ReviewComputational and structural biotechnology journal2020
Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods.
Review in Computational and structural biotechnology journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
42 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Breast cancer and microbiome: a systematic review highlighting challenges for clinical translation.BMC women's health · 2025Pooled it
- Integrated Foodomics Reveals Gut Microbiota-Metabolite-Gene Interactions Associated with the Immunoprotective Effects of Ganoderma lucidum Polysaccharide Peptide.Foods (Basel, Switzerland) · 2026Article
- Full-Length 16S rRNA Amplicon Sequencing for the Simple and Simultaneous Detection of Multiple Probiotic Species in Commercial Products.Journal of microbiology and biotechnology · 2026Article
- Benchmarking short- and long-read sequencing technologies for metagenomic profiling of microbiomes.Scientific reports · 2026Article
- Comparative Analysis of Gastrointestinal Microbiota Along the Digestive Tract in Sika Deer and Reindeer and Prediction of Their Potential Function.Animals : an open access journal from MDPI · 2026Article
- Enhancing inference of differential gene expression in metatranscriptomes from human microbial communities.Nature communications · 2026Article
- Microbiota, Gender-Affirming Hormone Therapy, and Inflammatory Biomarkers in Transgender Women with HIV: Potential Implications for Cardiovascular Disease.Transgender health · 2026Article
- Miscarriage and the Microbiome: Host Genetics, Immunity, and the Reproductive Tract Ecosystem.Genes · 2026Review
- Personalized Nutrition Through the Gut Microbiome in Metabolic Syndrome and Related Comorbidities.Nutrients · 2026Review
- Microbial dysbiosis in cholangiocarcinoma.Frontiers in microbiology · 2026Review
- Immune-oncology-microbiome axis in lung cancer: from carcinogenesis to therapy-a narrative review.Translational lung cancer research · 2025Review
- Systematic evaluation of metatranscriptomic differential gene expressionbioRxiv : the preprint server for biology · 2025Article
- QIIME2 enhances multi-amplicon sequencing data analysis: a standardized and validated open-source pipeline for comprehensive 16S rRNA gene profiling.Microbiology spectrum · 2025Article
- Why Are Long-Read Sequencing Methods Revolutionizing Microbiome Analysis?Microorganisms · 2025Review
- Untrimmed ITS2 metabarcode sequences cause artificially reduced abundances of specific fungal taxa.Applied and environmental microbiology · 2025Article
- The human microbiome in clinical translation: from bench to bedside.Frontiers in microbiology · 2025Review
- The researcher's guide to selecting biomarkers in mental health studies.BioEssays : news and reviews in molecular, cellular and developmental biology · 2024Review
- A Comprehensive View of Food Microbiota: Introducing FoodMicrobionet v5.Foods (Basel, Switzerland) · 2024Article
- Challenges and best practices in omics benchmarking.Nature reviews. Genetics · 2024Review
- An in-depth evaluation of metagenomic classifiers for soil microbiomes.Environmental microbiome · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbiomes are integral components of diverse ecosystems, and increasingly recognized for their roles in the health of humans, animals, plants, and other hosts. Given their complexity (both in composition and function), the effective study of microbiomes (microbiomics) relies on the development, optimization, and validation of computational methods for analyzing microbial datasets, such as from marker-gene (e.g., 16S rRNA gene) and metagenome data. This review describes best practices for benchmarking and implementing computational methods (and software) for studying microbiomes, with particular focus on unique characteristics of microbiomes and microbiomics data that should be taken into account when designing and testing microbiomics methods.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.