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Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning
We present RBPNet, a novel deep learning method, which predicts CLIP-seq crosslink count distribution from RNA sequence at single-nucleotide...
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Identification of RNA–RBP Interactions in Subcellular Compartments by CLIP-Seq
Cross-linking immunoprecipitation and high-throughput sequencing (CLIP-seq) allows the identification of RNA targets bound by a specific RNA-binding...
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Improving CLIP-seq data analysis by incorporating transcript information
BackgroundCurrent peak callers for identifying RNA-binding protein (RBP) binding sites from CLIP-seq data take into account genomic read profiles,...
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SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins
Advances in high-throughput profiling of RNA-binding proteins (RBPs) have resulted inCLIP-seq datasets coupled with transcriptome profiling by...
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Evaluation of methods to detect circular RNAs from single-end RNA-sequencing data
BackgroundCircular RNA (circRNA), a class of RNA molecule with a loop structure, has recently attracted researchers due to its diverse biological...
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CPA-seq reveals small ncRNAs with methylated nucleosides and diverse termini
High-throughput sequencing reveals the complex landscape of small noncoding RNAs (sRNAs). However, it is limited by requiring 5′-monophosphate and...
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A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation
BackgroundCellular RNA-binding proteins (RBPs) have multiple roles in post-transcriptional control, and some are shown to bind DNA. However, the...
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omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data
CLIP-seq methods allow the generation of genome-wide maps of RNA binding protein – RNA interaction sites. However, due to differences between...
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RNA m6A reader YTHDF2 facilitates lung adenocarcinoma cell proliferation and metastasis by targeting the AXIN1/Wnt/β-catenin signaling
Lung adenocarcinoma (LUAD) remains a leading cause of cancer-related deaths worldwide. YTHDF2 is a reader of N 6 -methyladenosine (m 6 A) on RNA and...
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Map** RNA Modifications Using Photo-Crosslinking-Assisted Modification Sequencing
Epitranscriptomic RNA modifications function as an important layer of gene regulation that modulates the function of RNA transcripts. A key step in...
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Predicting dynamic cellular protein–RNA interactions by deep learning using in vivo RNA structures
Interactions with RNA-binding proteins (RBPs) are integral to RNA function and cellular regulation, and dynamically reflect specific cellular...
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Genome-Scale Analysis of the Structure and Function of RNA Pathways and Networks in Pseudomonas aeruginosa
In recent years, several genome-wide approaches based on RNA sequencing (RNA-seq) have been developed. These methods allow a comprehensive and...
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GKLOMLI: a link prediction model for inferring miRNA–lncRNA interactions by using Gaussian kernel-based method on network profile and linear optimization algorithm
BackgroundThe limited knowledge of miRNA–lncRNA interactions is considered as an obstruction of revealing the regulatory mechanism. Accumulating...
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Detection of transcriptome-wide microRNA–target interactions in single cells with agoTRIBE
MicroRNAs (miRNAs) exert their gene regulatory effects on numerous biological processes based on their selection of target transcripts. Current...
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Role of Bioinformatics in Non-coding RNA Analysis
The transcriptome, comprising RNA molecules expressed in cells or tissues, is predominantly composed of non-coding RNAs (ncRNAs), which has most of...
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Biclustering for Epi-Transcriptomic Co-functional Analysis
Dynamic and reversible N6-methyladenosine (m6A) modifications are associated with many essential cellular functions as well as physiological and...
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Profiling of RNA-binding protein binding sites by in situ reverse transcription-based sequencing
RNA-binding proteins (RBPs) regulate diverse cellular processes by dynamically interacting with RNA targets. However, effective methods to capture...
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Epitranscriptomic technologies and analyses
RNA can interact with RNA-binding proteins (RBPs), mRNA, or other non-coding RNAs (ncRNAs) to form complex regulatory networks. High-throughput...
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Immunoprecipitation Methods to Isolate Messenger Ribonucleoprotein Complexes (mRNP)
Throughout their life cycle, messenger RNAs (mRNAs) associate with proteins to form ribonucleoproteins (mRNPs). Each mRNA is part of multiple...