Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Next-generation Sequencing

Next-generation Sequencing

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....

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

Modern Molecular Taxonomy

Modern Molecular Taxonomy

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...

Sanger Sequencing

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

You might also read

Related Articles

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

Sort by

Same author

Reference-free discovery with barcoded single-cell sequencing.

Nature biotechnology·2026

Same author

A Reference-Free Algorithm Discovers Regulation in the Plant Transcriptome.

Plant direct·2026

Same author

sc-SPLASH provides ultra-efficient reference-free discovery in barcoded single-cell sequencing.

bioRxiv : the preprint server for biology·2025

Same author

Statistical analysis supports pervasive RNA subcellular localization and alternative 3' UTR regulation.

eLife·2024

Same author

Scalable and unsupervised discovery from raw sequencing reads using SPLASH2.

Nature biotechnology·2024

Same author

Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung.

The Journal of experimental medicine·2024

Same journal

Another 10 years of PLOS Computational Biology: A data-driven reflection on trends in genomics research.

PLoS computational biology·2026

Same journal

Mobility data resolution needed to inform predictive models of spatial epidemic spread from mobile phone data.

PLoS computational biology·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

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 2, 2026

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Published on: August 29, 2014

Molecular sampling at logarithmic rates for next-generation sequencing.

Caroline Horn¹, Julia Salzman^1,2

¹Department of Biochemistry, Stanford University, Stanford, California, United States of America.

Plos Computational Biology

|December 13, 2019

Summary

This summary is machine-generated.

Next-generation sequencing depth can be reduced using SeQUential depletIon and enriCHment (SQUICH). This novel biophysical method achieves high precision molecular measurements at a logarithmic sampling rate, significantly cutting costs.

More Related Videos

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Related Experiment Videos

Last Updated: Jan 2, 2026

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Published on: August 29, 2014

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Area of Science:

Molecular Biology
Biophysics
Genomics

Background:

Next-generation sequencing (NGS) requires high sampling depth to accurately quantify diverse RNA and DNA species.
Prohibitive costs arise from physical limitations in sequencer molecular throughput, necessitating deeper sequencing for dynamic abundance ranges.

Purpose of the Study:

Introduce a novel sampling theory, SeQUential depletIon enriCHment (SQUICH), to address the cost and depth limitations of NGS.
Enable precise molecular measurements at significantly reduced sequencing depths.

Main Methods:

Developed a general sampling theory based on biophysical principles.
Functionally encoded species abundance prior to sampling.
Implemented a proof-of-principle experiment using a complex oligonucleotide system.

Main Results:

Theoretical and simulation analyses demonstrate SQUICH enables sampling at a logarithmic rate.
Achieved equivalent precision to conventional sequencing methods with reduced sampling depth.
Experimental validation showed a 10-fold reduction in sequencing depth in a complex system.

Conclusions:

SQUICH offers a general solution to fundamental molecular sampling challenges.
This method paves the way for a new generation of efficient and precise molecular measurements.
Logarithmic or better sampling depth is achievable, reducing sequencing costs and improving efficiency.