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 Experiment Videos

Viral population estimation using pyrosequencing.

Nicholas Eriksson1, Lior Pachter, Yumi Mitsuya

  • 1Department of Statistics, University of Chicago, Chicago, Illinois, United States of America. eriksson@galton.uchicago.edu

Plos Computational Biology
|April 26, 2008
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

Efficacy of robot-assisted stereotactic aspiration in moderate basal ganglia hemorrhage: a retrospective cohort study.

Frontiers in surgery·2026
Same author

Regulated Cell Death in Prostate Cancer: Immunometabolic Crosstalk, Therapeutic Resistance, and Biomarker-Guided Combination Strategies.

Cancers·2026
Same author

Dual inhibition of tubulin and DNMT by the novel letermovir derivative H62 blocks leukemia.

Biochemical pharmacology·2026
Same author

Corrigendum to " Knockdown of TRPM2 promotes osteogenic differentiation of Human Periodontal Ligament Stem Cells by modulating NF-κB /NLRP3 pathway", Tissue Cell, 2023, 84: 102184.

Tissue & cell·2026
Same author

A Machine Learning Framework Integrating DeepLabCut and SimBA for Quantifying Aggressive Behavior in Swimming Crab <i>Portunus trituberculatus</i>.

Animals : an open access journal from MDPI·2026
Same author

Comparison of mRNA-based and next-generation sequencing HPV assays in a population-based cervical cancer screening program in China.

Journal of gynecologic oncology·2026
Same journal

DeepMethylation: A deep learning framework for tissue-specific DNA methylation prediction and functional variant annotation.

PLoS computational biology·2026
Same journal

Redefining and estimating the early-phase reproduction ratio for epidemic outbreaks in spatially structured populations.

PLoS computational biology·2026
Same journal

Optimized phenotype definitions boost GWAS power.

PLoS computational biology·2026
Same journal

Detection, communication, and individual identification with deep audio embeddings: A case study with North Atlantic right whales.

PLoS computational biology·2026
Same journal

Exploring the structural lexicon of the Proteome via Metric Geometry.

PLoS computational biology·2026
Same journal

Linking retinal sampling in neural encoding models to temporal profiles of visual processing in humans.

PLoS computational biology·2026
See all related articles

New computational methods analyze pyrosequencing data to reveal virus population structures. This approach aids in understanding viral diversity and drug resistance, improving disease control strategies.

Area of Science:

  • Virology
  • Computational Biology
  • Genetics

Background:

  • Viral diversity within hosts complicates immune responses, vaccine development, and antiviral therapies.
  • Accurate characterization of viral populations is crucial for effective treatment and disease management.

Purpose of the Study:

  • To develop and validate computational methods for analyzing pyrosequencing data to reconstruct virus population structures.
  • To apply these methods to understand the population dynamics of drug-resistant HIV strains.

Main Methods:

  • Utilized pyrophosphate-based sequencing (pyrosequencing) for ultra-deep sequencing of viral samples.
  • Developed statistical error correction and combinatorial algorithms for haplotype reconstruction.
  • Employed an expectation-maximization (EM) algorithm to infer haplotype frequencies.

Related Experiment Videos

Main Results:

  • Successfully estimated the population structure of HIV strains from pyrosequencing reads.
  • Demonstrated the effectiveness of pyrosequencing for population reconstruction through simulations and comparison with clonal sequencing.
  • Validated the computational methods on diverse HIV populations from patients with drug-resistant strains.

Conclusions:

  • Pyrosequencing offers a cost-effective method for estimating virus population structures.
  • This approach provides valuable insights into viral evolutionary dynamics and can inform disease control strategies.
  • The developed computational tools enhance the utility of pyrosequencing in clinical and research settings.