Comparative RNA Genomics (Q47177746)

11 January 2018

title

Comparative RNA Genomics (English)

1 reference

11 January 2018

1 reference

Jan Gorodkin

2

0 references

Ivo L. Hofacker

object named as

Ivo L Hofacker

series ordinal

3

0 references

Peter F. Stadler

series ordinal

4

object named as

Peter F Stadler

1 reference

11 January 2018

1

Rolf Backofen

1 reference

11 January 2018

language of work or name

English

0 references

publication date

1 January 2018

1 reference

11 January 2018

Methods in Molecular Biology

published in

1 reference

11 January 2018

volume

1704

1 reference

11 January 2018

page(s)

363-400

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11 January 2018

Genome-wide transcription and the implications for genomic organization

cites work

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

The transcriptional landscape of the mammalian genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

An integrated encyclopedia of DNA elements in the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

The reality of pervasive transcription

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Pervasive transcription – Lessons from yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Non-coding RNAs in Saccharomyces cerevisiae: what is the function?

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

A global non-coding RNA system modulates fission yeast protein levels in response to stress.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

PLNlncRbase: A resource for experimentally identified lncRNAs in plants

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

The parasite Trichomonas vaginalis expresses thousands of pseudogenes and long non-coding RNAs independently from functional neighbouring genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

The primary transcriptome of the major human pathogen Helicobacter pylori

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Pervasive transcription: detecting functional RNAs in bacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Pervasive transcription: illuminating the dark matter of bacterial transcriptomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

21 January 2018

Visiting "noncodarnia".

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Long non-coding RNAs: insights into functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Identification of novel small RNAs using comparative genomics and microarrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Animal snoRNAs and scaRNAs with exceptional structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Evolutionary patterns of non-coding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

The Expansion of Animal MicroRNA Families Revisited

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Plant snoRNAs: functional evolution and new modes of gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Matching of Soulmates: coevolution of snoRNAs and their targets

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

An updated human snoRNAome

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Phylogenetic distribution of plant snoRNA families

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

RNA folding and combinatory landscapes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

From sequences to shapes and back: a case study in RNA secondary structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

On finding all suboptimal foldings of an RNA molecule

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Complete suboptimal folding of RNA and the stability of secondary structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Secondary structure prediction for aligned RNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

RNAalifold: improved consensus structure prediction for RNA alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Noncoding RNA genes identified in AT-rich hyperthermophiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Fast and reliable prediction of noncoding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

RNASurface: fast and accurate detection of locally optimal potentially structured RNA segments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Neutral evolution of mutational robustness

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Plasticity, evolvability, and modularity in RNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Direct evolution of genetic robustness in microRNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Sampled ensemble neutrality as a feature to classify potential structured RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Strategies for measuring evolutionary conservation of RNA secondary structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Sensitive measurement of single-nucleotide polymorphism-induced changes of RNA conformation: application to disease studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

A benchmark of multiple sequence alignment programs upon structural RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

ddbRNA: detection of conserved secondary structures in multiple alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

The identification and functional annotation of RNA structures conserved in vertebrates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Measuring covariation in RNA alignments: physical realism improves information measures

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

RILogo: visualizing RNA-RNA interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Selective Constraints in Conserved Folded RNAs of Drosophilid and Hominid Genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

A model of compensatory molecular evolution involving multiple sites in RNA molecules.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

The vast, conserved mammalian lincRNome

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Non-coding RNAs: hope or hype?

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Non-coding RNA: what is functional and what is junk?

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Evolutionary conservation of long non-coding RNAs; sequence, structure, function

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Purifying selection on splice-related motifs, not expression level nor RNA folding, explains nearly all constraint on human lincRNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Structure and function of long noncoding RNAs in epigenetic regulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Widespread purifying selection on RNA structure in mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Rapid turnover of long noncoding RNAs and the evolution of gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

The evolution of lncRNA repertoires and expression patterns in tetrapods

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Conservation and tissue-specific transcription patterns of long noncoding RNAs.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Nonclassical splicing mutations in the coding and noncoding regions of the ATM Gene: maximum entropy estimates of splice junction strengths

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

U6 snRNA intron insertion occurred multiple times during fungi evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

IGD: a resource for intronless genes in the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Androgen responsive intronic non-coding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Conserved tissue expression signatures of intronic noncoding RNAs transcribed from human and mouse loci

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Hidden treasures in unspliced EST data

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

The transcriptional activity of human Chromosome 22

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

The intronic long noncoding RNA ANRASSF1 recruits PRC2 to the RASSF1A promoter, reducing the expression of RASSF1A and increasing cell proliferation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Evolution of the Long Non-coding RNAs MALAT1 and MENβ/ε

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Association of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

EGF stimulates annexin 1-dependent inward vesiculation in a multivesicular endosome subpopulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Silencing and transcriptional properties of the imprinted Airn ncRNA are independent of the endogenous promoter

