Bioinformatics of Non-Coding RNAs with Applications to Biomedicine: Recent Advances and Open Challenges

Front Cover
Carlo Maria Croce, Alfredo Ferro, Alessandro Laganà
Frontiers Media SA, Jan 27, 2017

 The recent discovery of small and long non-coding RNAs (ncRNAs) has represented a major breakthrough in the life sciences. These molecules add a new layer of complexity to biological processes and pathways by revealing a sophisticated and dynamic interconnected system whose structure is just beginning to be uncovered. Genetic and epigenetic aberrations affecting ncRNA gene sequences and their expression have been linked to a variety of pathological conditions, including cancer, cardiovascular and neurological diseases. Latest advances in the development of high throughput analysis techniques may help to shed light on the complex regulatory mechanisms in which ncRNA molecules are involved. Bioinformatics tools constitute a unique and essential resource for non-coding RNA studies, providing a powerful technology to organize, integrate and analyze the huge amount of data produced daily by wet biology experiments in order to discover patterns, identify relationships among heterogeneous biological elements and formulate functional hypotheses. 

This Research Topic reviews current knowledge, introduces novel methods, and discusses open challenges of this exciting and innovative field in connection with the most important biomedical applications. It consists of four reviews and six original research and methods articles, spanning the full scope of the Research Topic.
 

Selected pages

Contents

Bioinformatics of noncoding RNAs with applications to biomedicine recent advances and open challenges
4
Computational approaches for the analysis of ncRNA through deep sequencing techniques
6
Computational prediction of miRNA genes from small RNA sequencing data
12
current knowledge sources and computational approaches with special emphasis on noncoding RNA molecules
26
design principles and computational tools
33
from functional classification to differential expression of miRNA isoforms
40
Uncovering RNA editing sites in long noncoding RNAs
50
Comprehensive reconstruction and visualization of noncoding regulatory networks in human
56
ncRNAdisease association prediction through tripartite networkbased inference
67
Discovery of proteinlncRNA interactions by integrating largescale CLIPSeq and RNASeq datasets
75
Discovering miRNA Regulatory Networks in HoltOram Syndrome Using a Zebrafish Model
86
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Common terms and phrases

A-to-I editing ADAR algorithm aliases alignment analysis annotation antisense associated Bartel Bioengineering and Biotechnology biogenesis Bioinformatics Biol biological Biotechnol cancer canonical miRNAs Cell Chen CLIP-Seq complex computational CRISPR Cytoscape database datasets deep sequencing detection diseases Drosha duplex entities Figure Friedländer functional gene expression Genet Genome Res genome-wide hairpin Helwak high-throughput identified integrated IsomiRage isomiRs Laganà lncRNAs long non-coding RNAs mapping mature miRNA methods microRNA miRDeep miRNA modifications molecules mRNAs ncPred ncRNA-DB next-generation sequencing Nishikura nodes non-coding RNAs non-templated Northern blot novel Nucleic Acids Nucleic Acids Res nucleotide pipeline post-transcriptional potential predicted miRNA protein protein-coding RBP binding sites RBPs reads regions regulation regulatory RNA editing RNA editing sites RNA interference RNA sequencing RNA-seq data role sequencing data sgRNA silencing siRNA small RNA SNPs specific splicing sRNAs strand structure studies Supplementary Material target Tbx5 tool transcription factor University of Catania variants Wang zebrafish Zhang

Bibliographic information

TitleBioinformatics of Non-Coding RNAs with Applications to Biomedicine: Recent Advances and Open Challenges
Frontiers Research Topics
EditorsCarlo Maria Croce, Alfredo Ferro, Alessandro Laganà
PublisherFrontiers Media SA, 2017
ISBN2889450961, 9782889450961
  
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