Methods

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 ...

Read More »

Identification and prioritization of long non-coding RNAs associated with autism

Genetic studies have identified many risk loci for autism spectrum disorder (ASD) although causal factors in the majority of cases are still unknown. Currently, known ASD risk genes are all protein-coding genes; however, the vast majority of transcripts in humans are non-coding RNAs (ncRNAs) which do not encode proteins. Recently, long non-coding RNAs (lncRNAs) were shown to be highly expressed ...

Read More »

Identification and validation long non-coding RNAs of oral squamous cell carcinoma by bioinformatics method

lncRNA

Gene markers of oral squamous cell carcinoma (OSCC) have great significance on early diagnosis and treatment of clinical oral cancer. In this study, researchers from the Children Hospital of Chongqing Medical University used RNA-Seq data from OSCC patients and filtered differentially-expressed long non-coding RNA (lncRNA) to further clarify the molecular mechanism. First, they downloaded datasets of OSCC from National Center ...

Read More »

lncRNA-screen – an interactive platform for computationally screening long non-coding RNAs in large genomics datasets

lncrna

Long non-coding RNAs (lncRNAs) have emerged as a class of factors that are important for regulating development and cancer. Computational prediction of lncRNAs from ultra-deep RNA sequencing has been successful in identifying candidate lncRNAs. However, the complexity of handling and integrating different types of genomics data poses significant challenges to experimental laboratories that lack extensive genomics expertise. To address this ...

Read More »

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, ...

Read More »

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 ...

Read More »

A Pipeline for Discovery of DNA methylation patterns in long non-coding RNAs

lncRNA

A systematic pipeline is proposed to discover methylation patterns for lncRNAs. Subtype specific and common lncRNAs differ greatly in functions and structures. Methylation modules enhances the accuracy of prediction of cancers. Despite growing evidence demonstrates that the long non-coding ribonucleic acids (lncRNAs) are critical modulators for cancers, the knowledge about the DNA methylation patterns of lncRNAs is quite limited. Researchers ...

Read More »

LncRNAs2Pathways – Identifying the pathways influenced by a set of lncRNAs of interest based on a global network propagation method

Long non-coding RNAs (lncRNAs) have been demonstrated to play essential roles in diverse cellular processes and biological functions. Exploring the functions associated with lncRNAs may help provide insight into their underlying biological mechanisms. The current methods primarily focus on investigating the functions of individual lncRNAs; however, essential biological functions may be affected by the combinatorial effects of multiple lncRNAs. Here, ...

Read More »

ASSA – Transcriptome-Wide Prediction Of lncRNA-RNA Interactions By Thermodynamics

lncRNA

The discovery of thousands of long noncoding RNAs (lncRNAs) in mammals raises a question about their functionality. It has been shown that some of them function post-transcriptionally via formation of inter-molecular duplexes. Sequence alignment tools are frequently used for transcriptome-wide prediction of RNA-RNA interactions. However, such approaches have poor prediction accuracy since they ignore RNA secondary structure and interaction energy. ...

Read More »

LncFunNet – an integrated computational framework for identification of functional long noncoding RNAs

lncRNA

Long noncoding RNAs (lncRNAs) are key regulators of diverse cellular processes. Recent advances in high-throughput sequencing have allowed for an unprecedented discovery of novel lncRNAs. To identify functional lncRNAs from thousands of candidates for further functional validation is still a challenging task. Here, researchers from the Chinese University of Hong Kong present a novel computational framework, lncFunNet (lncRNA Functional inference ...

Read More »