ArticleAmerican journal of epidemiology2019
HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor.
Article in American journal of epidemiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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
25 citing papers in PubMed, 49 citations in OpenAlex.
- mbSparse: an autoencoder-based imputation method to address sparsity in microbiome data.Gut microbes · 2025Article
- TphPMF: A microbiome data imputation method using hierarchical Bayesian Probabilistic Matrix Factorization.PLoS computational biology · 2025Article
- Multidimensional scaling improves distance-based clustering for microbiome data.Bioinformatics (Oxford, England) · 2025Article
- ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models.Bioinformatics (Oxford, England) · 2024Article
- Article
- Taxanorm: a novel taxa-specific normalization approach for microbiome data.BMC bioinformatics · 2024Article
- Obesity-associated microbiomes instigate visceral adipose tissue inflammation by recruitment of distinct neutrophils.Nature communications · 2024Article
- ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models.bioRxiv : the preprint server for biology · 2024Article
- Microbial Biosurfactant as an Alternate to Chemical Surfactants for Application in Cosmetics Industries in Personal and Skin Care Products: A Critical Review.BioMed research international · 2023Review
- Article
- Human Microbiome Mixture Analysis Using Weighted Quantile Sum Regression.International journal of environmental research and public health · 2022Article
- A comprehensive evaluation of microbial differential abundance analysis methods: current status and potential solutions.Microbiome · 2022Article
- CBEA: Competitive balances for taxonomic enrichment analysis.PLoS computational biology · 2022Article
- Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seeding.Med (New York, N.Y.) · 2021Observational
- mbImpute: an accurate and robust imputation method for microbiome data.Genome biology · 2021Article
- treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses.Genome biology · 2021Article
- Beyond samples: A metric revealing more connections of gut microbiota between individuals.Computational and structural biotechnology journal · 2021Article
- Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data.Genome biology · 2020Article
- The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health.FEMS microbiology reviews · 2020Review
- Comparison of lung microbiota between antineutrophil cytoplasmic antibody-associated vasculitis and sarcoidosis.Scientific reports · 2020Article
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Authors and funding
9 authors at 4 institutions in 3 countries.
Funding
Abstract
Phase 1 of the Human Microbiome Project (HMP) investigated 18 body subsites of 242 healthy American adults to produce the first comprehensive reference for the composition and variation of the "healthy" human microbiome. Publicly available data sets from amplicon sequencing of two 16S ribosomal RNA variable regions, with extensive controlled-access participant data, provide a reference for ongoing microbiome studies. However, utilization of these data sets can be hindered by the complex bioinformatic steps required to access, import, decrypt, and merge the various components in formats suitable for ecological and statistical analysis. The HMP16SData package provides count data for both 16S ribosomal RNA variable regions, integrated with phylogeny, taxonomy, public participant data, and controlled participant data for authorized researchers, using standard integrative Bioconductor data objects. By removing bioinformatic hurdles of data access and management, HMP16SData enables epidemiologists with only basic R skills to quickly analyze HMP data.
Indexed as
Identifiers
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.