ArticleBioinformatics (Oxford, England)2016
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT05469997 (Ketogenic Diet Interventions in Parkinson's Disease), which is not on this map. Cited by 106 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.
Ketogenic Diet Interventions in Parkinson's Disease: Safeguarding the Gut Microbiome
Who cites it
106 citing papers in PubMed.
- Effects of fecal microbiota transplantation in subjects with irritable bowel syndrome are mirrored by changes in gut microbiome.Gut microbes · 2020Trial
- Trial
- Impact of Combined Botanical Functional Ingredients on the Canine Gut Microbiome.Veterinary sciences · 2026Article
- Can the leafhopper microbiome unlock new strategies for its control?Journal of economic entomology · 2026Review
- Gut health in broiler chickens fed a mixture of Hermetia illucens and Tenebrio molitor meals: does it have a key role in shaping bird performance?Poultry science · 2026Article
- 16S rRNA sequence captures microbial functional potential.bioRxiv : the preprint server for biology · 2026Article
- Urban forest restoration enhances soil microbial functional potential and functional insurance via shifts in β-diversity.Environmental microbiome · 2026Article
- Article
- Gut microbiome modulation by cricket, pea, and whey protein using the SHIME in vitro simulator.NPJ science of food · 2026Article
- Soil Microbial Functions Indicate Persistent Agricultural Legacies and Potential Alternative States Following Restoration Plantings.Ecology and evolution · 2026Article
- DUOX2-Driven Oxidative Stress Alters the Gut Redox Niche and Promotes Microbial Dysbiosis in Crohn's Disease.Antioxidants (Basel, Switzerland) · 2026Article
- From predisposition to recovery: field evidence of interactions between the gut microbiota and Brachyspira hyodysenteriae infection.Veterinary research · 2026Article
- Advances in Shotgun Metagenomics for Cheese Microbiology: From Microbial Dynamics to Functional Insights.Foods (Basel, Switzerland) · 2026Review
- A genome-resolved cyanobacterial consortium from the Atacama Desert reveals novel bacterial diversity, stress-resilience potential, chromatic flexibility, and photoprotection.Frontiers in bioengineering and biotechnology · 2026Article
- Contrasting Microbial Taxonomic and Functional Colonisation Patterns in Wild Populations of the Pan-Palaeotropical C4 Grass, Themeda triandra.Plant, cell & environment · 2026Article
- Compositional maturation of the microbiome and adaptive immunity in the postnatal period.Frontiers in immunology · 2026Article
- Indigenous infants in remote Australia retain an ancestral gut microbiome despite encroaching Westernization.Nature communications · 2025Article
- MeTAline: enabling reproducible and scalable metagenomic analyses.NAR genomics and bioinformatics · 2025Article
- The Role of Omics Technology in Evaluating Plastic Pollution's Effects on Plants: A Comprehensive Review.International journal of molecular sciences · 2025Review
- Severity of Brachyspira hyodysenteriae colitis correlates to the changes observed in the microbiota composition and its associated functionality in the large intestine.Animal microbiome · 2025Article
46 more citing papers are in PubMed but not listed here.
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
summaryAnalyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms present in the original sample, answering the question what they can do. Currently, available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keep increasing. Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with over 70 real metagenomes, the results showing that it accurately predicts the subsystems present in the profiled microbial communities, and is up to 1000 times faster than other tools. AVAILABILITY AND IMPLEMENTATION: SUPER-FOCUS was implemented in Python, and its source code and the tool website are freely available at https://edwards.sdsu.edu/SUPERFOCUS. CONTACT: redwards@mail.sdsu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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.