Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Ribosome Profiling

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...

Experimental RNAi

Experimental RNAi

RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...

lncRNA - Long Non-coding RNAs

lncRNA - Long Non-coding RNAs

Ribozymes

Ribozymes

Ribosomal RNA Synthesis

Ribosomal RNA Synthesis

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

PATO: genome-wide prediction of lncRNA-DNA triple helices.

Bioinformatics (Oxford, England)·2023

Same author

PyToxo: a Python tool for calculating penetrance tables of high-order epistasis models.

BMC bioinformatics·2022

Same author

HSRA: Hadoop-based spliced read aligner for RNA sequencing data.

PloS one·2018

Same author

ParBiBit: Parallel tool for binary biclustering on modern distributed-memory systems.

PloS one·2018

Same journal

Tracking Synthetic Adhesins on Bacterial Surfaces with Immunofluorescence Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Post-Selection Methods for Analyzing mRNA Display Selections and Optimization of Hits.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

High-Performance Computing in Tandem Mass Spectrometry (MS/MS) Peptide Identification.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Engineering and Adapting Disulfide-Containing Proteins to Enable Intracellular Functionality.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

AI-Driven Protein Research: From Prediction to Design.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Methods for the In Vitro Selection of Protein and Peptide Libraries Using mRNA Display.

Methods in molecular biology (Clifton, N.J.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 12, 2026

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Published on: April 30, 2011

Hybrid MPI/OpenMP Implementation of RIblast for Transcriptome-Scale lncRNA-RNA Interaction Prediction.

Iñaki Amatria-Barral¹, Jorge González-Domínguez², Juan Touriño²

¹Computer Architecture Group, CITIC, Universidade da Coruña, Coruña, Spain. i.amatria@udc.es.

Methods in Molecular Biology (Clifton, N.J.)

|November 1, 2025

Summary

This summary is machine-generated.

Researchers developed pRIblast, a faster tool for predicting long noncoding RNA (lncRNA) interactions. This computational method significantly reduces costs and enables large-scale lncRNA analysis, previously impossible.

Keywords:

High-performance computing MPI OpenMP Transcriptome-scale analysis lncRNA lncRNA–RNA interaction

More Related Videos

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

Published on: December 2, 2009

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

Related Experiment Videos

Last Updated: Jan 12, 2026

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Published on: April 30, 2011

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

Published on: December 2, 2009

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

Area of Science:

Bioinformatics
Computational Biology
Molecular Biology

Background:

Identifying long noncoding RNA (lncRNA) interaction partners is crucial for understanding lncRNA functions.
Existing tools for predicting lncRNA-RNA interactions face computational cost limitations, hindering transcriptome-scale analyses.
High-throughput prediction of lncRNA interactions is essential for advancing functional genomics.

Purpose of the Study:

To introduce pRIblast, an optimized computational tool for large-scale lncRNA-RNA interaction analysis.
To address the computational bottlenecks associated with transcriptome-wide lncRNA interaction prediction.
To enable efficient analysis of massive datasets for inferring lncRNA functions.

Main Methods:

Development of pRIblast, a hybrid MPI/OpenMP implementation of the RIblast algorithm.
Leveraging cluster environments and supercomputing facilities for reduced computational costs.
Optimization of the algorithm for handling large-scale biological datasets.

Main Results:

pRIblast significantly reduces computational costs for lncRNA-RNA interaction analyses.
The tool enables the analysis of datasets previously too large for existing methods.
Demonstrated feasibility of large-scale lncRNA interaction studies.

Conclusions:

pRIblast offers a powerful and efficient solution for transcriptome-wide lncRNA-RNA interaction prediction.
The optimized algorithm facilitates deeper insights into lncRNA functions through large-scale analysis.
This advancement overcomes previous computational barriers in lncRNA functional genomics research.