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 Video

Updated: Jul 31, 2025

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

1.0K

An improved algorithm for inferring mutational parameters from bar-seq evolution experiments.

Fangfei Li1, Aditya Mahadevan2, Gavin Sherlock3

  • 1Department of Genetics, Stanford University, Stanford, California, US.

BMC Genomics
|May 6, 2023
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

The germline MLH1 c.2054 C>T mutation disrupts DNA mismatch repair and is detectable by digital PCR.

Cancer letters·2026
Same author

Prepregnancy GLP-1RA Exposure and Risk of Hypertensive Disorders of Pregnancy Among Women With Obesity and Diabetes.

Obesity (Silver Spring, Md.)·2026
Same author

Pressure-induced formation of KBr monohydrate and bromide substitution effects in alkali halide monohydrates.

iScience·2026
Same author

Pressure-Induced Evolution of Structure and Conduction Mechanism Transition in Ba<sub>0.5</sub>Sr<sub>0.5</sub>TiO<sub>3</sub>.

Inorganic chemistry·2026
Same author

Intracellular sclerostin promotes tumor progression and metastasis as a potential therapeutic target in triple-negative breast cancer.

Cell reports. Medicine·2026
Same author

Icariin Enhances the Enzymatic Activity of N-acetylgalactosaminidase to Augment Akkermansia Abundance in Gut Microbiota for Improved PD-1 Blockade Efficacy in Tumor Suppression.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same journal

Chromosomal scale genome assembly of medicinal plant Sophora tonkinensis.

BMC genomics·2026
Same journal

Variant-specific RNA testing resolves variants of uncertain significance in exome testing.

BMC genomics·2026
Same journal

Kaiso overexpression promotes an interferon immune response in murine intestines.

BMC genomics·2026
Same journal

Genomic evidence of ecological flexibility and cross-niche CRISPR spacerome targeting phage-plasmid hybrids in Latilactobacillus curvatus.

BMC genomics·2026
Same journal

Fgf evolution in vertebrates: insights from cyclostomes.

BMC genomics·2026
Same journal

Metabolic reprogramming, oxidative stress, and mitophagy in JSRV Env-transformed BEAS-2B cells: insights from integrated transcriptomics and metabolomics.

BMC genomics·2026
See all related articles

This study introduces a new algorithm to infer beneficial mutations from genetic barcode sequencing data. The improved method accurately identifies more adaptive mutations and their parameters, even with low read depth.

Area of Science:

  • Microbial Evolution
  • Computational Biology
  • Genomics

Background:

  • Genetic barcoding enables high-throughput tracking of microbial lineage frequencies.
  • Inferring evolutionary dynamics from barcode data remains challenging.

Purpose of the Study:

  • To develop an algorithm for inferring fitness effects and establishment times of beneficial mutations from barcode sequencing data.
  • To improve upon existing Bayesian inference methods for microbial evolution.

Main Methods:

  • Developed a novel algorithm building on Bayesian inference.
  • Enforced self-consistency between population mean fitness and individual mutation effects.
  • Tested the method on simulations of 40,000 barcoded lineages in serial batch culture.
Keywords:
Experimental evolutionGenetic barcodingInference

More Related Videos

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.1K
Competitive Genomic Screens of Barcoded Yeast Libraries
11:59

Competitive Genomic Screens of Barcoded Yeast Libraries

Published on: August 11, 2011

18.4K

Related Experiment Videos

Last Updated: Jul 31, 2025

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

1.0K
Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.1K
Competitive Genomic Screens of Barcoded Yeast Libraries
11:59

Competitive Genomic Screens of Barcoded Yeast Libraries

Published on: August 11, 2011

18.4K

Main Results:

  • The new algorithm outperforms its predecessor in inferring mutational parameters.
  • Identified a greater number of adaptive mutations.
  • Achieved more accurate inference of mutational parameters, especially with low read depth.

Conclusions:

  • The algorithm is particularly effective for low read depth data.
  • The Python code for simulations and inference methods is available on GitHub.
  • Aims to facilitate broader use within the microbial evolution community.