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

You might also read

Related Articles

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

Sort by
Same author

A murine cytomegalovirus cell cycle regulator (m54.5p) evolved within the conserved viral DNA polymerase gene.

PLoS pathogens·2026
Same author

Analysis and visualization of expression patterns with fuzzy sets as FlowSets.

NAR genomics and bioinformatics·2026
Same author

Identification of Viral Variants from Functional Genomics Data.

F1000Research·2026
Same author

Divergent granulopoiesis at extramedullary sites safeguards antibacterial host defense.

Science immunology·2026
Same author

Phosphorylation of SF3B1 by CDK11 orchestrates spliceosome activation via SNIP1-dependent RES complex recruitment.

Nature communications·2026
Same author

High rates of viral co-detection in outpatient children with acute respiratory infections after the easing of preventive measures against Covid-19 in Germany.

BMC infectious diseases·2026

Related Experiment Video

Updated: Jun 14, 2026

Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay in Cell Culture
11:00

Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay in Cell Culture

Published on: August 8, 2013

HALO--a Java framework for precise transcript half-life determination.

Caroline C Friedel1, Stefanie Kaufmann, Lars Dölken

  • 1Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany. caroline.friedel@bio.ifi.lmu.de

Bioinformatics (Oxford, England)
|March 20, 2010
PubMed
Summary
This summary is machine-generated.

New software, HALO (Half-life Organizer), precisely determines transcript half-lives from RNA sequencing data. This tool aids understanding gene expression regulation and RNA dynamics.

More Related Videos

Fluorescence In Situ Hybridization on DNA Halo Preparations to Reveal Whole Chromosomes, Telomeres and Gene Loci
09:07

Fluorescence In Situ Hybridization on DNA Halo Preparations to Reveal Whole Chromosomes, Telomeres and Gene Loci

Published on: March 4, 2021

Single-Molecule Measurement of Protein Interaction Dynamics Within Biomolecular Condensates
06:48

Single-Molecule Measurement of Protein Interaction Dynamics Within Biomolecular Condensates

Published on: January 5, 2024

Related Experiment Videos

Last Updated: Jun 14, 2026

Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay in Cell Culture
11:00

Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay in Cell Culture

Published on: August 8, 2013

Fluorescence In Situ Hybridization on DNA Halo Preparations to Reveal Whole Chromosomes, Telomeres and Gene Loci
09:07

Fluorescence In Situ Hybridization on DNA Halo Preparations to Reveal Whole Chromosomes, Telomeres and Gene Loci

Published on: March 4, 2021

Single-Molecule Measurement of Protein Interaction Dynamics Within Biomolecular Condensates
06:48

Single-Molecule Measurement of Protein Interaction Dynamics Within Biomolecular Condensates

Published on: January 5, 2024

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Advancements in experimental technologies enable whole-transcriptome measurements of transcription and RNA decay.
  • Transcript half-lives are crucial for understanding biological process regulation and gene expression dynamics.

Purpose of the Study:

  • To introduce HALO (Half-life Organizer), the first software for precise transcript half-life determination.
  • To provide tools for quality control, filtering, and normalization of RNA sequencing data.

Main Methods:

  • Utilizes measurements of de novo transcription or RNA decay.
  • Supports data from microarrays and RNA-sequencing (RNA-seq).
  • Offers a graphical user interface, command-line tools, and a Java API.

Main Results:

  • Enables fast and reliable determination of transcript half-lives.
  • Facilitates integration into existing gene expression profiling pipelines.
  • Provides comprehensive quality control and data processing methods.

Conclusions:

  • HALO is a versatile tool for biologists and software developers.
  • Enhances the analysis of gene expression regulation through accurate transcript half-life measurement.
  • Streamlines the process of analyzing RNA dynamics from high-throughput sequencing data.