Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

In-vitro Mutagenesis

In-vitro Mutagenesis

To learn more about the function of a gene, researchers can observe what happens when the gene is inactivated or “knocked out,” by creating genetically engineered knockout animals. Knockout mice have been particularly useful as models for human diseases such as cancer, Parkinson’s disease, and diabetes.

You might also read

Related Articles

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

Sort by

Same author

Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals <i>Lactobacillus crispatus</i> accessory genes associated with cervical dysplasia.

mSystems·2026

Same author

Linkage of nucleotide and functional diversity varies across gut bacteria.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

Machine learning-predicted chromatin organization landscape across pediatric tumors.

Scientific reports·2026

Same author

Structural variants in human congenital heart disease disrupt distal genomic regulatory contacts of developmental genes.

bioRxiv : the preprint server for biology·2026

Same author

Species-specific chromatin architecture and neurogenesis mediated by a human enhancer.

Cell stem cell·2026

Same author

An integrated view of the structure and function of the human 4D nucleome.

Nature·2025

Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026

Same journal

SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping.

Bioinformatics (Oxford, England)·2026

Same journal

CSCN: Inference of Cell-Specific Causal Networks Using Single-Cell RNA-Seq Data.

Bioinformatics (Oxford, England)·2026

Same journal

Sparse CCA-Based Mediation Analysis with High-Dimensional Exposures and Mediators.

Bioinformatics (Oxford, England)·2026

Same journal

Enhancing Cross-Context Generalization in Drug Perturbation Prediction with a Multimodal Conditional Diffusion Framework.

Bioinformatics (Oxford, England)·2026

Same journal

Primer Design through Submodular Function Estimation.

Bioinformatics (Oxford, England)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 25, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models.

Ketrin Gjoni^1,2, Katherine S Pollard^1,2,3

¹Institute of Data Science and Biotechnology, Gladstone Institutes, 1650 Owens Street, San Francisco, CA 94158, United States.

Bioinformatics (Oxford, England)

|May 25, 2024

Summary

This summary is machine-generated.

Sequence Mutator for Predictive Models (SuPreMo) is a new tool for in silico mutagenesis experiments. It helps prioritize pathogenic variants and discover functional sequences using machine learning models.

More Related Videos

Implementation of In Vitro Drug Resistance Assays: Maximizing the Potential for Uncovering Clinically Relevant Resistance Mechanisms

Implementation of In Vitro Drug Resistance Assays: Maximizing the Potential for Uncovering Clinically Relevant Resistance Mechanisms

Published on: December 9, 2015

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

Published on: August 20, 2019

Related Experiment Videos

Last Updated: Jun 25, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Implementation of In Vitro Drug Resistance Assays: Maximizing the Potential for Uncovering Clinically Relevant Resistance Mechanisms

Implementation of In Vitro Drug Resistance Assays: Maximizing the Potential for Uncovering Clinically Relevant Resistance Mechanisms

Published on: December 9, 2015

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

Published on: August 20, 2019

Area of Science:

Genomics
Bioinformatics
Machine Learning

Background:

Sequence-based machine learning models require effective sequence manipulation tools.
Existing genome editing tools have limitations with structural variants and identifying causative sequence changes.

Purpose of the Study:

To introduce Sequence Mutator for Predictive Models (SuPreMo), a tool designed to overcome limitations in current in silico mutagenesis methods.
To enable efficient manipulation and evaluation of genome sequences for machine learning applications.

Main Methods:

SuPreMo is a Python-based tool that generates reference and perturbed sequences.
It supports in silico mutagenesis experiments and provides 3D genome disruption scores.
The tool is designed for scalability and ease of use, runnable with a single line of code.

Main Results:

SuPreMo facilitates the use of machine learning models with edited genome sequences.
It aids in prioritizing pathogenic variants.
The tool assists in the discovery of novel functional sequences.

Conclusions:

SuPreMo addresses key bottlenecks in sequence manipulation for predictive modeling.
It offers a comprehensive and scalable solution for in silico mutagenesis.
The tool enhances the application of machine learning in genomic research.