ArticlePeerJ2014
FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares.
Article in PeerJ, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 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
52 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Advances in phage-host interaction prediction: in silico method enhances the development of phage therapies.Briefings in bioinformatics · 2024Pooled it
- Chromosome-level assembly and phylophenetic insights of Cladosporium oxysporum A3.I.1, a fungus with the ability to degrade polyurethane polymers.G3 (Bethesda, Md.) · 2026Article
- Genetically engineered lipases: advances in expression and upscaling for industrial applications.Archives of microbiology · 2026Review
- Artificial Intelligence Applications in Bacteriophage Genomics and Host Interaction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Metagenomic Insights Into the Role of Gut Microbes in the Defensive Ink "Tsunabi" of Physeteroid Whales.Ecology and evolution · 2025Article
- Viralization as a microbial approach for enhancing coral reef restoration.The ISME journal · 2025Article
- Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes.Nature communications · 2024Article
- YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample.Bioinformatics (Oxford, England) · 2024Article
- Article
- Draft genomes of 3 cyanobacteria strains and 17 co-habiting proteobacteria assembled from metagenomes.Microbiology resource announcements · 2023Article
- Emergent community architecture despite distinct diversity in the global whale shark (Rhincodon typus) epidermal microbiome.Scientific reports · 2023Article
- Lactiplantibacillus plantarum, lactiplantibacillus pentosus and inulin meal inclusion boost the metagenomic function of broiler chickens.Animal microbiome · 2023Article
- Stingray epidermal microbiomes are species-specific with local adaptations.Frontiers in microbiology · 2023Article
- TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles.GigaScience · 2022Article
- Epidermal Microbiomes of Leopard Sharks (Microorganisms · 2022Article
- Deep-Sea Sediments from the Southern Gulf of Mexico Harbor a Wide Diversity of PKS I Genes.Antibiotics (Basel, Switzerland) · 2022Article
- Critical Assessment of Metagenome Interpretation: the second round of challenges.Nature methods · 2022Article
- Article
- Influence of Taxonomic and Functional Content of Microbial Communities on the Quality of Fermented Cocoa Pulp-Bean Mass.Applied and environmental microbiology · 2021Article
- Metagenome SNP calling via read-colored de Bruijn graphs.Bioinformatics (Oxford, England) · 2021Article
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
One of the major goals in metagenomics is to identify the organisms present in a microbial community from unannotated shotgun sequencing reads. Taxonomic profiling has valuable applications in biological and medical research, including disease diagnostics. Most currently available approaches do not scale well with increasing data volumes, which is important because both the number and lengths of the reads provided by sequencing platforms keep increasing. Here we introduce FOCUS, an agile composition based approach using non-negative least squares (NNLS) to report the organisms present in metagenomic samples and profile their abundances. FOCUS was tested with simulated and real metagenomes, and the results show that our approach accurately predicts the organisms present in microbial communities. FOCUS was implemented in Python. The source code and web-sever are freely available at http://edwards.sdsu.edu/FOCUS.
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.