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

Harmonic Mean01:09

Harmonic Mean

3.6K
The arithmetic mean is usually skewed towards the larger values in the data set. Therefore, to avoid this inherent bias towards smaller values, the harmonic mean is used.
Take the example of the speed of a car, which is the measure of the rate of distance traveled. If the vehicle traverses the same distance back-and-forth, its average speed equals the total distance traveled divided by the total time taken. However, if the car moves with varying speeds, then the arithmetic mean is more skewed...
3.6K
Genomics02:02

Genomics

39.8K
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...
39.8K
Energy in Simple Harmonic Motion01:23

Energy in Simple Harmonic Motion

12.6K
To determine the energy of a simple harmonic oscillator, consider all the forms of energy it can have during its simple harmonic motion. According to Hooke's Law, the energy stored during the compression/stretching of a string in a simple harmonic oscillator is potential energy. As the simple harmonic oscillator has no dissipative forces, it also possesses kinetic energy. In the presence of conservative forces, both energies can interconvert during oscillation, but the total energy remains...
12.6K
Simple Harmonic Motion01:21

Simple Harmonic Motion

14.7K
Simple harmonic motion is the name given to oscillatory motion for a system where the net force can be described by Hooke's law. If the net force can be described by Hooke's law and there is no damping (by friction or other non-conservative forces), then a simple harmonic oscillator will oscillate with equal displacement on either side of the equilibrium position. To derive an equation for period and frequency, the equation of motion is used. The period of a simple harmonic oscillator is given...
14.7K
Genomic Imprinting and Inheritance02:30

Genomic Imprinting and Inheritance

36.9K
Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
36.9K
Characteristics of Simple Harmonic Motion01:17

Characteristics of Simple Harmonic Motion

17.6K
The key characteristic of the simple harmonic motion is that the acceleration of the system and, therefore, the net force are proportional to the displacement and act in the opposite direction to the displacement. Additionally, the period and frequency of a simple harmonic oscillator are independent of its amplitude. For example, diving boards move faster or slower based on their thickness. A stiff, thick diving board has a large force constant, which causes it to have a smaller period, while a...
17.6K

You might also read

Related Articles

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

Sort by
Same author

Ring artifacts removal in X-ray-induced acoustic computed tomography.

Journal of innovative optical health sciences·2024
Same author

Investigation on Mechanism of Microstructure Evolution during Multi-Process Hot Forming of GH4169 Superalloy Forging.

Materials (Basel, Switzerland)·2024
Same author

Xiebai San alleviates acute lung injury by inhibiting the phosphorylation of the ERK/Stat3 pathway and regulating multiple metabolisms.

Phytomedicine : international journal of phytotherapy and phytopharmacology·2024
Same author

Pharmacological effects and target analysis of Guipi wan in the treatment of cerebral ischemia-reperfusion injury.

Frontiers in pharmacology·2024
Same author

Toxicity of urban stormwater on Chlorella pyrenoidosa: Implications for reuse safety.

The Science of the total environment·2024
Same author

Ginkgolides with anti-PAF activity from Ginkgo biloba L.

Fitoterapia·2024

Related Experiment Video

Updated: Jan 23, 2026

Harmonic Nanoparticles for Regenerative Research
09:23

Harmonic Nanoparticles for Regenerative Research

Published on: May 1, 2014

12.1K

Harmonizing single-cell 3D genome data with STARK and scNucleome.

Wen-Jie Jiang1, KangWen Cai2, YuanChen Sun2

  • 1Department of Cardiology and Institute of Vascular Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, NHC Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University Third Hospital, Peking University, Beijing, 100191, China.

Genome Biology
|January 22, 2026
PubMed
Summary

A new toolkit called STARK offers universal analysis for single-cell 3D genome sequencing (sc3DG-seq) data. It benchmarks technologies, improves quality control, and establishes a foundational data repository for 3D genome research.

Keywords:
BenchmarkSTARKScNucleomeSingle cell 3D genomeSingle cell Hi-C

More Related Videos

Target Cell Pre-enrichment and Whole Genome Amplification for Single Cell Downstream Characterization
10:12

Target Cell Pre-enrichment and Whole Genome Amplification for Single Cell Downstream Characterization

Published on: May 15, 2018

9.5K
An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
10:00

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

18.3K

Related Experiment Videos

Last Updated: Jan 23, 2026

Harmonic Nanoparticles for Regenerative Research
09:23

Harmonic Nanoparticles for Regenerative Research

Published on: May 1, 2014

12.1K
Target Cell Pre-enrichment and Whole Genome Amplification for Single Cell Downstream Characterization
10:12

Target Cell Pre-enrichment and Whole Genome Amplification for Single Cell Downstream Characterization

Published on: May 15, 2018

9.5K
An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
10:00

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

18.3K

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Single-cell three-dimensional genome sequencing (sc3DG-seq) is crucial for understanding genome regulation and cellular heterogeneity.
  • A lack of universal analysis tools hinders the widespread adoption and comparability of sc3DG-seq data.

Purpose of the Study:

  • To develop a versatile toolkit (STARK) for processing, quality control, and analyzing diverse sc3DG-seq data.
  • To benchmark existing sc3DG-seq technologies and introduce new metrics for data quality assessment.

Main Methods:

  • Development of the STARK toolkit for sc3DG-seq data analysis.
  • Benchmarking of 15 different sc3DG-seq technologies.
  • Introduction of EmptyCells for barcode filtering and Spatial Structure Capture Efficiency (SSCE) for quality assessment.
  • Establishment of scNucleome, a standardized sc3DG-seq data repository.

Main Results:

  • STARK provides a unified platform for sc3DG-seq data analysis.
  • Quantitative comparison of 15 sc3DG-seq technologies, highlighting their strengths and limitations.
  • Improved empty barcode removal and chromatin structure quality assessment using EmptyCells and SSCE.
  • Creation of scNucleome, a valuable resource for the research community.

Conclusions:

  • STARK addresses the need for a universal analysis tool in sc3DG-seq research.
  • The toolkit and new metrics enhance data processing, quality control, and technology evaluation.
  • scNucleome serves as a foundational resource, promoting standardization and accelerating future 3D genome studies.