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

You might also read

Related Articles

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

Sort by

Same author

Prevalence aware feature selection improves biomarker identification in microbiome studies.

Bioinformatics (Oxford, England)·2026

Same author

Flexible and scalable inference of spatially varying correlation in spatial transcriptomics with spCorr.

Genome research·2026

Same author

Φ-Space ST: A platform-agnostic method to identify cell states in spatial transcriptomics studies.

Cell reports methods·2026

Same author

Multi-Omics Reveals Early Pregnancy Placental Dysfunction Associated With Preterm and Term Preeclampsia.

MedComm·2026

Same author

CIPHER: An end-to-end framework for designing optimized aggregated spatial transcriptomics experiments.

PLoS computational biology·2026

Same author

IntegrateRigor: annotation-free integration optimization for cell identity recovery reveals cancer-immune interface niches.

bioRxiv : the preprint server for biology·2026

Same journal

STED: flexible cross-modal topic modeling infers cell-type-specific regulatory landscapes from bulk epigenomics.

Briefings in bioinformatics·2026

Same journal

A knowledge-guided deep learning framework for quantitative nucleic acid testing.

Briefings in bioinformatics·2026

Same journal

Optimal transport for label transfer in single-cell multi-omics integration.

Briefings in bioinformatics·2026

Same journal

Continuous multi-omics pathway enrichment analysis resolves hidden functional heterogeneity.

Briefings in bioinformatics·2026

Same journal

Evaluating completeness, coherence, and consistency of genome-scale function annotations.

Briefings in bioinformatics·2026

Same journal

Transformers for single-cell RNA sequencing: a survey.

Briefings in bioinformatics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 28, 2025

Assessing the Viability of a Synthetic Bacterial Consortium on the In Vitro Gut Host-microbe Interface

Assessing the Viability of a Synthetic Bacterial Consortium on the In Vitro Gut Host-microbe Interface

Published on: July 4, 2018

Semisynthetic simulation for microbiome data analysis.

Kris Sankaran¹, Saritha Kodikara², Jingyi Jessica Li^3,4,5

¹Department of Statistics, University of Wisconsin-Madison, 1300 University Ave, Madison,WI 53703, United States.

Briefings in Bioinformatics

|February 10, 2025

Summary

This summary is machine-generated.

Simulation provides a crucial testing ground for analyzing high-throughput sequencing data in microbiome research. This approach helps validate methods for detecting subtle signals and ensuring reliable results from complex datasets.

Keywords:

methods assessment methods selection microbiome power analysis simulation

More Related Videos

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

Individualized Reconstitution of Human Milk Microbiota: A Feasible Approach in Real-World Settings

Individualized Reconstitution of Human Milk Microbiota: A Feasible Approach in Real-World Settings

Published on: February 7, 2025

Related Experiment Videos

Last Updated: May 28, 2025

Assessing the Viability of a Synthetic Bacterial Consortium on the In Vitro Gut Host-microbe Interface

Assessing the Viability of a Synthetic Bacterial Consortium on the In Vitro Gut Host-microbe Interface

Published on: July 4, 2018

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

Individualized Reconstitution of Human Milk Microbiota: A Feasible Approach in Real-World Settings

Individualized Reconstitution of Human Milk Microbiota: A Feasible Approach in Real-World Settings

Published on: February 7, 2025

Area of Science:

Microbiome research
Computational biology
Bioinformatics

Background:

High-throughput sequencing is central to modern microbiome research.
Analyzing microbiome data requires robust methods to avoid spurious associations and detect subtle signals.
Simulation offers a controlled environment to test and validate analytical approaches.

Purpose of the Study:

To review the utility of simulation as a sandbox for microbiome data analysis.
To explain the statistical underpinnings of microbiome data simulators.
To demonstrate the application of simulation in various microbiome analysis tasks.

Main Methods:

Explanation of probability, multivariate analysis, and regression concepts in simulator design.
Discussion of trade-offs in simulator implementations (generality, faithfulness, controllability).
Review of methods for evaluating simulator accuracy against real-world data properties.

Main Results:

Simulation is valuable for power analysis, methods benchmarking, and reliability analysis.
Case studies illustrate simulation's utility in differential abundance testing, dimensionality reduction, network analysis, and data integration.
An online tutorial with adaptable code examples is provided.

Conclusions:

Simulation is an indispensable tool for developing and validating microbiome data analysis methods.
Careful evaluation of simulators is necessary to ensure their reflection of real-world data characteristics.
Simulation enhances the reliability and interpretability of microbiome research findings.