference

PubMed ID

17786447

maintained by WikiProject

17 August 2017

WikiProject Mathematics

0 references

exact match

https://scigraph.springernature.com/pub.10.1007/s00285-007-0122-6

0 references

cites work

A novel method for finding tRNA genes

1 reference

12 December 2020

Discovering common stem-loop motifs in unaligned RNA sequences

1 reference

12 December 2020

snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome

1 reference

12 December 2020

The language of genes

1 reference

12 December 2020

Small subunit ribosomal RNA modeling using stochastic context-free grammars

1 reference

12 December 2020

Non-coding RNAs: hope or hype?

1 reference

12 December 2020

Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes

1 reference

12 December 2020

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

1 reference

12 December 2020

Hidden Markov models in computational biology. Applications to protein modeling

1 reference

12 December 2020

Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs.

1 reference

12 December 2020

T-Coffee: A novel method for fast and accurate multiple sequence alignment

1 reference

12 December 2020

Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change

1 reference

12 December 2020

Using CLUSTAL for multiple sequence alignments

1 reference

12 December 2020

Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy

1 reference

12 December 2020

1 reference

12 December 2020

Secondary structure prediction for aligned RNA sequences

1 reference

12 December 2020

Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics

1 reference

12 December 2020

Noncoding RNA genes identified in AT-rich hyperthermophiles

1 reference

12 December 2020

Second eigenvalue of the Laplacian matrix for predicting RNA conformational switch by mutation

1 reference

12 December 2020

1 reference

12 December 2020

BRUCE: a program for the detection of transfer-messenger RNA genes in nucleotide sequences

1 reference

12 December 2020

Sfold web server for statistical folding and rational design of nucleic acids

1 reference

12 December 2020

Rfam: annotating non-coding RNAs in complete genomes

1 reference

12 December 2020

RNA structure prediction

1 reference

12 December 2020

RNA secondary structure prediction using stochastic context-free grammars and evolutionary history

1 reference

12 December 2020

Predicting a set of minimal free energy RNA secondary structures common to two sequences

1 reference

12 December 2020

A new distance for high level RNA secondary structure comparison.

1 reference

12 December 2020

A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure

1 reference

12 December 2020

Prediction of RNA secondary structure, including pseudoknotting, by computer simulation

1 reference

12 December 2020

A program for predicting significant RNA secondary structures.

1 reference

12 December 2020

CONTRAfold: RNA secondary structure prediction without physics-based models

1 reference

12 December 2020

The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription

1 reference

12 December 2020

Computational complexity of multiple sequence alignment with SP-score

1 reference

12 December 2020

Description of RNA folding by "simulated annealing".

1 reference

12 December 2020

No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution

1 reference

12 December 2020

Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences.

1 reference

12 December 2020

The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts

1 reference

12 December 2020

Consensus folding of unaligned RNA sequences revisited

1 reference

12 December 2020

Dial tm for rescue: tmRNA engages ribosomes stalled on defective mRNAs

1 reference

12 December 2020

Fast and reliable prediction of noncoding RNAs

1 reference

12 December 2020

A comparative method for finding and folding RNA secondary structures within protein-coding regions

1 reference

12 December 2020

Using multiple alignments and phylogenetic trees to detect RNA secondary structure

1 reference

12 December 2020

Stochastic context-free grammars for tRNA modeling

1 reference

12 December 2020

A new method to predict the consensus secondary structure of a set of unaligned RNA sequences.

1 reference

12 December 2020

Finding the common structure shared by two homologous RNAs.

1 reference

12 December 2020

Cofolga: a genetic algorithm for finding the common folding of two RNAs.

1 reference

12 December 2020

Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics

1 reference

12 December 2020

Beyond Mfold: recent advances in RNA bioinformatics

1 reference

12 December 2020

Rfam: an RNA family database

1 reference

12 December 2020

Searching for RNA genes using base-composition statistics

1 reference

12 December 2020

RAGA: RNA sequence alignment by genetic algorithm

1 reference

12 December 2020

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

1 reference

12 December 2020

RNA pseudoknot prediction in energy-based models

1 reference

12 December 2020

Identifying potential tRNA genes in genomic DNA sequences.

1 reference

12 December 2020

As antisense RNA gets intronic

1 reference

12 December 2020

Statistical and Bayesian approaches to RNA secondary structure prediction

1 reference

12 December 2020

FastR: fast database search tool for non-coding RNA.

1 reference

12 December 2020

Sequence-based heuristics for faster annotation of non-coding RNA families.

1 reference

12 December 2020

MicroRNA identification based on sequence and structure alignment

1 reference

12 December 2020

An expanding universe of noncoding RNAs

1 reference

12 December 2020

Accelerated probabilistic inference of RNA structure evolution

1 reference

12 December 2020

The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy

1 reference

12 December 2020

A computational screen for methylation guide snoRNAs in yeast

1 reference

12 December 2020

RNAmute: RNA secondary structure mutation analysis tool

1 reference

12 December 2020

CARNAC: folding families of related RNAs

1 reference

12 December 2020

ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences

1 reference

12 December 2020

Tracking down noncoding RNAs

1 reference

12 December 2020

ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs

1 reference

12 December 2020

Complete suboptimal folding of RNA and the stability of secondary structures.

1 reference

12 December 2020

Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency

1 reference

12 December 2020

ConStruct: a tool for thermodynamic controlled prediction of conserved secondary structure

1 reference

12 December 2020

An RNA folding method capable of identifying pseudoknots and base triples.

1 reference

12 December 2020

Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data

1 reference

12 December 2020

1 reference

12 December 2020

Distinguishing protein-coding from non-coding RNAs through support vector machines

1 reference

12 December 2020

Alignment of RNA base pairing probability matrices

1 reference

12 December 2020

SRPDB: Signal Recognition Particle Database

1 reference

12 December 2020

ddbRNA: detection of conserved secondary structures in multiple alignments.

