AIMC Topic: RNA, Long Noncoding

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SubLocEP: a novel ensemble predictor of subcellular localization of eukaryotic mRNA based on machine learning.

Briefings in bioinformatics
MOTIVATION: mRNA location corresponds to the location of protein translation and contributes to precise spatial and temporal management of the protein function. However, current assignment of subcellular localization of eukaryotic mRNA reveals import...

A comprehensive survey on computational methods of non-coding RNA and disease association prediction.

Briefings in bioinformatics
The studies on relationships between non-coding RNAs and diseases are widely carried out in recent years. A large number of experimental methods and technologies of producing biological data have also been developed. However, due to their high labor ...

Predicting the interaction biomolecule types for lncRNA: an ensemble deep learning approach.

Briefings in bioinformatics
Long noncoding RNAs (lncRNAs) play significant roles in various physiological and pathological processes via their interactions with biomolecules like DNA, RNA and protein. The existing in silico methods used for predicting the functions of lncRNA ma...

Predicting microRNA-disease associations from lncRNA-microRNA interactions via Multiview Multitask Learning.

Briefings in bioinformatics
MOTIVATION: Identifying microRNAs that are associated with different diseases as biomarkers is a problem of great medical significance. Existing computational methods for uncovering such microRNA-diseases associations (MDAs) are mostly developed unde...

MLCDForest: multi-label classification with deep forest in disease prediction for long non-coding RNAs.

Briefings in bioinformatics
The long non-coding RNAs (lncRNAs) are subject of intensive recent studies due to its association with various human diseases. It is desirable to build the artificial intelligence-based models for prediction of diseases or tissues based on the lncRNA...

DeepCPP: a deep neural network based on nucleotide bias information and minimum distribution similarity feature selection for RNA coding potential prediction.

Briefings in bioinformatics
The development of deep sequencing technologies has led to the discovery of novel transcripts. Many in silico methods have been developed to assess the coding potential of these transcripts to further investigate their functions. Existing methods per...

m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome.

Nucleic acids research
N 6-Methyladenosine (m6A) is the most prevalent RNA modification on mRNAs and lncRNAs. It plays a pivotal role during various biological processes and disease pathogenesis. We present here a comprehensive knowledgebase, m6A-Atlas, for unraveling the ...

Gene set analysis methods for the functional interpretation of non-mRNA data-Genomic range and ncRNA data.

Briefings in bioinformatics
Gene set analysis (GSA) is one of the methods of choice for analyzing the results of current omics studies; however, it has been mainly developed to analyze mRNA (microarray, RNA-Seq) data. The following review includes an update regarding general me...

DeepLGP: a novel deep learning method for prioritizing lncRNA target genes.

Bioinformatics (Oxford, England)
MOTIVATION: Although long non-coding RNAs (lncRNAs) have limited capacity for encoding proteins, they have been verified as biomarkers in the occurrence and development of complex diseases. Recent wet-lab experiments have shown that lncRNAs function ...

Screening key lncRNAs with diagnostic and prognostic value for head and neck squamous cell carcinoma based on machine learning and mRNA-lncRNA co-expression network analysis.

Cancer biomarkers : section A of Disease markers
BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) is the seventh most common type of cancer around the world. The aim of this study was to seek the long non-coding RNAs (lncRNAs) acting as diagnostic and prognostic biomarker of HNSCC.