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

Mapping Mammalian 3D Genome Interactions with Micro-C-XL11:41

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

3.6K
A protocol for mapping the three-dimensional genome organization with nucleosome resolution using the genome-wide chromosome conformation capture method Micro-C-XL is presented here.
3.6K
Genomics02:02

Genomics

39.7K
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...
39.7K
A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types12:39

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

11.7K
Our Bayesian Change Point (BCP) algorithm builds on state-of-the-art advances in modeling change-points via Hidden Markov Models and applies them to chromatin immunoprecipitation sequencing (ChIPseq) data analysis. BCP performs well in both broad and punctate data types, but excels in accurately identifying robust, reproducible islands of diffuse histone...
11.7K
3D Printing of Preclinical X-ray Computed Tomographic Data Sets11:06

3D Printing of Preclinical X-ray Computed Tomographic Data Sets

41.0K
Using modern plastic extrusion and printing technologies, it is now possible to quickly and inexpensively produce physical models of X-ray CT data taken in a laboratory. The three -dimensional printing of tomographic data is a powerful visualization, research, and educational tool that may now be accessed by the preclinical imaging...
41.0K
Ultra-long Read Sequencing for Whole Genomic DNA Analysis10:34

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

23.9K
Long-read sequences greatly facilitate the assembly of complex genomes and characterization of structural variation. We describe a method to generate ultra-long sequences by nanopore-based sequencing platforms. The approach adopts an optimized DNA extraction followed by modified library preparations to generate hundreds of kilobase reads with moderate coverage from human...
23.9K
Methodology for Accurate Detection of Mitochondrial DNA Methylation12:11

Methodology for Accurate Detection of Mitochondrial DNA Methylation

13.9K
Here, we present a protocol to allow accurate quantification of mitochondrial DNA (mtDNA) methylation. In this protocol, we describe an enzymatic digestion of DNA with BamHI coupled with a bioinformatic analysis pipeline which can be used to avoid overestimation of mtDNA methylation levels caused by the secondary structure of...
13.9K

You might also read

Related Articles

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

Sort by
Same author

Immunopathogenesis of antibody-mediated rejection in liver transplantation.

Frontiers in immunology·2026
Same author

Elevated TFR1 is associated with inflammatory burden and ferroptosis in ulcerative colitis.

Frontiers in medicine·2026
Same author

GlycoBond X enables isomer-resolved milk oligosaccharide glycomics and reveals evolutionary divergence across four mammalian species.

Cell reports·2026
Same author

Study on transdermal delivery system of sulforaphane chitosan nanoparticles based on methacryloylated chitosan microneedles: application in the treatment of irritant contact dermatitis.

International journal of pharmaceutics·2026
Same author

A ZBTB26-Integrator Axis Mediates Targeted Transcriptional Activation.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology·2026
Same author

Correction: Differential analysis of virulence and antibiotic resistance genes in ST11 CRKP and ST15 CRKP isolates from a tertiary hospital.

Frontiers in microbiology·2026
Same journal

Biomedical Concept Recognition with Error-aware Negative-enhanced Ranking Framework.

Bioinformatics (Oxford, England)·2026
Same journal

TEDLH: Domain HMMs for sensitive detection of remote homologues.

Bioinformatics (Oxford, England)·2026
Same journal

PLNFGL: Joint Estimation of Multi-Condition Gene Networks from Single-cell RNA-seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
Same journal

EDEL: Enhancing Dense Retrievers for Curation of Biomedical Knowledge Bases.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Jan 19, 2026

Mapping Mammalian 3D Genome Interactions with Micro-C-XL
11:41

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

3.6K

Accurate loop calling for 3D genomic data with cLoops.

Yaqiang Cao1, Zhaoxiong Chen1,2, Xingwei Chen1

  • 1CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

Bioinformatics (Oxford, England)
|September 11, 2019
PubMed
Summary
This summary is machine-generated.

cLoops is a new tool that accurately identifies 3D genome loops from sequencing data. It works across various data types and requires less computing power, improving the detection of regulatory element interactions.

More Related Videos

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types
12:39

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

Published on: December 10, 2012

11.7K
3D Printing of Preclinical X-ray Computed Tomographic Data Sets
11:06

3D Printing of Preclinical X-ray Computed Tomographic Data Sets

Published on: March 22, 2013

41.0K

Related Experiment Videos

Last Updated: Jan 19, 2026

Mapping Mammalian 3D Genome Interactions with Micro-C-XL
11:41

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

3.6K
A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types
12:39

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

Published on: December 10, 2012

11.7K
3D Printing of Preclinical X-ray Computed Tomographic Data Sets
11:06

3D Printing of Preclinical X-ray Computed Tomographic Data Sets

Published on: March 22, 2013

41.0K

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • 3D genome mapping technologies identify interactions between distant regulatory elements.
  • Existing loop-calling tools have limitations in data type compatibility, accuracy, and hardware requirements.

Purpose of the Study:

  • To introduce cLoops, a novel tool for identifying 3D genome loops.
  • To overcome the limitations of existing loop-calling methods.

Main Methods:

  • cLoops utilizes the cDBSCAN clustering algorithm to directly analyze paired-end tags (PETs).
  • It employs a permuted local background for statistical significance estimation.
  • The tool is data-type independent, supporting various sequencing data like ChIA-PET, Hi-C, HiChIP, and Trac-looping.

Main Results:

  • cLoops reliably identifies loops from both sharp and broad peak data.
  • Loops detected by cLoops exhibit reduced distance-dependent bias and higher enrichment compared to existing tools.
  • The tool demonstrates improved accuracy, versatility, flexibility, and efficiency with modest hardware needs.

Conclusions:

  • cLoops offers an accurate, versatile, and efficient solution for 3D genome loop detection.
  • The tool addresses key limitations of previous methods, making advanced genomic analysis more accessible.