IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction (Q30376610)

18 August 2017

IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction (English)

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18 August 2017

computational biology

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Xiaoyong Pan

1

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18 August 2017

Yong-Xian Fan

series ordinal

2

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18 August 2017

Junchi Yan

series ordinal

3

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18 August 2017

Hong-Bin Shen

series ordinal

4

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18 August 2017

language of work or name

English

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publication date

9 August 2016

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18 August 2017

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18 August 2017

17

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18 August 2017

582

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describes a project that uses

18 August 2017

scikit-learn

object named as

Scikit-learn

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CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Predicting effects of noncoding variants with deep learning-based sequence model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

Transcriptomic landscape of lncRNAs in inflammatory bowel 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=4979166

Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

A comprehensive comparative review of sequence-based predictors of DNA- and RNA-binding residues.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

Computationally predicting protein-RNA interactions using only positive and unlabeled examples

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

RPI-Pred: predicting ncRNA-protein interaction using sequence and structural 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=4979166

High-throughput characterization of 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=4979166

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=4979166

Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary 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=4979166

Methods for comprehensive experimental identification of RNA-protein 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=4979166

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale 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=4979166

NPInter v2.0: an updated database of ncRNA 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=4979166

Computational prediction of associations between long non-coding RNAs and 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=4979166

catRAPID omics: a web server for large-scale prediction of 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=4979166

A compendium of RNA-binding motifs for decoding gene 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=4979166

Representation learning: a review and new perspectives

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

GENCODE: the reference human genome annotation for The ENCODE Project

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

Predicting RNA-protein interactions using only sequence 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=4979166

20 June 2018

ViennaRNA Package 2.0

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

Non-coding RNAs 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=4979166

Long noncoding RNAs and 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=4979166

Diverse roles of host RNA binding proteins in RNA virus replication

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

In silico characterization and prediction of global protein-mRNA interactions in yeast

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

Towards better accuracy for missing value estimation of epistatic miniarray profiling data by a novel ensemble approach

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

CLIPZ: a database and analysis environment for experimentally determined binding 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=4979166

PRIDB: a Protein-RNA interface database

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

Large-scale prediction of human protein-protein interactions from amino acid sequence based on latent topic features

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

Signatures of RNA binding proteins globally coupled to effective microRNA target 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=4979166

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=4979166

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

CD-HIT Suite: a web server for clustering and comparing biological sequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

Rapid and systematic analysis of the RNA recognition specificities 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=4979166

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

RNA-binding proteins: modular design for efficient function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

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=4979166

RNA-protein interactions in the control of stability and localization of messenger RNA (review).

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

20 June 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4979166

Predicting protein associations with long noncoding RNAs

20 June 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12864-016-2931-8

Predicting protein-RNA interaction amino acids using random forest based on submodularity subset selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12864-016-2931-8

Identifying Important Risk Factors for Survival in Kidney Graft Failure Patients Using Random Survival Forests

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12864-016-2931-8

De novo prediction of RNA-protein interactions from sequence information

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12864-016-2931-8

Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12864-016-2931-8

A global view of network of lncRNAs and their binding proteins

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27506469

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S12864-016-2931-8

1 reference

Dimensions Publication ID

18 August 2017

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/s12864-016-2931-8

1 reference

18 August 2017

PubMed publication ID

27506469

1 reference