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

CRISPR01:59

CRISPR

Genome editing technologies allow scientists to modify an organism’s DNA via the addition, removal, or rearrangement of genetic material at specific genomic locations. These types of techniques could potentially be used to cure genetic disorders such as hemophilia and sickle cell anemia. One popular and widely used DNA-editing research tool that could lead to safe and effective cures for genetic disorders is the CRISPR-Cas9 system. CRISPR-Cas9 stands for Clustered Regularly Interspaced Short...
CRISPR01:59

CRISPR

Genome editing technologies allow scientists to modify an organism’s DNA via the addition, removal, or rearrangement of genetic material at specific genomic locations. These types of techniques could potentially be used to cure genetic disorders such as hemophilia and sickle cell anemia. One popular and widely used DNA-editing research tool that could lead to safe and effective cures for genetic disorders is the CRISPR-Cas9 system. CRISPR-Cas9 stands for Clustered Regularly Interspaced Short...
CRISPR and crRNAs02:53

CRISPR and crRNAs

Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...
CRISPR/Cas9 Genome Editing01:28

CRISPR/Cas9 Genome Editing

The CRISPR-Cas system serves as a bacterial defense mechanism against invading genetic elements such as viruses and plasmids, forming the foundation for its adaptation as a powerful genome-editing tool. Originally discovered in prokaryotes, this system has been repurposed to revolutionize genetic engineering across a wide range of organisms, including plants, animals, and humans. The core component, Cas9, is an endonuclease derived from Streptococcus pyogenes, capable of introducing...

You might also read

Related Articles

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

Sort by
Same author

Digital tools and biomarkers for cognitive screening: A systematic review.

Digital health·2026
Same author

Enhanced B-N coordinated dynamic boronate chemistry for recyclable thermosets with elevated stability.

Nature communications·2026
Same author

On the robustness of truncated negative binomial regression model: application to field epidemiology.

Journal of applied statistics·2026
Same author

CerS2 is a druggable target in triple-negative breast cancer.

Molecular cancer therapeutics·2026
Same author

Aberrant immune regulation and enrichment of stem-like CD8<sup>+</sup> T cells in the pancreatic lymph node during type 1 diabetes development.

bioRxiv : the preprint server for biology·2026
Same author

scDEcrypter: Uncertainty-aware differential expression analysis for viral infection in scRNA-seq.

bioRxiv : the preprint server for biology·2026
Same journal

Layered social competition coordinates reproductive hierarchy formation in ants.

bioRxiv : the preprint server for biology·2026
Same journal

Combination epigenetic-targeted therapy increases the immunogenicity of poorly immunogenic sarcomas.

bioRxiv : the preprint server for biology·2026
Same journal

Loss of LanC-like proteins delays post-injury regeneration of aging skeletal muscles.

bioRxiv : the preprint server for biology·2026
Same journal

Integrative Transfer Network: Deep Transfer Learning Across Populations and Prediction Targets.

bioRxiv : the preprint server for biology·2026
Same journal

Confidence-supported label-free metabolic imaging with FPhaS phase autofluorescence microscopy.

bioRxiv : the preprint server for biology·2026
Same journal

Sequence-encoded autoinhibition couples mRNA decapping activity to phase separation.

bioRxiv : the preprint server for biology·2026
See all related articles

Related Experiment Video

Updated: May 26, 2026

Pooled CRISPR-Based Genetic Screens in Mammalian Cells
09:05

Pooled CRISPR-Based Genetic Screens in Mammalian Cells

Published on: September 4, 2019

simCRISPR: Modeling Experimental Complexity in Pooled CRISPR Screens.

Zhaohan Zhu1, Xiaoru Dong2,3, Chanhee Kim4

  • 1Department of Biostatistics, University of Florida, Gainesville, FL, USA.

Biorxiv : the Preprint Server for Biology
|May 25, 2026
PubMed
Summary
This summary is machine-generated.

Pooled CRISPR screens help study gene function. A new tool, simCRISPR, aids in analyzing gene-by-environment interactions by simulating screen data, improving analysis accuracy.

More Related Videos

Genome-Wide CRISPR Screen for Unveiling Radiosensitive and Radioresistant Genes
08:32

Genome-Wide CRISPR Screen for Unveiling Radiosensitive and Radioresistant Genes

Published on: May 23, 2025

Related Experiment Videos

Last Updated: May 26, 2026

Pooled CRISPR-Based Genetic Screens in Mammalian Cells
09:05

Pooled CRISPR-Based Genetic Screens in Mammalian Cells

Published on: September 4, 2019

Genome-Wide CRISPR Screen for Unveiling Radiosensitive and Radioresistant Genes
08:32

Genome-Wide CRISPR Screen for Unveiling Radiosensitive and Radioresistant Genes

Published on: May 23, 2025

Area of Science:

  • Genomics
  • Computational Biology
  • Genetic Screening

Background:

  • Pooled CRISPR screens are essential for gene function and interaction studies.
  • Analyzing gene-by-environment (GxE) interactions is challenging due to lack of ground truth and inadequate simulation tools.

Purpose of the Study:

  • To develop a flexible simulation framework, simCRISPR, for generating pooled CRISPR screen data.
  • To benchmark computational methods for GxE interaction detection using simulated data.

Main Methods:

  • Developed simCRISPR, a simulation framework for complex CRISPR screen designs.
  • Evaluated analysis methods, comparing safe-harbor vs. non-targeting sgRNA normalization.
  • Assessed empirical log2 fold-change (FC) thresholds as an effect-size criterion.

Main Results:

  • Safe-harbor normalization enhanced GxE interaction detection, especially with DNA damage effects.
  • Combining safe-harbor normalization with empirical log2 FC thresholding improved DESeq2 analysis.
  • Applied workflow to doxorubicin GxE screen, reducing bias and identifying relevant candidates.

Conclusions:

  • simCRISPR provides a robust platform for simulating CRISPR screen data for GxE interaction analysis.
  • Safe-harbor normalization is a valuable strategy for improving the accuracy of GxE interaction detection in pooled CRISPR screens.
  • The developed workflow enhances the identification of biologically relevant genetic interactions under environmental stress.