Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.

  PMID 18682527 · PMC2532719 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  Biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA analysis

  faecal rsr 16s sargasso shotgun blastn-based 16s

• Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.

  PMID 17916580 · PMC2533590 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 7 claims · 7 setups

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  Adult and weaned-children gut microbiota show high functional (gene-content) uniformity despite taxonomic differences, while unweaned infant microbiota show high inter-individual variation in both taxonomic and gene composition.

  fecal assembled predicted gut whole-genome gene reciprocal

• Dental Plaque Microbial Resistomes of Periodontal Health and Disease and Their Changes after Scaling and Root Planing Therapy.

  PMID 34287005 · PMC8386447 · mSphere · 2021 · 8 claims · 7 setups

  Has reproduction · 76

  Periodontitis significantly alters dental plaque microbial community diversity and structure compared to healthy and treated states

  dental metagenomic taxonomic arg

• Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.

  PMID 19796657 · PMC3568755 · Journal of microbiological methods · 2009 · 8 claims · 6 setups

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  The 16S rRNA V5 hypervariable region, amplified as a short ~82-base segment, provides reliable taxonomic identification of oral bacteria against public databases like HOMD.

  pooled 16s sequenced topo 16s primer taxonomic

• Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.

  PMID 42098796 · PMC13154700 · Microbiome · 2026 · 8 claims · 5 setups

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  Poly(A)-enriched mRNA-seq can reliably reconstruct microbiome composition, validated against a quantitative mock community standard and metagenomic analysis

  zymobiomics vls-vscc vulvar subset mrna-seq rna-seq poly

• Correlations between gut microbiota and serum metabolomics in patients with neurogenic rosacea.

  PMID 40676500 · PMC12272963 · BMC microbiology · 2025 · 6 claims · 3 setups

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  Patients with neurogenic rosacea exhibit significant gut microbiota dysbiosis compared to healthy controls

  serum fecal paired lc-ms 16s spearman

• A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).

  PMID 22719821 · PMC3374610 · PloS one · 2012 · 8 claims · 7 setups

  Has reproduction · 78

  METAREP version 1.3.1 is an open-source, scalable tool for querying, browsing and comparing extremely large volumes of metagenomic annotations, with an extended data model, dynamic weighting, distributed searches and advanced clustering.

  microbiome pooled hmp metarep genome assembly-based enzymatic

• Shotgun metagenomic analysis of the oral microbiomes of children with noma.

  PMID 41860897 · PMC13029773 · PLoS neglected tropical diseases · 2026 · 8 claims · 6 setups

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  Noma oral microbiomes show marked dysbiosis with significant enrichment of Treponema, Porphyromonas, and Bacteroides, and depletion of Streptococcus and Rothia, compared to healthy controls

  oral saliva noma previously shotgun comparative metagenome

• metaTraits: a large-scale integration of microbial phenotypic trait information.

  PMID 41296543 · PMC12807735 · Nucleic acids research · 2026 · 8 claims · 6 setups

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  metaTraits integrates culture-derived trait data from BacDive, BV-BRC, JGI IMG, and GOLD with genome-based predictions for isolate genomes (proGenomes) and MAGs (SPIRE)

  high-quality medium isolate genomes genome-based genome taxonomic

• TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.

  PMID 42277027 · PMC13260335 · Nature communications · 2026 · 8 claims · 5 setups

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  TOFU-MAaPO yields significantly more high-quality MAGs than metaFun, nf-core/mag, and ATLAS due to integration of multiple complementary binning tools with unified MAGScoT refinement

  gut same uniquely metagenome quality assembly-free

• metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.

  PMID 41530917 · PMC12818822 · Gut microbes · 2026 · 8 claims · 8 setups

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  metaFun is an open-source, end-to-end Nextflow/Apptainer pipeline integrating quality control, taxonomic profiling, functional profiling, de novo assembly, binning, genome assessment, comparative genomics, network analysis, and strain-level microdiversity analysis into a unified framework

  simulated selected gut mags novo binning pangenome-based

• Aryl Hydrocarbon Receptor (AhR) Activation by 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (TCDD) Dose-Dependently Shifts the Gut Microbiome Consistent with the Progression of Non-Alcoholic Fatty Liver Disease.

  PMID 34830313 · PMC8625315 · International journal of molecular sciences · 2021 · 8 claims · 2 setups

  Has reproduction · 79

  TCDD dose-dependently enriches Lactobacillus species, particularly L. reuteri, in the mouse cecum microbiome

  cecum fecal shotgun humann