Prediction

A deep learning method for lincRNA detection using auto-encoder algorithm

lncRNA

RNA sequencing technique (RNA-seq) enables scientists to develop novel data-driven methods for discovering more unidentified lincRNAs. Meantime, knowledge-based technologies are experiencing a potential revolution ignited by the new deep learning methods. By scanning the newly found data set from RNA-seq, scientists have found that: (1) the expression of lincRNAs appears to be regulated, that is, the relevance exists along the ...

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A computational approach to predict scaffolding lncRNAs at large scale

lncRNA

The human transcriptome contains thousands of long non-coding RNAs (lncRNAs). Characterizing their function is a current challenge. An emerging concept is that lncRNAs serve as protein scaffolds, forming ribonucleoproteins and bringing proteins in proximity. However, only few scaffolding lncRNAs have been characterized and the prevalence of this function is unknown. Here, researchers from the Aix-Marseille University, Inserm propose the first computational ...

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Fusing multiple protein-protein similarity networks can effectively boost the performance of predicting lncRNA-protein interactions

lncrna

Long non-coding RNA (lncRNA) plays important roles in many biological and pathological processes, including transcriptional regulation and gene regulation. As lncRNA interacts with multiple proteins, predicting lncRNA-protein interactions (lncRPIs) is an important way to study the functions of lncRNA. Up to now, there have been a few works that exploit protein-protein interactions (PPIs) to help the prediction of new lncRPIs. ...

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EPLMI – large-scale lncRNA-miRNA interaction profiling

lncrna

The interaction of miRNA and lncRNA is known to be important for gene regulations. However, not many computational approaches have been developed to analyse known interactions and predict the unknown ones. Given that there are now more evidences that suggest that lncRNA-miRNA interactions are closely related to their relative expression levels in the form of a titration mechanism, researchers from ...

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LPI-ETSLP – lncRNA-protein interaction prediction using eigenvalue transformation-based semi-supervised link prediction

RNA-protein interactions are essential for understanding many important cellular processes. In particular, lncRNA-protein interactions play important roles in post-transcriptional gene regulation, such as splicing, translation, signaling and even the progression of complex diseases. However, the experimental validation of lncRNA-protein interactions remains time-consuming and expensive, and only a few theoretical approaches are available for predicting potential lncRNA-protein associations. Here, researchers from ...

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PLPIHS – prediction of lncRNA-protein interactions using HeteSim scores

lncRNA

Massive studies have indicated that long non-coding RNAs (lncRNAs) are critical for the regulation of cellular biological processes by binding with RNA-related proteins. However, only a few experimentally supported lncRNA-protein associations have been reported. Existing network-based methods are typically focused on intrinsic features of lncRNA and protein but ignore the information implicit in the topologies of biological networks associated with ...

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A Review of Recent Computational Methods for Predicting Noncoding RNAs

lncrna

Noncoding RNAs (ncRNAs) play important roles in various cellular activities and diseases. Researchers from Hebei University of Science and Technology, present a comprehensive review on computational methods for ncRNA prediction, which are generally grouped into four categories: (1) homology-based methods, that is, comparative methods involving evolutionarily conserved RNA sequences and structures, (2) de novo methods using RNA sequence and structure features, ...

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RPI-Bind – a structure-based method for accurate identification of RNA-protein binding sites

lncRNA

RNA and protein interactions play crucial roles in multiple biological processes, while these interactions are significantly influenced by the structures and sequences of protein and RNA molecules. A large class of long noncoding RNAs (lncRNAs) can bind and modulate the activity of chromatin proteins, and play roles in chromatin modifications. In this process, lncRNAs, e.g. the Xist, with specific structures ...

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