1 reference

12 December 2020

Noncoding RNA gene detection using comparative sequence analysis

1 reference

12 December 2020

A dynamic programming algorithm for RNA structure prediction including pseudoknots

1 reference

12 December 2020

Estimation of Secondary Structure in Ribonucleic Acids

1 reference

12 December 2020

An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots.

1 reference

12 December 2020

RNA multi-structure landscapes. A study based on temperature dependent partition functions.

1 reference

12 December 2020

Vienna RNA secondary structure server

1 reference

12 December 2020

The equilibrium partition function and base pair binding probabilities for RNA secondary structure

1 reference

12 December 2020

RNA sequence analysis using covariance models

1 reference

12 December 2020

RNA secondary structure: physical and computational aspects

1 reference

12 December 2020

The signal recognition particle

1 reference

12 December 2020

Structure clustering features on the Sfold Web server

1 reference

12 December 2020

Phylogenetic comparative analysis of RNA secondary structure

1 reference

12 December 2020

On finding all suboptimal foldings of an RNA molecule

1 reference

12 December 2020

Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix analysis of transcriptional control regions.

1 reference

12 December 2020

RNA folding energy landscapes.

1 reference

12 December 2020

RDfolder: a web server for prediction of RNA secondary structure

1 reference

12 December 2020

RNA pseudoknot modeling using intersections of stochastic context free grammars with applications to database search.

1 reference

12 December 2020

A partition function algorithm for nucleic acid secondary structure including pseudoknots

1 reference

12 December 2020

The microRNAs of Caenorhabditis elegans

1 reference

12 December 2020

Dynalign: an algorithm for finding the secondary structure common to two RNA sequences

1 reference

12 December 2020

Co-transcriptional folding is encoded within RNA genes

1 reference

12 December 2020

Pairwise RNA structure comparison with stochastic context-free grammars.

1 reference

12 December 2020

Prediction of signal recognition particle RNA genes

1 reference

12 December 2020

A statistical sampling algorithm for RNA secondary structure prediction

1 reference

12 December 2020

A general edit distance between RNA structures.

1 reference

12 December 2020

RNALOSS: a web server for RNA locally optimal secondary structures

1 reference

12 December 2020

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information

1 reference

12 December 2020

Prediction of common secondary structures of RNAs: a genetic algorithm approach

1 reference

12 December 2020

The Ribonuclease P Database

1 reference

12 December 2020

An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots

1 reference

12 December 2020

Evolutionary models for insertions and deletions in a probabilistic modeling framework

1 reference

12 December 2020

HotKnots: heuristic prediction of RNA secondary structures including pseudoknots.

1 reference

12 December 2020

RSEARCH: finding homologs of single structured RNA sequences

1 reference

12 December 2020

RNAKinetics: a web server that models secondary structure kinetics of an elongating RNA

1 reference

12 December 2020

RNAshapes: an integrated RNA analysis package based on abstract shapes.

1 reference

12 December 2020

Method for predicting RNA secondary structure

1 reference

12 December 2020

Identification of novel genes coding for small expressed RNAs

1 reference

12 December 2020

Complete probabilistic analysis of RNA shapes

1 reference

12 December 2020

RAG: RNA-As-Graphs database--concepts, analysis, and features

1 reference

12 December 2020

BayesFold: rational 2 degrees folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences

1 reference

12 December 2020

PSoL: a positive sample only learning algorithm for finding non-coding RNA genes.

1 reference

12 December 2020

Finding the most significant common sequence and structure motifs in a set of RNA sequences

1 reference

12 December 2020

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

1 reference

12 December 2020

ILM: a web server for predicting RNA secondary structures with pseudoknots

1 reference

12 December 2020

RNA folding at elementary step resolution

1 reference

12 December 2020

Non–coding RNA genes and the modern RNA world

1 reference

12 December 2020

How do RNA folding algorithms work?

1 reference

12 December 2020

Pfold: RNA secondary structure prediction using stochastic context-free grammars

1 reference

12 December 2020

Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome

1 reference

12 December 2020

RNA polymerase II synthesizes antisense RNA in Plasmodium falciparum

1 reference

12 December 2020

Antisense intronic non-coding RNA levels correlate to the degree of tumor differentiation in prostate cancer

1 reference

12 December 2020

Comparing multiple RNA secondary structures using tree comparisons

1 reference

12 December 2020

MSARI: multiple sequence alignments for statistical detection of RNA secondary structure

1 reference

12 December 2020

RNA secondary structure prediction based on free energy and phylogenetic analysis

1 reference

12 December 2020

A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences

1 reference

12 December 2020

Pure multiple RNA secondary structure alignments: a progressive profile approach

1 reference

12 December 2020

Computational genomics of noncoding RNA genes

1 reference

12 December 2020

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%

1 reference

12 December 2020

Mfold web server for nucleic acid folding and hybridization prediction

1 reference

12 December 2020

Local RNA base pairing probabilities in large sequences.

1 reference

12 December 2020

An efficient algorithm to compute the landscape of locally optimal RNA secondary structures with respect to the Nussinov-Jacobson energy model

1 reference

12 December 2020

The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs

1 reference

12 December 2020

MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons.

1 reference

12 December 2020

Computational identification of Drosophila microRNA genes

1 reference

12 December 2020

NONCODE: an integrated knowledge database of non-coding RNAs

1 reference

12 December 2020

Phylogenetically enhanced statistical tools for RNA structure prediction.

1 reference

12 December 2020

10.1007/S00285-007-0122-6

Identifiers

DOI

1 reference

17 August 2017

1 reference

PubMed ID

17786447