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

Fermentation01:29

Fermentation

Most eukaryotic organisms require oxygen to survive and function adequately. Such organisms produce large amounts of energy during aerobic respiration by metabolizing glucose and oxygen into carbon dioxide and water. However, most eukaryotes can generate some energy in the absence of oxygen by anaerobic metabolism.
Fermentation is a type of metabolic process that occurs in the absence of oxygen, where organic molecules such as glucose are broken down to produce energy. During this process, the...
Microbial Fermentation01:23

Microbial Fermentation

Fermentation is a crucial anaerobic metabolic process that enables microbes to derive energy from sugar without relying on oxygen or an electron transport chain. This process is fundamental to various biological and industrial applications and is classified based on the metabolic products generated.Role of Pyruvate in FermentationPyruvate and its derivatives serve as key electron acceptors in fermentative pathways. The oxidation of NADH to regenerate NAD+ is essential for the continuation of...
Microbes in the Production of Fermented Foods01:27

Microbes in the Production of Fermented Foods

Lactic acid bacteria (LAB) and molds are instrumental in fermenting plant-based foods to enhance preservation and ensure year-round availability. These microbial processes convert plant carbohydrates into organic acids and other metabolites that inhibit spoilage organisms and contribute to the sensory qualities of the final product.In sauerkraut production, cabbage goes through a microbial succession that starts with cocci such as Leuconostoc mesenteroides. These microbes begin fermentation by...
Methods to Assess Microbial Communities01:19

Methods to Assess Microbial Communities

Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
Automated Microbial Diagnostics01:24

Automated Microbial Diagnostics

Automated diagnostic analyzers have transformed clinical microbiology by providing rapid and reliable methods for pathogen identification and antibiotic susceptibility testing. Among these systems, the Vitek 2 is widely used because it automates the traditionally labor-intensive processes of microbial identification (ID) and antibiotic susceptibility testing (AST), delivering standardized and timely results that are essential for effective patient care.Microbial Identification with ID CardsThe...
Microbes in Beverage Production01:25

Microbes in Beverage Production

Alcoholic beverages such as wine, beer, and spirits are the products of microbial fermentation processes that transform simple sugars into ethanol and a wide array of complex flavor compounds. These transformations rely on the metabolic activities of specific yeasts and bacteria, which are selected and controlled to yield the desired beverage characteristics.Wine Fermentation and MaturationWine production begins with the crushing of grapes to release juice and pulp, forming a must that is...

You might also read

Related Articles

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

Sort by
Same author

Human CD8-iTreg are potent GVHD suppressors and tumoricidal effectors by release of Granzyme-K <sup>+</sup> Supramolecular Attack Particles.

bioRxiv : the preprint server for biology·2026
Same author

PTPN22 regulates T cell synapse formation through PSTPIP1-dependent actin remodeling.

Science signaling·2026
Same author

PD-1 signaling and PD-1 blockade-mediated tumor control are established at microvillar T cell contacts.

Science immunology·2026
Same author

<i>Trans</i>-eQTLs reveal the architecture of human gene regulatory networks.

medRxiv : the preprint server for health sciences·2026
Same author

Kv1.3 palmitoylation regulates spatial distribution and channel removal from the immunological synapse.

Cellular and molecular life sciences : CMLS·2026
Same author

isMap - immunological synapse map analysis program.

Frontiers in immunology·2026

Related Experiment Video

Updated: Jul 9, 2026

Profiling the Bacterial Community of Fermenting Traminette Grapes during Wine Production using Metagenomic Amplicon Sequencing
07:34

Profiling the Bacterial Community of Fermenting Traminette Grapes during Wine Production using Metagenomic Amplicon Sequencing

Published on: December 1, 2023

VDJ-REMIX: REpertoire Module Identification and eXploration.

Sakina Amin1, Lauren Overend2, Felicia Tucci2

  • 1Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.

Bioinformatics (Oxford, England)
|July 7, 2026
PubMed
Summary
This summary is machine-generated.

VDJ-REMIX is a new R package that analyzes adaptive immune receptor repertoire data. It identifies distinct immune cell signatures in various diseases, aiding biomarker discovery.

More Related Videos

Workflow Based on the Combination of Isotopic Tracer Experiments to Investigate Microbial Metabolism of Multiple Nutrient Sources
12:47

Workflow Based on the Combination of Isotopic Tracer Experiments to Investigate Microbial Metabolism of Multiple Nutrient Sources

Published on: January 22, 2018

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
15:07

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

Published on: December 28, 2015

Related Experiment Videos

Last Updated: Jul 9, 2026

Profiling the Bacterial Community of Fermenting Traminette Grapes during Wine Production using Metagenomic Amplicon Sequencing
07:34

Profiling the Bacterial Community of Fermenting Traminette Grapes during Wine Production using Metagenomic Amplicon Sequencing

Published on: December 1, 2023

Workflow Based on the Combination of Isotopic Tracer Experiments to Investigate Microbial Metabolism of Multiple Nutrient Sources
12:47

Workflow Based on the Combination of Isotopic Tracer Experiments to Investigate Microbial Metabolism of Multiple Nutrient Sources

Published on: January 22, 2018

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
15:07

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

Published on: December 28, 2015

Area of Science:

  • Immunology
  • Bioinformatics
  • Computational Biology

Background:

  • High-throughput sequencing of adaptive immune receptor repertoires (AIRR) offers deep insights into immunity.
  • Interpreting complex, high-dimensional AIRR data is challenging due to multi-collinearity, diverse data types, and missing values.
  • Existing dimensionality reduction methods are often inadequate for AIRR data.

Purpose of the Study:

  • To introduce VDJ-REMIX, an R package designed for robust analysis of AIRR data.
  • To provide a network-based framework for deconstructing complex repertoire features into interpretable modules.
  • To enable systematic exploration of immunological variation and facilitate biomarker discovery.

Main Methods:

  • VDJ-REMIX refactors weighted correlation network analysis (WGCNA) for immune repertoire data.
  • It offers a tailored workflow including preprocessing, imputation, and modularization.
  • The package is implemented in R and available on GitHub.

Main Results:

  • VDJ-REMIX identified distinct B cell signatures in autoimmune patients, stratifying diseases and responses to therapy.
  • It differentiated disease-specific signatures from shared severe infection responses in sepsis and COVID-19 patients.
  • Analysis of B cell populations and single-cell multi-omics data revealed biologically coherent immune repertoire modules linked to specific immune programs and disease contexts.

Conclusions:

  • VDJ-REMIX is a versatile tool for analyzing complex immune repertoire data.
  • The package facilitates the discovery of biologically interpretable modules and potential biomarkers.
  • It enhances the understanding of adaptive immunity across diverse immunological contexts.