Research Articles
Beyond the Sample: Incorporating Cage Effects into Mouse Microbiome Study Power Calculations for Robust Preclinical Research
This article provides a comprehensive guide for researchers on integrating cage effects into power analysis for mouse microbiome studies.
Beyond Closure: Mastering L∞ Normalization for Robust Analysis of Microbiome and High-Throughput Biomedical Data
This article provides a comprehensive guide to L∞ normalization for compositional data in biomedical research.
LUPINE Method: A Comprehensive Guide to Accurate Microbial Network Inference for Researchers and Drug Developers
This article provides a detailed guide to the LUPINE method for microbial network inference.
LUPINE Longitudinal Microbiome Network Inference: A Comprehensive Guide for Biomedical Researchers
This article provides a detailed exploration of LUPINE (Longitudinal Profiling and INference Engine), a computational framework designed for inferring dynamic microbial association networks from longitudinal microbiome data.
A Comprehensive Guide to Kraken2: Building, Optimizing, and Validating Your Metagenomic Classification Workflow for Biomedical Research
This guide provides a detailed, step-by-step framework for implementing the Kraken2 metagenomic classifier, tailored for researchers, scientists, and drug development professionals.
Kraken2 for Shotgun Metagenomics: A Complete Guide for Researchers and Drug Developers
This comprehensive guide provides researchers and drug development professionals with an in-depth analysis of Kraken2 for taxonomic classification of shotgun metagenomic data.
Koch's Postulates Reimagined: Establishing Causality for Commensal Pathogens and Microbiome-Associated Diseases
This article explores the critical challenge of establishing causal relationships between commensal microorganisms and disease states—a paradigm that traditional Koch's postulates fail to address.
Compositional Data Analysis in Microbiome Studies: A Complete Guide for Biomedical Researchers
This comprehensive guide explores the critical importance of compositional data analysis in microbiome research.
Beyond the Hype: Advanced Strategies for Robust False Discovery Rate Control in Microbiome Differential Abundance Analysis
This article provides a comprehensive guide for researchers and bioinformaticians tackling the critical challenge of false discovery rate (FDR) control in microbiome differential abundance (DA) analysis.
Unlocking Microbial Correlations: A Practical Guide to ISCAZIM Analysis for Zero-Inflated Microbiome Data
This comprehensive guide provides researchers, scientists, and drug development professionals with an in-depth analysis of the ISCAZIM (Integrated Sparse Canonical Correlation Analysis for Zero-Inflated Microbiomes) method.