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).

• Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.

  PMID 40170038 · PMC11963311 · BMC medical genomics · 2025 · 7 claims · 7 setups

  Has reproduction

  Differential DNA methylation occurs predominantly in intergenic regions and low methylated regions (LMRs), highlighting the role of distal regulatory elements in COVID-19 severity.

  nasal aggregated genes differentially whole-genome methylation tiling

• Insights into the physiology of childbirth using transcriptomics.

  PMID 16752954 · PMC1475648 · PLoS medicine · 2006 · 7 claims · 4 setups

  Full-text index only

  Labor results in a change in the transcriptome in each component of the uterus studied

  uterine lower microarray quantitative re-analysis

• Metatranscriptomics of the human oral microbiome during health and disease.

  PMID 24692635 · PMC3977359 · mBio · 2014 · 8 claims · 8 setups

  Has reproduction · 62

  Disease-associated periodontal communities display conserved community-level metabolic gene expression profiles between patients, whereas the metabolic gene expression of individual species is highly variable between patients.

  patient-matched subset health rna-seq rrna comparison metatranscriptomics

• Grass supplementation to a pellet-based diet fails to enrich gut microbiomes with wild-like functions in captive-bred hares.

  PMID 41784373 · PMC13055366 · Microbiology spectrum · 2026 · 8 claims · 6 setups

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  Significant taxonomic and functional differences exist between the gut microbiota of wild and captive-bred European hares

  fecal gut mag mags shotgun alpha differential

• The oxazolidinone derivative locostatin induces cytokine appeasement.

  PMID 19917702 · PMC2799496 · Journal of immunology (Baltimore, Md. : 1950) · 2009 · 7 claims · 7 setups

  Full-text index only

  RKIP is differentially localized (not differentially expressed) on the proteomic map after in vivo T cell recall compared to resting state

  ot-i splenocytes fractions serum intracellular proteomics sds-page

• Tracing the early bacterial settlers in preterm and very-low birth-weight infants: first report of microbiota dynamics in South American neonates.

  PMID 41563098 · PMC12890024 · Infection and immunity · 2026 · 7 claims · 7 setups

  Full-text index only

  Klebsiella pneumoniae species complex and Escherichia coli dominate the gut microbial composition of VLBW infants

  stool 16s fecal full-length taxonomic alpha

• miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline.

  PMID 34308351 · PMC8294687 · NAR genomics and bioinformatics · 2021 · 8 claims · 6 setups

  Has reproduction

  miRge3.0 is a Python 3-based small RNA-seq and tRF analysis pipeline that improves on miRge2.0 (which was Python 2.7-based)

  sra synthetic qiagen-processed same small umi mirna

• Report on the Molecular Approaches to Osteoarthritis Symposium, Imperial College London, UK, 18-20 April 2004.

  PMID 15380034 · PMC546282 · Arthritis research & therapy · 2004 · 8 claims · 8 setups

  Full-text index only

  OA cartilage and synovium show an 'IL-1 signature' of upregulated inflammatory cytokines/chemokines, with peripheral blood leukocytes possibly activated by trafficking through affected joints

  cartilage knee mesenchymal chondrocytes transcriptional clinical overexpression

• Elevated phenylacetylglutamine caused by gut dysbiosis associated with type 2 diabetes increases neutrophil extracellular traps formation and exacerbates brain infarction.

  PMID 40471587 · PMC12599254 · Clinical science (London, England : 1979) · 2025 · 7 claims · 8 setups

  Full-text index only

  Plasma PAGln levels are significantly higher in ischemic stroke patients with T2D than in those without T2D

  fecal plasma sprague-dawley cerebral 16s metagenome targeted

• Monocarboxylate Transporter-2 Expression Restricts Tumor Growth in a Murine Model of Lung Cancer: A Multi-Omic Analysis.

  PMID 34638954 · PMC8508890 · International journal of molecular sciences · 2021 · 8 claims · 8 setups

  Has reproduction · 53

  MCT2 knockout (KO) increases tumor weight, volume, and local invasiveness in the TC1 lung carcinoma model

  testis tc1 tumor tumor-associated western tumor electron

• Niche Modification by Sulfate-Reducing Bacteria Drives Microbial Community Assembly in Anoxic Marine Sediments.

  PMID 36988509 · PMC10128000 · mBio · 2023 · 7 claims · 7 setups

  Has reproduction · 100

  SRB modify niches (e.g., pH) to affect species coexistence during organic matter degradation

  coastal marine marinilabiliales srb-inhibited 16s molecular physicochemical

• Critical care: applying genomics to inflammation outcomes.

  PMID 16330338 · PMC1314943 · Environmental health perspectives · 2005 · 8 claims · 6 setups

  Full-text index only

  Genetic factors drive key aspects of an individual's inflammatory outcome after trauma, burns, or sepsis

  leukocytes whole-blood healthy peripheral genomewide whole-genome microarray

• Proteomic approaches to cancer biomarkers.

  PMID 19931265 · PMC2873613 · Gastroenterology · 2010 · 8 claims · 8 setups

  Full-text index only

  Combining abundant-protein depletion, offline fractionation, and subproteome (e.g., glycoproteome) enrichment with 2D LC-MS/MS increases the dynamic range and depth of blood proteome analysis for biomarker discovery.

  plasma serum capan-2 apcδ580 lectin silac elisa

• Standing on the shoulders of microbes: microbiome thermal priming buffers the effects of heatwaves on clams by preventing stress overreaction.

  PMID 41987828 · PMC13077298 · ISME communications · 2026 · 8 claims · 5 setups

  Full-text index only

  Transplantation of a microbiome from heat-primed donor clams into non-acclimated recipients is sufficient to enhance host resilience during a subsequent simulated heatwave.

  ruditapes philippinarum 16s host enzymatic

• A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.

  PMID 18631455 · PMC2727981 · Immunity · 2008 · 7 claims · 8 setups

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  Transcriptional modules constructed from coordinately expressed genes across 8 diseases form stable, biologically coherent functional units

  pbmc genes monocytes original microarray literature stimulation

• 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

• 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

  Full-text index only

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

  influent card pubmlst targeted shotgun arg