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

Next-generation Sequencing03:00

Next-generation Sequencing

88.0K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
88.0K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

865
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...
865

You might also read

Related Articles

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

Sort by
Same author

How to measure copresent ammonia and inorganic chloramines reliably: Some fundamental issues and novel solutions.

Journal of hazardous materials·2026
Same author

Alcohols as reactive species modulators: Rethinking quenching in UV/chlorine process.

Water research·2025
Same author

Why hypochlorite in water cannot be detected by ion chromatography?

Journal of hazardous materials·2025
Same author

Insights into the pH-dependent mechanism of peracetic acid activation by biochar-supported zero-valent iron/cobalt bimetallic nanoparticles: The shift of reactive sites and the dual role of hydrogen peroxide.

Journal of hazardous materials·2024
Same author

Characterization of the complete chloroplast genome of a chinese endangered species <i>Cymbidium wenshanense</i> Y. S. Wu et F. Y. Liu.

Mitochondrial DNA. Part B, Resources·2023
Same author

Over-expression of

PeerJ·2023

Related Experiment Video

Updated: May 5, 2026

Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

38.3K

A classification approach for DNA methylation profiling with bisulfite next-generation sequencing data.

Longjie Cheng1, Yu Zhu

  • 1Department of Statistics, Purdue University, West Lafayette, IN 47906, USA.

Bioinformatics (Oxford, England)
|November 26, 2013
PubMed
Summary

We developed a new methylation status calling (MSC) procedure for analyzing bisulfite sequencing data. This method improves accuracy and controls false discovery rates, outperforming existing methods in simulations and real data applications.

More Related Videos

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

27.3K
DNA Methylation: Bisulphite Modification and Analysis
12:34

DNA Methylation: Bisulphite Modification and Analysis

Published on: October 21, 2011

108.9K

Related Experiment Videos

Last Updated: May 5, 2026

Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

38.3K
Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

27.3K
DNA Methylation: Bisulphite Modification and Analysis
12:34

DNA Methylation: Bisulphite Modification and Analysis

Published on: October 21, 2011

108.9K

Area of Science:

  • Genomics
  • Computational Biology
  • Statistical Genetics

Background:

  • High-throughput sequencing enables genome-wide DNA methylation profiling with single-base resolution.
  • Existing statistical methods for bisulfite sequencing data are underdeveloped and inadequate for noise and binary status calls.
  • Proportion-based methods lack statistical rigor and biological satisfaction for methylation status determination.

Purpose of the Study:

  • To develop statistically sound and biologically relevant methods for analyzing bisulfite sequencing data.
  • To propose a classification-based procedure for accurate binary methylation status calls.
  • To control the false discovery rate (FDR) in methylation status determination.

Main Methods:

  • Utilized a mixture of binomial model to characterize bisulfite sequencing data.
  • Developed the methylation status calling (MSC) procedure for binary methylation status calls.
  • Created an FDR-controlled MSC procedure by integrating a local FDR-based adaptive method.

Main Results:

  • The MSC procedure maximizes the correct allocation rate and allows estimation of FDR and false non-discovery rate (FNDR).
  • Simulation studies confirmed the accuracy of MSC's FDR/FNDR estimates and the validity of the FDR-controlled MSC procedure.
  • The FDR-controlled MSC procedure demonstrated superior power compared to individual binomial testing and achieved an overall correct allocation rate >0.97 in real data.

Conclusions:

  • The proposed MSC procedure and its FDR-controlled variant are effective for analyzing bisulfite sequencing data.
  • These methods provide statistically adequate and biologically meaningful binary methylation status calls.
  • The developed procedures offer improved accuracy and reliable FDR control for methylation analysis.