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Expression of distinct RNAs from 3' untranslated regions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Evolution of the unspliced transcriptome

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

The tedious task of finding homologous noncoding RNA genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Rfam 12.0: updates to the RNA families database

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Basic local alignment search tool

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Non-coding RNA annotation of the genome of Trichoplax adhaerens

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Structure and function of the smallest vertebrate telomerase RNA from teleost fish.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

BlastR--fast and accurate database searches for non-coding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Fragrep: an efficient search tool for fragmented patterns in genomic sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

RNAMotif, an RNA secondary structure definition and search algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Searching for patterns in genomic data

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Locomotif: from graphical motif description to RNA motif search

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

The Pfam protein families database: towards a more sustainable future

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Introduction to stochastic context free grammars

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

SCFGs in RNA secondary structure prediction RNA secondary structure prediction: a hands-on approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Infernal 1.1: 100-fold faster RNA homology searches

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Structured RNAs and synteny regions in the pig genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

RNAlien - Unsupervised RNA family model construction

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Dinucleotide controlled null models for comparative RNA gene prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Noncoding RNA gene detection using comparative sequence analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Identification and classification of conserved RNA secondary structures in the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

How accurately is ncRNA aligned within whole-genome multiple alignments?

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Discovering common stem-loop motifs in unaligned RNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Dynalign II: common secondary structure prediction for RNA homologs with domain insertions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

LocARNA-P: accurate boundary prediction and improved detection of structural RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

RNA structural alignments, part I: Sankoff-based approaches for structural alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

CMfinder--a covariance model based RNA motif finding algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Fast folding and comparison of RNA secondary structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

De novo discovery of structured ncRNA motifs in genomic sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Structure-based whole-genome realignment reveals many novel noncoding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

When one is better than two: RNA with dual functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

A translation-independent role of oskar RNA in early Drosophila oogenesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

A new type of IRES within gag coding region recruits three initiation complexes on HIV-2 genomic RNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

cncRNAs: Bi-functional RNAs with protein coding and non-coding functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory RNA RyhB and a peptide, RyhP

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Conflicting selection pressures on synonymous codon use in yeast suggest selection on mRNA secondary structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Considerations in the identification of functional RNA structural elements in genomic alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Structured RNAs in the ENCODE selected regions of the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Computational RNomics of drosophilids

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Computational searches for splicing signals.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Conserved introns reveal novel transcripts in Drosophila melanogaster

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Computational discovery of human coding and non-coding transcripts with conserved splice sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

ARNold: a web tool for the prediction of Rho-independent transcription terminators.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

An in silico model for identification of small RNAs in whole bacterial genomes: characterization of antisense RNAs in pathogenic Escherichia coli and Streptococcus agalactiae strains

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

A multiobjective method for robust identification of bacterial small non-coding RNAs.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

NAPP: the Nucleic Acid Phylogenetic Profile Database

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

A widespread self-cleaving ribozyme class is revealed by bioinformatics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

New classes of self-cleaving ribozymes revealed by comparative genomics analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

An assessment of bacterial small RNA target prediction programs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Target prediction for small, noncoding RNAs in bacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Fast and effective prediction of microRNA/target duplexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

RNA-RNA interaction prediction and antisense RNA target search

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Prediction of hybridization and melting for double-stranded nucleic acids

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Partition function and base pairing probabilities of RNA heterodimers

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Thermodynamics of RNA-RNA binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

RNA Accessibility in cubic time

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

RNAplex: a fast tool for RNA-RNA interaction search

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Fast prediction of RNA-RNA interaction

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

A partition function algorithm for interacting nucleic acid strands

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Partition function and base pairing probabilities for RNA-RNA interaction prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

RNA-RNA interaction prediction based on multiple sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics - assessment and update

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

PLEXY: efficient target prediction for box C/D snoRNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

RNAsnoop: efficient target prediction for H/ACA snoRNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Accessibility and conservation: general features of bacterial small RNA-mRNA interactions?

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Comparative genomics boosts target prediction for bacterial small RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Accurate SHAPE-directed RNA structure determination

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Genome-wide measurement of RNA secondary structure in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Landscape and variation of RNA secondary structure across the human transcriptome

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

RNA folding with hard and soft constraints

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

A compendium of RNA-binding motifs for decoding gene regulation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Insight into lncRNA biology using hybridization capture analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Nucleotide-Level Profiling of m5C RNA Methylation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Regulation of PKR by RNA: formation of active and inactive dimers

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

A cis-acting element in the 3'-untranslated region of human TNF-alpha mRNA renders splicing dependent on the activation of protein kinase PKR.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

Dynamic refolding of IFN-gamma mRNA enables it to function as PKR activator and translation template.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-1-4939-7463-4_14

10.1007/978-1-4939-7463-4_14

21 January 2018

Identifiers

DOI

1 reference

11 January 2018

1 reference

11 January 2018