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 Experiment Videos

Text-mining assisted regulatory annotation.

Stein Aerts1, Maximilian Haeussler, Steven van Vooren

  • 1Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven, B-3000, Belgium. stein.aerts@med.kuleuven.be

Genome Biology
|February 15, 2008
PubMed
Summary
This summary is machine-generated.

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

Case Report: Synchronous Manifestations of Kaposi Sarcoma Herpesvirus-Associated Disorders.

Cancer reports (Hoboken, N.J.)·2026
Same author

Intrinsic coordination of dynamic molecular signatures shape the human prefrontal cortex.

bioRxiv : the preprint server for biology·2026
Same author

Adjuvant personalized multivalent neoantigen DNA vaccination for MGMT unmethylated glioblastoma: a phase 1 trial.

Nature cancer·2026
Same author

ClinGen API platform for classification of human genetic variants.

Cell genomics·2026
Same author

An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory network dynamics across cardiac development, aging, and disease.

Genome biology·2026
Same author

NT-I7, a Long-Acting Interleukin 7, Increases Lymphocyte Counts and Induces CD8+ T-cell Clonotype Expansion in Patients with Newly Diagnosed High-Grade Gliomas.

Clinical cancer research : an official journal of the American Association for Cancer Research·2026
Same journal

Integrated lipidomic and transcriptomic profiling of the host response in human malaria.

Genome biology·2026
Same journal

Centromeric satellite expansion drives genome evolution in the snowy owl.

Genome biology·2026
Same journal

Mapping the landscape of allele-specific expression in porcine genomes.

Genome biology·2026
Same journal

Genomic sequence evolution underlying human neocortical interareal diversification.

Genome biology·2026
Same journal

Regulatory mechanisms driven by functional 3'-UTR variants in alcohol use disorder and related traits.

Genome biology·2026
Same journal

A longitudinal single-nucleus transcriptomic atlas of bovine placentation reveals dynamic cellular hierarchies and regulatory programs.

Genome biology·2026
See all related articles

We developed text-mining methods to unlock vast amounts of hidden cis-regulatory data in scientific literature. This approach aids in annotating transcriptional regulatory networks, advancing gene regulation research.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Decoding transcriptional regulatory networks and their genomic cis-regulatory logic is a key challenge in genome biology.
  • Current analyses heavily depend on prior experimental data, with much existing regulatory information inaccessible in the literature.

Purpose of the Study:

  • To develop and apply text-mining strategies for extracting cis-regulatory sequence information from biomedical literature.
  • To enhance the annotation of transcriptional regulatory networks by leveraging previously undiscovered data.

Main Methods:

  • Utilized a vector space model to identify Medline abstracts with high cis-regulatory content.
  • Developed text-mining approaches to extract DNA sequences and associated genomic information from publications.

Related Experiment Videos

  • Mapped extracted DNA sequences to genome sequences for annotation.

    • Main Results:

    • Demonstrated that relevance ranking of documents can aid in curating transcriptional regulatory networks.
    • Estimated that at least 30,000 papers contain unannotated cis-regulatory data.
    • Successfully extracted DNA sequences and mapped them to identify organism, location, and target gene information.

    Conclusions:

    • Text-mining technologies can be integrated with genome annotation systems.
    • This integration increases the availability of annotated cis-regulatory data.
    • Accelerates advancements in the field of gene regulation research.