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).

• The gene expression landscape of disease genes.

  PMID 41664080 · PMC12983648 · Genome biology · 2026 · 8 claims · 8 setups

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  In tissues and cell types with established disease relevance, disease genes show higher and more specific gene expression than control genes

  gtex pubmed tabula archs4 differential magma anderson-darling

• Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci.

  PMID 41807385 · PMC12979833 · Nature communications · 2026 · 8 claims · 8 setups

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  Integration of CAD GWAS summary statistics with epigenetic data from 45 cell types identifies 1580 candidate CAD genes

  cad-associated disease-relevant types cad variant epigenetic tf-snv

• A genome-wide association analysis identifies 16 novel susceptibility loci for carpal tunnel syndrome.

  PMID 30833571 · PMC6399342 · Nature communications · 2019 · 6 claims · 8 setups

  Has reproduction · 90

  A GWAS of 12,312 CTS cases and 389,344 controls in UK Biobank identifies 16 novel genome-wide significant susceptibility loci for CTS

  biobank surgically gwas transformed genome-wide sequencing gene-based

• Prostate cancer genomics: towards a new understanding.

  PMID 19104501 · PMC2721916 · Nature reviews. Genetics · 2009 · 8 claims · 8 setups

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  Multiple GWAS have identified over a dozen replicated germline SNPs each associated with a modest increase in prostate cancer risk

  germline families african-american combined genome-wide linkage admixture

• Cross-ancestry genome-wide association studies of liver function biomarkers uncover pleiotropic variants, systemic disease links and therapeutic targets.

  PMID 41689074 · PMC13005531 · Genome medicine · 2026 · 8 claims · 8 setups

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  5,507 lead signals (P<5x10^-9) were identified for seven LFQBs across ancestries, including 210 novel loci

  hope biobank combined cross-ancestry gwas cross-ancestry functional-informed

• Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets.

  PMID 37563310 · PMC10457199 · Nature immunology · 2023 · 8 claims · 8 setups

  Has reproduction · 93

  Genome-wide pQTL mapping of 91 inflammation-related plasma proteins in 14,824 participants identified 180 significant pQTLs (59 cis, 121 trans) across 108 genomic regions and 70 proteins

  plasma blood tissues gut genome-wide pqtl cis-eqtl

• Protocol to perform cell-type-specific transcriptome-wide association study using scPrediXcan framework.

  PMID 41689808 · PMC12925207 · STAR protocols · 2026 · 6 claims · 6 setups

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  scPrediXcan enables cell-type-specific transcriptome-wide association studies (TWAS) by integrating deep learning-based prediction of gene expression from DNA sequence and epigenetic features.

  acinar individual-level geuvadis beta mlp-based personalized elastic-net

• Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation.

  PMID 41688638 · PMC12987725 · Nature genetics · 2026 · 8 claims · 8 setups

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  Variants in the OR51E1–OR51E2 locus, encoding microbiome-derived fatty acid chemosensors expressed in enteroendocrine cells, are associated with gut microbial richness

  adults subset intestinal enteroendocrine genome-wide sanger single-cell

• Cell type-specific eQTL analysis of COVID-19 based on single-cell transcriptomic data.

  PMID 41064594 · PMC12501775 · NAR genomics and bioinformatics · 2025 · 8 claims · 8 setups

  Has reproduction · 51

  Single-cell eQTL analysis across eight immune cell types identified 2593 genes whose expression is significantly associated with common genetic polymorphisms, with most genes showing cell type-specific effects

  pbmcs eight pbmc monocytes scrna-seq genetic cis-eqtl

• Systems spatiotemporal dynamics of traumatic brain injury at single-cell resolution reveals humanin as a therapeutic target.

  PMID 35951114 · PMC9372016 · Cellular and molecular life sciences : CMLS · 2022 · 8 claims · 8 setups

  Has reproduction · 98

  Coordinated gene expression patterns across cell types are disrupted and re-organized by mTBI with distinct regional, cellular, and temporal (24-h vs 7-day) specificity.

  hippocampus frontal peripheral cell-type single-cell svm-based ligand-receptor

• