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

• Expression spectrum of TE-driven transcripts in human adult tissues.

  PMID 41593763 · PMC12924553 · Genome biology · 2026 · 8 claims · 8 setups

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  TE-driven transcripts are broadly expressed across human adult tissues and contribute to both housekeeping and tissue-specific gene regulation

  tissues paired sequences genome bulk differential chip-seq

• Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles.

  PMID 37444556 · PMC10340377 · Cancers · 2023 · 8 claims · 6 setups

  Has reproduction · 90

  EV extraction methods vary in reproducibility for isolating small RNAs, with effects on small RNA composition

  evs matched plasma cell-line small differential adapter

• Eduomics: a Nextflow pipeline to simulate -omics data for education.

  PMID 41816779 · PMC12972896 · NAR genomics and bioinformatics · 2026 · 8 claims · 4 setups

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  Eduomics is a Nextflow DSL2 pipeline that automates generation of validated variant-calling and RNA-seq datasets for education while abstracting away technical requirements

  chromosome full simulated exome rna-seq pipeline

• Single-cell analysis of signalling and transcriptional responses to type I interferons.

  PMID 41896367 · PMC13172048 · EMBO reports · 2026 · 7 claims · 6 setups

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  Different immune cell types show cell-type-specific patterns of STAT phosphorylation and gene expression changes in response to type I IFN

  freshly pbmcs mass rt-qpcr bulk