Research Articles
Targeted Sequencing Face-Off: When to Choose PCR Amplicon vs. Hybridization Capture for Precision Variant Detection
This article provides a comprehensive comparison of PCR amplicon sequencing and hybridization capture, the two dominant approaches for targeted next-generation sequencing (NGS) in research and drug development.
Polymerase Choice in Amplicon Sequencing: A Critical Review of Error Sources, Artifacts, and Best Practices
Amplicon sequencing is fundamental to biomedical research, from microbiome profiling to cancer mutation detection.
Degenerate Primer Bias in 16S rRNA Sequencing: Sources, Impacts, and Mitigation Strategies for Accurate Microbiome Analysis
This article provides a comprehensive analysis of how degenerate primers introduce bias in 16S rRNA gene sequencing, a critical concern for researchers and drug development professionals.
Co-Occurrence Networks Demystified: From Core Algorithms to Biomedical Applications in Omics Research
This comprehensive guide explains the fundamental principles and algorithmic workings of co-occurrence networks, a pivotal tool in systems biology and drug discovery.
Homotrimeric Nucleotide UMI Design: A Novel Strategy for Ultra-Accurate PCR Error Correction in NGS
This article provides a comprehensive guide to homotrimeric nucleotide Unique Molecular Identifiers (UMIs) for researchers and drug development professionals.
High-Throughput 16S Amplicon Sequencing: A Comprehensive Guide to Optimized Protocols for Researchers
This article provides a detailed guide to high-throughput 16S rRNA gene amplicon sequencing for microbiome analysis.
Beyond the Gap: A Modern Guide to Structural Zeros in High-Dimensional Microbiome Data Analysis
This article provides a comprehensive guide for researchers and biomedical professionals on handling structural zeros—true biological absences—in high-dimensional microbiome datasets.
Overcoming High Sparsity in Microbiome Data: Advanced Strategies for Robust Analysis in Biomedical Research
High sparsity, characterized by a vast majority of zero counts, is an inherent and formidable challenge in real-world microbiome composition data from 16S rRNA and shotgun metagenomic sequencing.
Co-Occurrence Networks for New Researchers: A 2024 Guide to Inference Algorithms, Tools, and Best Practices
This comprehensive guide demystifies co-occurrence network inference for new researchers in biomedical and drug discovery fields.
Microbial Trait Integration: A Genome-to-Ecosystem (G2E) Framework for Next-Generation Biogeochemical and Biomedical Models
This article introduces and details a Genome-to-Ecosystem (G2E) framework designed to systematically integrate microbial functional traits, derived from genomic and metagenomic data, into predictive biogeochemical models.