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

Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.2K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

3.9K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
3.9K
DNA as a Genetic Template02:05

DNA as a Genetic Template

21.7K
Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
21.7K

You might also read

Related Articles

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

Sort by
Same author

Decoding Immune Regulation: From Genetic Variation to Mechanism Through Single-Cell Genomics.

Immune network·2026
Same author

Artificial intelligence and machine learning: an important new set of tools for clinical shoulder arthroplasty research.

JSES international·2026
Same author

Replaying germinal center evolution on a quantified affinity landscape.

Cell·2026
Same author

Extending structural surfaceomics to identify aberrant conformations of tumor surface proteins as potential immunotherapy targets.

bioRxiv : the preprint server for biology·2026
Same author

FastGxC: Fast and powerful context-specific eQTL mapping in bulk and single-cell data.

Cell genomics·2026
Same author

Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining.

Genome research·2026

Related Experiment Video

Updated: Jun 8, 2025

Use of Alu Element Containing Minigenes to Analyze Circular RNAs
13:10

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Published on: March 10, 2020

7.3K

Learning antibody sequence constraints from allelic inclusion.

Milind Jagota1, Chloe Hsu1, Thomas Mazumder2

  • 1Computer Science Division, UC Berkeley, Berkeley, CA USA.

Biorxiv : the Preprint Server for Biology
|November 1, 2024
PubMed
Summary
This summary is machine-generated.

Allelic inclusion in naive B cells reveals novel antibody sequence constraints. Machine learning models trained on these rare cells predict antibody properties more accurately than existing methods.

More Related Videos

Immunoglobulin Gene Sequence Analysis In Chronic Lymphocytic Leukemia: From Patient Material To Sequence Interpretation
09:02

Immunoglobulin Gene Sequence Analysis In Chronic Lymphocytic Leukemia: From Patient Material To Sequence Interpretation

Published on: November 26, 2018

21.0K
Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation
08:07

Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation

Published on: September 6, 2017

10.1K

Related Experiment Videos

Last Updated: Jun 8, 2025

Use of Alu Element Containing Minigenes to Analyze Circular RNAs
13:10

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Published on: March 10, 2020

7.3K
Immunoglobulin Gene Sequence Analysis In Chronic Lymphocytic Leukemia: From Patient Material To Sequence Interpretation
09:02

Immunoglobulin Gene Sequence Analysis In Chronic Lymphocytic Leukemia: From Patient Material To Sequence Interpretation

Published on: November 26, 2018

21.0K
Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation
08:07

Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation

Published on: September 6, 2017

10.1K

Area of Science:

  • Immunology
  • Computational Biology
  • Genomics

Background:

  • B cells produce antibodies and B-cell receptors (BCRs) comprising heavy and light chains.
  • Allelic exclusion typically ensures a single heavy and light chain pair per B cell.
  • Allelic inclusion, where B cells express two productive light chains, is a rare but informative phenomenon.

Purpose of the Study:

  • To investigate the potential of allelic inclusion in naive B cells for learning antibody sequence constraints.
  • To develop machine learning models for identifying abnormal antibody sequences from allelic inclusion data.
  • To compare the predictive power of models trained on allelic inclusion data with existing antibody modeling approaches.

Main Methods:

  • Analysis of large-scale single-cell sequencing data from human naive B cells.
  • Training machine learning models to identify aberrant light chain sequences in B cells exhibiting allelic inclusion.
  • Evaluating model correlations with antibody properties like polyreactivity, surface expression, and affinity maturation usage.
  • Investigating heavy chain diversity and selection forces in mice, considering surrogate light chain pairing.

Main Results:

  • Thousands of human naive B cells with light chain allelic inclusion were identified, significantly expanding available datasets.
  • Trained machine learning models demonstrated strong correlations with antibody properties not used in training.
  • These correlations surpassed those achieved by current antibody modeling techniques, highlighting the value of allelic inclusion data.
  • Heavy chain diversity in mice was found to be significantly restricted by pairing with surrogate light chains.

Conclusions:

  • Allelic inclusion in naive B cells provides a valuable source of information for understanding antibody sequence constraints.
  • Machine learning models leveraging allelic inclusion data offer improved prediction of antibody characteristics.
  • The findings suggest that allelic inclusion is a more prevalent phenomenon than previously thought and holds significant potential for antibody engineering and research.