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

Genomics02:02

Genomics

36.8K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
36.8K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.1K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.1K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

77
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
77
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

19.1K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
19.1K
Synteny and Evolution02:31

Synteny and Evolution

3.3K
John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
3.3K
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

8.1K
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
8.1K

You might also read

Related Articles

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

Sort by
Same author

CD4/CD8 ratio is associated with structural reorganization of vaccine-induced immune responses in people living with HIV.

Frontiers in immunology·2026
Same author

Sulfur mustard exposure induces inflammatory injury by Dnmt3b-mediated DNA methylation via oleic acid accumulation in Treg cells.

Chemico-biological interactions·2026
Same author

An in vivo fitness gene of Toxoplasma, MIC11, is essential for PLP1-mediated egress from host cells.

Nature communications·2026
Same author

Human DHX29 detects nonoptimal codon usage to regulate mRNA stability.

Science (New York, N.Y.)·2026
Same author

Regnase-1-mediated regulation of neutrophils modulates SARS-CoV-2 pneumonia.

PLoS pathogens·2026
Same author

Multiple protease-activated probody-drug conjugates for treating CD147-positive ovarian cancer with limited toxicity.

Pharmacological research·2026
Same journal

Navigating the labyrinth of drugging the disordered.

Biophysical reviews·2026
Same journal

<i>Biophysical Reviews</i>: a forum for publication of review articles from the international biophysics community.

Biophysical reviews·2026
Same journal

Mitochondrial potassium channels: mitochondria-specific mechanism of regulation.

Biophysical reviews·2026
Same journal

Biomolecular condensates in living systems: from function to disease. What to do next.

Biophysical reviews·2026
Same journal

Astrocyte morphology: complex or trivial?

Biophysical reviews·2026
Same journal

Correction to: A quest for greater thermodynamic rigour in the quantitative characterization of protein self-association by direct assessment of sedimentation equilibrium distributions.

Biophysical reviews·2026
See all related articles

Related Experiment Video

Updated: Aug 16, 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

The evolution of structural genomics.

Daron M Standley1, Tokuichiro Nakanishi1, Zichang Xu1

  • 1Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, 565-0871 Japan.

Biophysical Reviews
|December 20, 2022
PubMed
Summary
This summary is machine-generated.

Structural genomics initiatives generated numerous protein structures, driving advancements in data science and deep learning. This led to a revolution in computational molecular biology, with research from Protein Data Bank Japan (PDBj) continuing to impact the field.

Keywords:
Deep learningFold spaceProtein Data BankProtein structure predictionStructural alignmentStructural genomics

More Related Videos

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.3K
A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

9.7K

Related Experiment Videos

Last Updated: Aug 16, 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
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.3K
A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

9.7K

Area of Science:

  • Computational molecular biology
  • Structural genomics
  • Bioinformatics and data science

Background:

  • The 1990s saw the rise of structural genomics, aiming to map all protein structures.
  • This effort yielded a vast number of protein structures, many with unassigned functions.
  • The initial value of structural genomics was debated, but its impact extended beyond solved structures.

Purpose of the Study:

  • To review computational research from the Protein Data Bank Japan (PDBj) during the Protein 3000 project.
  • To highlight the long-term impact of structural genomics on computational molecular biology.
  • To showcase the contributions of Haruki Nakamura's leadership at PDBj.

Main Methods:

  • Analysis of computational research outputs from the Protein Data Bank Japan (PDBj).
  • Review of infrastructure and data science efforts spurred by structural genomics.
  • Integration of advances in Deep Learning with structural biology data.

Main Results:

  • Structural genomics projects generated a large volume of protein structure data.
  • These efforts catalyzed significant developments in data science and computational infrastructure.
  • The synergy between structural data and Deep Learning has revolutionized computational molecular biology.

Conclusions:

  • The legacy of structural genomics, particularly the Protein 3000 project at PDBj, continues to influence computational molecular biology.
  • The integration of structural data with advanced computational techniques has unlocked new research avenues.
  • Ongoing research demonstrates the enduring value and transformative impact of early structural genomics efforts.