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).

• Characterization of Human Genes Modulated by Porphyromonas gingivalis Highlights the Ribosome, Hypothalamus, and Cholinergic Neurons.

  PMID 34194426 · PMC8236716 · Frontiers in immunology · 2021 · 8 claims · 8 setups

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  Genes in the SRP-dependent cotranslational protein targeting to membrane (ER translocation) pathway and ribosomal subunit genes are strongly and specifically enriched for arginine and lysine residues, suggesting high susceptibility to gingipain cleavage.

  protein-coding coli recombinant postmortem proteome-wide gene gingipain

• Antimicrobial resistance dissemination via horizontal gene transfer is constrained in stratified waters.

  PMID 41813906 · PMC13022341 · Communications biology · 2026 · 8 claims · 7 setups

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  No evidence for recent HGT-mediated dissemination of ARGs across depth layers was detected, despite genetic compatibility among co-occurring bacteria.

  stratified freshwater predicted arg-carrying depth-resolved horizontal arg

• A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58.

  PMID 35115531 · PMC8813906 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 95

  ST58 contains a major sub-lineage (BAP2, n=363) characterized by near-ubiquitous carriage of ColV plasmids

  coli st58 novo draft whole-genome pan-genome-wide plasmid

• Biomarker discovery in neurodegenerative diseases: a proteomic approach.

  PMID 18938247 · PMC2939006 · Neurobiology of disease · 2009 · 6 claims · 8 setups

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  Proteomic profiling of CSF and plasma can identify candidate protein biomarkers that distinguish AD patients from controls with high sensitivity and specificity

  csf plasma brain 2-dge lc-ms seldi-tof-ms

• Metagenomic Assessment of Full-Scale Wastewater Treatment Plants Identifies Sentinel Antibiotic Resistance Gene Families for Monitoring Reclaimed Wastewater and Treated Sludge.

  PMID 41636304 · PMC12918712 · Environmental science & technology · 2026 · 7 claims · 6 setups

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  Reclaimed effluents show lower AMR exposure (<0.5 ARGs/cell) than typically reported for secondary effluents

  influent card pubmlst targeted shotgun arg

• 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

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  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

• Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs.

  PMID 15817567 · PMC1074747 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  966 pseudogenes derived from the four human Y (hY) RNAs were characterized in the human genome

  genome chimpanzee pseudogenes genomic megablast blat sequence