(Q30390089)

15 August 2017

A deep learning framework for modeling structural features of RNA-binding protein targets (English)

1 reference

15 August 2017

1 reference

1 reference

Sai Zhang

1

1 reference

15 August 2017

Jingtian Zhou

2

1 reference

15 August 2017

Hailin Hu

3

1 reference

15 August 2017

Haipeng Gong

4

1 reference

15 August 2017

Ligong Chen

5

1 reference

15 August 2017

Chao Cheng

6

1 reference

15 August 2017

Jianyang Zeng

7

1 reference

15 August 2017

language of work or name

English

0 references

publication date

13 October 2015

1 reference

15 August 2017

Nucleic Acids Research

1 reference

15 August 2017

44

1 reference

15 August 2017

4

1 reference

15 August 2017

e32

1 reference

Creative Commons Attribution 4.0 International

15 August 2017

start time

6 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Stabilization of the G-quadruplex at the VEGF IRES represses cap-independent translation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

CLIPdb: a CLIP-seq database for protein-RNA interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Role of the N6-methyladenosine RNA mark in gene regulation and its implications on development and disease

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Deep learning of the tissue-regulated splicing code

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Structures of Human ALKBH5 Demethylase Reveal a Unique Binding Mode for Specific Single-stranded N 6 -Methyladenosine RNA Demethylation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Identifying mRNA sequence elements for target recognition by human Argonaute proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

GraphProt: modeling binding preferences of RNA-binding proteins.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

New insights into functional roles of the polypyrimidine tract-binding protein.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Finding the target sites of RNA-binding proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Deep architectures and deep learning in chemoinformatics: the prediction of aqueous solubility for drug-like molecules

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

N6-methyl-adenosine modification in messenger and long non-coding RNA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Reversible RNA adenosine methylation in biological regulation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Annexin A2 and PSF proteins interact with p53 IRES and regulate translation of p53 mRNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Secondary RNA structure and nucleotide specificity contribute to internal initiation mediated by the human tau 5' leader

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

TDP-43 and FUS RNA-binding proteins bind distinct sets of cytoplasmic messenger RNAs and differently regulate their post-transcriptional fate in motoneuron-like cells.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Global or local? Predicting secondary structure and accessibility in mRNAs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

doRiNA: a database of RNA interactions in post-transcriptional regulation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

RNA targets of wild-type and mutant FET family proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

How to grow a mind: statistics, structure, and abstraction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

U1 snRNA directly interacts with polypyrimidine tract-binding protein during splicing repression

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Effect of mutations on the p53 IRES RNA structure: implications for de-regulation of the synthesis of p53 isoforms.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Characterization of a family of RanBP2-type zinc fingers that can recognize single-stranded RNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

R3D Align: global pairwise alignment of RNA 3D structures using local superpositions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

On the significance of an RNA tertiary structure prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

RNAstructure: software for RNA secondary structure prediction and analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

IRESite--a tool for the examination of viral and cellular internal ribosome entry sites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Next-generation SELEX identifies sequence and structural determinants of splicing factor binding in human pre-mRNA sequence

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

RNA-binding proteins in human genetic disease

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Structure-function relationships of the polypyrimidine tract binding protein

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

FR3D: finding local and composite recurrent structural motifs in RNA 3D structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

RNA regulons: coordination of post-transcriptional events

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Reducing the dimensionality of data with neural networks

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

A fast learning algorithm for deep belief nets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Evidence for an RNA chaperone function of polypyrimidine tract-binding protein in picornavirus translation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

UNR translation can be driven by an IRES element that is negatively regulated by polypyrimidine tract binding protein

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Bag-1 internal ribosome entry segment activity is promoted by structural changes mediated by poly(rC) binding protein 1 and recruitment of polypyrimidine tract binding protein 1.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

The thermodynamic stability of RNA duplexes and hairpins containing N6-alkyladenosines and 2-methylthio-N6-alkyladenosines

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Cell-specific RNA-binding proteins in human disease

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

The Apaf-1 internal ribosome entry segment attains the correct structural conformation for function via interactions with PTB and unr

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

HADDOCK: a protein-protein docking approach based on biochemical or biophysical information

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Training products of experts by minimizing contrastive divergence

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Protein factor requirements of the Apaf-1 internal ribosome entry segment: roles of polypyrimidine tract binding protein and upstream of N-ras

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Individual RNA recognition motifs of TIA-1 and TIAR have different RNA binding specificities

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770198

A multiple-feature framework for modelling and predicting transcription factor binding sites.

20 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV1025

Deep Neural Networks for Acoustic Modeling in Speech Recognition: The Shared Views of Four Research Groups

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV1025

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV1025

mRNAs containing the histone 3' stem-loop are degraded primarily by decapping mediated by oligouridylation of the 3' end.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV1025

Learning Deep Architectures for AI

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV1025

Identification of Ewing's sarcoma protein as a G-quadruplex DNA- and RNA-binding protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV1025

MOV10 Is a 5' to 3' RNA helicase contributing to UPF1 mRNA target degradation by translocation along 3' UTRs.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV1025

Effect of a natural mutation in the 5' untranslated region on the translational control of p53 mRNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV1025

21 January 2018

Identifiers

DOI

10.1093/NAR/GKV1025

1 reference

15 August 2017

1 reference

15 August 2017

PubMed publication ID

26467480

1 reference