ArticleGenome biology2018
HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed.
- Antiepileptic Effects ofBiology · 2025Article
- Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach.Bioinformatics (Oxford, England) · 2024Article
- Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research.Cell reports. Medicine · 2024Article
- A Machine Learning-Based Diagnostic Model for Crohn's Disease and Ulcerative Colitis Utilizing Fecal Microbiome Analysis.Microorganisms · 2023Article
- MaLiAmPi enables generalizable and taxonomy-independent microbiome features from technically diverse 16S-based microbiome studies.Cell reports methods · 2023Article
- A streamlined pipeline based on HmmUFOtu for microbial community profiling using 16S rRNA amplicon sequencing.Genomics & informatics · 2023Article
- Article
- Involucrin Modulates Vitamin D Receptor Activity in the Epidermis.The Journal of investigative dermatology · 2023Article
- MPrESS: An R-Package for Accurately Predicting Power for Comparisons of 16S rRNA Microbiome Taxa Distributions including Simulation by Dirichlet Mixture Modeling.Microorganisms · 2023Article
- Article
- Metagenomic Analysis Using Phylogenetic Placement-A Review of the First Decade.Frontiers in bioinformatics · 2022Review
- Cutaneous Effects of In Utero and Lactational Exposure of C57BL/6J Mice to 2,3,7,8-Tetrachlorodibenzo-Toxics · 2021Article
- Commensal microbiota regulates skin barrier function and repair via signaling through the aryl hydrocarbon receptor.Cell host & microbe · 2021Article
- Linking Plant Secondary Metabolites and Plant Microbiomes: A Review.Frontiers in plant science · 2021Review
- Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets.Microbiome · 2020Article
- Research Techniques Made Simple: Profiling the Skin Microbiota.The Journal of investigative dermatology · 2019Review
- Article
- IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences.Microbiome · 2018Article
- HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies.Genome biology · 2018Article
- Persistent gaps and errors in reference databases impede ecologically meaningful taxonomy assignments in 18S rRNA studies: a case study of terrestrial and marine nematodes.Environmental DNA (Hoboken, N.J.)Article
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
Abstract
Culture-independent analysis of microbial communities frequently relies on amplification and sequencing of the prokaryotic 16S ribosomal RNA gene. Typical analysis pipelines group sequences into operational taxonomic units (OTUs) to infer taxonomic and phylogenetic relationships. Here, we present HmmUFOtu, a novel tool for processing microbiome amplicon sequencing data, which performs rapid per-read phylogenetic placement, followed by phylogenetically informed clustering into OTUs and taxonomy assignment. Compared to standard pipelines, HmmUFOtu more accurately and reliably recapitulates microbial community diversity and composition in simulated and real datasets without relying on heuristics or sacrificing speed or accuracy.
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.