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

Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

6.9K
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
6.9K
What is Variation?01:14

What is Variation?

18.6K
Apart from the measures of central tendency, distribution, outliers, and the changing characteristics of data with time, an important characteristic of any data set is its variation or spread. In some data sets, the data values are concentrated closely near the mean; in others, the data values are more widely spread out from the mean.
The range, standard deviation, standard error, and variance are the different measures of variation.
Range: The range is the difference between its maximum and...
18.6K
Language01:16

Language

921
Language is a unique communication system that uses words and systematic rules to organize and transmit information. Unlike other forms of communication, which may involve postures, movements, odors, or vocalizations, language relies on symbols and grammar. This makes human communication distinct from that of other species, who also communicate but do not use language in the same way humans do.
Corballis and Suddendorf (2007) and Tomasello and Rakoczy (2003) highlight the role of language in...
921
Self Within Cultural Contexts01:30

Self Within Cultural Contexts

243
Cultural frameworks for understanding the self are often categorized into two broad orientations: individualism and collectivism. These paradigms influence how people define themselves, relate to others, and interpret their social worlds. Each orientation offers distinct perspectives on autonomy, responsibility, and the role of the individual within a community.Individualistic CulturesIn individualistic cultures like North America and Western Europe, identity is understood as autonomous and...
243
Variation01:19

Variation

8.1K
An important characteristic of any set of data is the variation in the data. In some data sets, the data values are concentrated closely near the mean; in other data sets, the data values are more widely spread out from the mean. The most common measure of variation, or spread, is the standard deviation, which is the square root of variance.
When independent and dependent variables are plotted on a scatter plot, the slope of a line is a value that describes the rate of change between the two...
8.1K
Components of Language01:24

Components of Language

830
Language, whether spoken, signed, or written, consists of specific components: lexicon and grammar. The lexicon is the vocabulary of a language, comprising its words. Grammar is the set of rules used to convey meaning through the lexicon. For example, English grammar adds “-ed” to most verbs to indicate past tense. Words are formed by combining phonemes, which are the basic sound units of a language. Different languages have different sets of phonemes (e.g., “ah” vs.
830

You might also read

Related Articles

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

Sort by
Same author

Imaging-Pathology Discordance During Neoadjuvant Chemotherapy for Pediatric Osteosarcoma.

Pediatrics international : official journal of the Japan Pediatric Society·2026
Same author

Forecasting virus evolution by integrating genotype-phenotype-epidemiology.

Nature microbiology·2026
Same author

Genetic diversity of pangolin coronaviruses reveals a key immuno-evasive substitution at spike residue 519.

Journal of virology·2026
Same author

Letter to the Editor: Primary Extraosseous Ewing Sarcoma of the Right L5 Nerve Root Mimicking a Schwannoma.

Journal of pediatric hematology/oncology·2026
Same author

Programmable antibody-based chimeric entry receptors for sarbecoviruses.

Communications biology·2026
Same author

Author Correction: Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant.

Nature·2026

Related Experiment Video

Updated: Feb 12, 2026

Augmenting Large Language Models via Vector Embeddings to Improve Domain-Specific Responsiveness
03:14

Augmenting Large Language Models via Vector Embeddings to Improve Domain-Specific Responsiveness

Published on: December 6, 2024

1.2K

Inferring context-specific site variation with evotuned protein language models.

Spyros Lytras1, Adam Strange1, Jumpei Ito1,2

  • 1Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.

NAR Genomics and Bioinformatics
|February 11, 2026
PubMed
Summary
This summary is machine-generated.

Protein language models (pLMs) offer a new way to study protein diversity from single sequences. A novel pLM-based entropy metric effectively predicts site variability, especially when models are fine-tuned on related proteins.

More Related Videos

Eye Tracking During Visually Situated Language Comprehension: Flexibility and Limitations in Uncovering Visual Context Effects
07:36

Eye Tracking During Visually Situated Language Comprehension: Flexibility and Limitations in Uncovering Visual Context Effects

Published on: November 30, 2018

16.4K
Split-BioID — Proteomic Analysis of Context-specific Protein Complexes in Their Native Cellular Environment
09:02

Split-BioID — Proteomic Analysis of Context-specific Protein Complexes in Their Native Cellular Environment

Published on: April 20, 2018

20.5K

Related Experiment Videos

Last Updated: Feb 12, 2026

Augmenting Large Language Models via Vector Embeddings to Improve Domain-Specific Responsiveness
03:14

Augmenting Large Language Models via Vector Embeddings to Improve Domain-Specific Responsiveness

Published on: December 6, 2024

1.2K
Eye Tracking During Visually Situated Language Comprehension: Flexibility and Limitations in Uncovering Visual Context Effects
07:36

Eye Tracking During Visually Situated Language Comprehension: Flexibility and Limitations in Uncovering Visual Context Effects

Published on: November 30, 2018

16.4K
Split-BioID — Proteomic Analysis of Context-specific Protein Complexes in Their Native Cellular Environment
09:02

Split-BioID — Proteomic Analysis of Context-specific Protein Complexes in Their Native Cellular Environment

Published on: April 20, 2018

20.5K

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Artificial Intelligence in Protein Science

Background:

  • Multiple sequence alignments (MSAs) traditionally analyze protein site-specific diversity.
  • Protein language models (pLMs) show promise in capturing protein properties from single sequences.
  • pLMs bypass the need for aligned sequences, offering a distinct advantage over MSAs.

Purpose of the Study:

  • To introduce a novel Context-Dependent Entropy metric utilizing pLM embeddings.
  • To assess protein site conservation and variability using the new pLM-based metric.
  • To evaluate the impact of fine-tuning pLMs on evolutionary related protein families.

Main Methods:

  • Developed a Context-Dependent Entropy metric leveraging pLM embeddings.
  • Employed two prominent pLMs (ESM-2, protT5) for metric calculation.
  • Fine-tuned pLMs ('evotuning') on hemagglutinin protein diversity from Influenza A virus subtypes.

Main Results:

  • The pLM entropy metric successfully identifies sites prone to change within specific sequence contexts.
  • Evotuning pLMs enhanced their ability to capture the diversity of related protein families.
  • Demonstrated the efficacy of pLM embeddings as an alternative to MSAs for diversity analysis.

Conclusions:

  • The pLM-based entropy metric is a viable tool for assessing protein site variability.
  • Fine-tuning pLMs improves their performance in understanding protein family-specific evolutionary dynamics.
  • This approach offers a powerful, sequence-centric alternative for protein diversity studies.