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 step forward for Shiga toxin-producing Escherichia coli identification and characterization in raw milk using long-read metagenomics.

  PMID 36748417 · PMC9836091 · Microbial genomics · 2022 · 8 claims · 6 setups

  Has reproduction · 75

  Long-read metagenomics enables isolation-independent identification and characterization of eae-positive STEC directly from raw milk.

  pure enriched stec-negative extracted ont real-time artificial

• Transposable elements are driving rapid adaptation of Enterococcus faecium.

  PMID 42020750 · PMC13216065 · Nature · 2026 · 8 claims · 8 setups

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  E. faecium has the highest IS density among ESKAPEE pathogens, dominated by replicative ISL3 family elements

  eskapee faecium ncbi single-hospital large-scale chromosome core

• Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring.

  PMID 42038409 · PMC13107125 · NAR genomics and bioinformatics · 2026 · 7 claims · 7 setups

  Has reproduction · 78

  Long-read shotgun metagenomic sequencing of eDNA can simultaneously detect and quantify organismal DNA from viruses to mammals in a single assay

  river edna extracted raw edna concentration quantitative

• Rapid identification of microbial pathogens and antimicrobial resistance from bloodstream infections using long-read sequencing.

  PMID 42274466 · PMC13256323 · Microbial genomics · 2026 · 8 claims · 8 setups

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  A novel ONT long-read sequencing laboratory and bioinformatic workflow rapidly identifies bacterial and fungal organisms and AMR determinants from positive blood cultures

  positive matching pure ont long-read short-read maldi-tof

• Microbial diversity of plant pathogens and insect endosymbionts in Reptalus artemisiae.

  PMID 41826827 · PMC13202766 · BMC microbiology · 2026 · 8 claims · 7 setups

  Has reproduction · 71

  R. artemisiae harbors six prokaryotic taxa: two plant pathogens ('Ca. P. solani' and 'Ca. A. phytopathogenicus') and four insect endosymbionts ('Ca. Vidania', 'Ca. Purcelliella', 'Ca. Karelsulcia', Wolbachia)

  whole-insect individual metagenomic endosymbiont pcr-free its2 taxonomic

• Wochenende - modular and flexible alignment-based shotgun metagenome analysis.

  PMID 36368923 · PMC9650795 · BMC genomics · 2022 · 8 claims · 6 setups

  Has reproduction · 88

  Wochenende is a modular, transparent alignment-based pipeline for shotgun metagenome analysis supporting short and long reads across all kingdoms of life

  zymo bacterial reference shotgun comparative reference

• The chromosomal genome sequence of the common sea fan, Gorgonia ventalina (Linnaeus, 1758) (Malacalcyonacea: Gorgoniidae).

  PMID 41625986 · PMC12856254 · Wellcome open research · 2026 · 7 claims · 6 setups

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  A chromosome-level genome assembly was produced for Gorgonia ventalina with a total length of 339.18 Mb

  gorgonia cobiont pacbio hi-c rna-seq

• StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution.

  PMID 42097292 · PMC13188985 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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  StrainMake is a Snakemake-based, Conda-managed workflow for de novo metagenomic analysis from short, long, or hybrid sequencing data.

  cami high-quality recovered gut metagenome metagenomic mag