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).

• TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes.

  PMID 34197621 · PMC8464036 · Nucleic acids research · 2021 · 8 claims · 8 setups

  Has reproduction · 60

  TRAPID 2.0 is a web application performing global characterization of de novo transcriptomes via structural, functional, and taxonomic annotation in an initial processing phase, followed by an exploratory phase of downstream analyses.

  mmetsp query putative ciliate taxonomic similarity non-coding

• taxize: taxonomic search and retrieval in R.

  PMID 24555091 · PMC3901538 · F1000Research · 2013 · 8 claims · 8 setups

  Has reproduction · 30

  taxize is an open-source R package (on CRAN) giving simple programmatic access to taxonomic data from 13 web data sources.

  package session name identifier upstream

• Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics.

  PMID 28097058 · PMC5228507 · PeerJ · 2017 · 8 claims · 8 setups

  Has reproduction · 95

  Similar virus-host interactions and glycerol metabolism gene associations (notably dihydroxyacetone kinase with Haloquadratum/Halorubrum) exist across geographically diverse solar salterns

  solar saltern combined individual metagenomic taxonomic functional

• Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes.

  PMID 36192523 · PMC9529974 · Communications biology · 2022 · 8 claims · 8 setups

  Has reproduction · 68

  Built an integrated horse gut microbiome gene catalog (~25 million unique genes) and 372 metagenome-assembled genomes (MAGs) spanning 4179 genera and 95 phyla

  fecal horse dominant plasma shotgun taxonomic functional

• The global landscape of sequence diversity.

  PMID 17996061 · PMC2258180 · Genome biology · 2007 · 7 claims · 5 setups

  Full-text index only

  Eukaryotic sequence datasets show substantially greater genetic diversity (higher sequence/gene family discovery rates) than bacterial datasets, likely related to differences in modes of genetic inheritance.

  fully eukaryotic complete gene blast-based est gene

• A survey of integral alpha-helical membrane proteins.

  PMID 19760129 · PMC2780624 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups

  Full-text index only

  An automated annotation pipeline defines the integral membrane genome and family associations for 21,379 proteins from 34 genomes, most belonging to 598 Pfam-derived membrane protein families.

  pfam-a organisms 34-genome integral transmembrane comparative sequence

• 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

  Full-text index only

  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

• Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification.

  PMID 35862823 · PMC9426513 · mSystems · 2022 · 8 claims · 5 setups

  Has reproduction · 56

  The vast majority of recovered gene cluster families (GCFs) in sponge microbiomes show no similarity to any characterized BGC, revealing extreme biosynthetic novelty

  microbiomes sponge shotgun nonpareil 16s

• Main Factors Influencing the Gut Microbiota of Datong Yaks in Mixed Group.

  PMID 35883324 · PMC9312300 · Animals : an open access journal from MDPI · 2022 · 7 claims · 6 setups

  Has reproduction · 84

  Gut microbial diversity (alpha and beta) differs significantly among domestic males, domestic females, and wild male Datong yaks.

  fresh fecal 16s alpha-diversity beta-diversity

• What the Phage: a scalable workflow for the identification and analysis of phage sequences.

  PMID 36399058 · PMC9673492 · GigaScience · 2022 · 8 claims · 7 setups

  Has reproduction · 76

  WtP combines 11 tools (14 approaches) for phage prediction in a parallel, containerized Nextflow workflow

  assembled illumina phage-predicted predicted multitool metagenome gene

• Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level.

  PMID 17090320 · PMC1654190 · BMC evolutionary biology · 2006 · 8 claims · 5 setups

  Full-text index only

  HHpred (HMM-HMM comparison) detects remote homologs in the human proteome with higher sensitivity than hmmpfam (HMMER), giving 10% more functional domain coverage and 20% higher residue coverage against Pfam-A families.

  proteome homo domains hmm-hmm hmm subtractive

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

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

  Full-text index only

  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

• Dual-platform metagenomic surveillance distinguishes pathogen and resistome hotspots across agricultural and mixed-use watersheds.

  PMID 41890980 · PMC13015239 · One health (Amsterdam, Netherlands) · 2026 · 8 claims · 7 setups

  Full-text index only

  Agricultural drainage ditches consistently harbor higher fecal-associated bacterial diversity than mixed-use or forested sites, with pronounced seasonal shifts (higher during spring/fall high-flow periods).

  surface shotgun trimmed co-assembled 16s shotgun short-read

• The effect of 16S rRNA region choice on bacterial community metabarcoding results.

  PMID 30720800 · PMC6362892 · Scientific data · 2019 · 8 claims · 8 setups

  Has reproduction · 59

  The V2-V3 16S rRNA fragment has higher resolution for lower-rank taxa (genera and species) than V3-V4, enabling more precise distance-based OTU clustering.

  bacterial extracted filtered combined 16s pcr extraction

• Kinetoplastid genomics: the thin end of the wedge.

  PMID 18675383 · PMC2676795 · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2008 · 8 claims · 8 setups

  Full-text index only

  Completion of the T. brucei, T. cruzi, and L. major genome sequencing projects enabled numerous studies that would otherwise have been difficult or impossible.

  brucei major cruzi kinetoplastid whole-genome gene shotgun

• Integrative multi-omics analysis of dietary fibre-induced modulations in the composition and function of chicken caecal microbiota.

  PMID 41741451 · PMC13046836 · NPJ biofilms and microbiomes · 2026 · 6 claims · 6 setups

  Full-text index only

  High inulin supplementation (4%) significantly altered caecal microbial composition and promoted broader microbial metabolic adaptations, indicating a strong fermentative response to soluble fibre

  caecal shotgun metatranscriptomics eukaryotic

• MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.

  PMID 41888223 · PMC13172421 · Scientific reports · 2026 · 8 claims · 8 setups

  Has reproduction · 24

  MiGPC is the first genome-resolved metagenomic gene and protein catalog specifically targeted to enzybiotics

  environmental quality-filtered assembled predicted metagenomic metagenome gene

• Metagenomic Comparison of Bat Colony Resistomes Across Anthropogenic and Pristine Habitats.

  PMID 41594088 · PMC12838372 · Antibiotics (Basel, Switzerland) · 2026 · 8 claims · 7 setups

  Full-text index only

  Anthropogenic exposure enhances the diversity and evenness of resistance mechanisms within bat-associated microbiomes, increasing their potential as AMR reservoirs.

  bat mag-derived shotgun metagenome arg