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

Logic functions of the genomic cis-regulatory code.

Sorin Istrail1, Eric H Davidson

  • 1Applied Biosystems/Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA.

Proceedings of the National Academy of Sciences of the United States of America
|March 25, 2005
PubMed
Summary

Regulatory elements in DNA act like logic gates, processing transcription factor inputs to control gene expression during development. This study explores these cis-regulatory logic operations to decode the genome.

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

Michael Waterman's Contributions to Computational Biology and Bioinformatics.

Journal of computational biology : a journal of computational molecular cell biology·2022
Same author

Proteinarium: Multi-sample protein-protein interaction analysis and visualization tool.

Genomics·2020
Same author

Combinatorial and statistical prediction of gene expression from haplotype sequence.

Bioinformatics (Oxford, England)·2020
Same author

Preface Special Issue: RECOMB 2018.

Journal of computational biology : a journal of computational molecular cell biology·2020
Same author

Eric Davidson's Regulatory Genome for Computer Science: Causality, Logic, and Proof Principles of the Genomic <i>cis</i>-Regulatory Code.

Journal of computational biology : a journal of computational molecular cell biology·2019
Same author

How Does the Regulatory Genome Work?

Journal of computational biology : a journal of computational molecular cell biology·2019

Area of Science:

  • Genomics
  • Developmental Biology
  • Systems Biology

Background:

  • Cis-regulatory modules are crucial for orchestrating gene expression during development.
  • These modules integrate signals from transcription factors via specific DNA binding sites.
  • Understanding their function is key to deciphering the genomic regulatory code.

Purpose of the Study:

  • To illustrate the diverse range of cis-regulatory logic operations.
  • To provide a framework for interpreting the functional logic of gene regulation.
  • To advance the understanding of the genomic regulatory code.

Main Methods:

  • Modeling cis-regulatory processing functions as logic operations.
  • Analyzing both combinatorial (multiple sites) and unitary (single site) logic gates.

Related Experiment Videos

  • Illustrating the repertoire of these logic operations.

    • Main Results:

    • Cis-regulatory modules function through logic operations, processing transcription factor inputs.
    • Both combinatorial and unitary logic operations are employed by these modules.
    • A comprehensive view of cis-regulatory logic operations is presented.

    Conclusions:

    • Cis-regulatory logic operations are fundamental to developmental gene expression.
    • This work offers a functional interpretation of the genomic regulatory code.
    • The study highlights the importance of logic-based analysis in genomics.