Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

RNA-seq03:21

RNA-seq

11.8K
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...
11.8K

You might also read

Related Articles

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

Sort by
Same author

Oral microbiome modulation mitigates hyperglycemia exacerbation in gestational diabetes mellitus.

Nature communications·2026
Same author

Genomic landscape of the human vaginal microbiome is linked to host genetics and population of origin.

Nature genetics·2026
Same author

HELIX: a scalable model for predicting context-dependent regulation of RNA splicing and isoform usage.

Nature computational science·2026
Same author

Modulating the gut-reproductive tract axis: microbial influence on gynaecological cancer pathogenesis and treatment.

Gut·2026
Same author

Single-cell Spatial Multiomics: Technologies, Methods, and Biological Applications.

Genomics, proteomics & bioinformatics·2026
Same author

Comprehensive mapping of RNA modification dynamics and crosstalk via deep learning and nanopore direct RNA-sequencing.

Nature communications·2026

Related Experiment Video

Updated: Jan 16, 2026

Identification of Circular RNAs using RNA Sequencing
08:25

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

12.7K

Detecting and quantifying circular RNAs in terabyte-scale RNA-seq datasets with CIRI3.

Xin Zheng1,2, Jinyang Zhang3, Lipu Song1

  • 1China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.

Nature Biotechnology
|October 1, 2025
PubMed
Summary
This summary is machine-generated.

CIRI3 is a new tool for analyzing circular RNA (circRNA) in large RNA sequencing datasets. It offers faster and more accurate detection and quantification of circRNAs, aiding cancer research.

More Related Videos

In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions
10:27

In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

Published on: October 21, 2022

2.0K
Quantification of Circular RNAs Using Digital Droplet PCR
08:39

Quantification of Circular RNAs Using Digital Droplet PCR

Published on: September 16, 2022

4.0K

Related Experiment Videos

Last Updated: Jan 16, 2026

Identification of Circular RNAs using RNA Sequencing
08:25

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

12.7K
In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions
10:27

In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

Published on: October 21, 2022

2.0K
Quantification of Circular RNAs Using Digital Droplet PCR
08:39

Quantification of Circular RNAs Using Digital Droplet PCR

Published on: September 16, 2022

4.0K

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Circular RNA (circRNA) analysis faces challenges with large datasets.
  • Accurate detection and quantification of circRNAs are crucial for biological insights.

Purpose of the Study:

  • To introduce CIRI3, a novel computational tool for circRNA detection and quantification.
  • To enhance the efficiency and accuracy of analyzing terabyte-scale RNA-sequencing data.

Main Methods:

  • Developed CIRI3 utilizing dynamic multithreaded task partitioning.
  • Implemented a blocking search strategy for efficient junction read processing.
  • Applied CIRI3 to analyze 2,535 cancer-related RNA sequencing samples.

Main Results:

  • CIRI3 demonstrates an order of magnitude speed improvement over existing tools.
  • Achieved increased accuracy in circRNA detection and quantification.
  • Identified differentially spliced circRNAs across a large cancer sample cohort.

Conclusions:

  • CIRI3 provides a powerful and efficient solution for large-scale circRNA analysis.
  • The tool facilitates the discovery of novel circRNA biomarkers.
  • The CIRIonco database offers valuable resources for cancer research.