(Q30985446)

15 October 2017

RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins (English)

1 reference

15 October 2017

Esther T Chan

3

0 references

Quaid D Morris

object named as

Quaid Morris

5

0 references

author name string

Hilal Kazan

1

1 reference

15 October 2017

Debashish Ray

2

1 reference

15 October 2017

Timothy R Hughes

4

1 reference

15 October 2017

1 July 2010

1 reference

PLOS Computational Biology

15 October 2017

1 reference

15 October 2017

6

1 reference

15 October 2017

e1000832

1 reference

Creative Commons Attribution 4.0 International

15 October 2017

start time

1 July 2010

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein

21 June 2018

1 reference

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Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Diversity and complexity in DNA recognition by transcription factors

21 June 2018

1 reference

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Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

RNA-binding proteins in human genetic disease

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

RNA regulons: coordination of post-transcriptional events

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Using RNA secondary structures to guide sequence motif finding towards single-stranded regions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

On counting position weight matrix matches in a sequence, with application to discriminative motif finding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

MEME: discovering and analyzing DNA and protein sequence motifs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Profiling condition-specific, genome-wide regulation of mRNA stability in yeast

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

CLIP: a method for identifying protein-RNA interaction sites in living cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Explicit equilibrium modeling of transcription-factor binding and gene regulation.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Structure of PTB bound to RNA: specific binding and implications for splicing regulation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

enoLOGOS: a versatile web tool for energy normalized sequence logos

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Rfam: annotating non-coding RNAs in complete genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

mRNA openers and closers: modulating AU-rich element-controlled mRNA stability by a molecular switch in mRNA secondary structure.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Identification of a target RNA motif for RNA-binding protein HuR.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

A statistical sampling algorithm for RNA secondary structure prediction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Integrating regulatory motif discovery and genome-wide expression analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

The SR protein SRp38 represses splicing in M phase cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Additivity in protein-DNA interactions: how good an approximation is it?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Crystal structure of a Pumilio homology domain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Mammalian staufen is a double-stranded-RNA- and tubulin-binding protein which localizes to the rough endoplasmic reticulum

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Combining evidence using p-values: application to sequence homology searches

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Mutation of PTB binding sites causes misregulation of alternative 3' splice site selection in vivo

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

The neuronal RNA binding protein Nova-1 recognizes specific RNA targets in vitro and in vivo

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

RNA sequence analysis using covariance models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

Selection of a subset of mRNAs from combinatorial 3' untranslated region libraries using neuronal RNA-binding protein Hel-N1

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

U1-snRNP-A protein selects a ten nucleotide consensus sequence from a degenerate RNA pool presented in various structural contexts

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895634

The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model.

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000832

Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000832

Predicting transcription factor affinities to DNA from a biophysical model

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000832

RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000832

A Limited Memory Algorithm for Bound Constrained Optimization

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000832

From promoter sequence to expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000832

10.1371/JOURNAL.PCBI.1000832

21 January 2018

Identifiers

DOI

1 reference

journals/ploscb/KazanRCHM10

15 October 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

15 October 2017

PubMed publication ID

20617199

1 reference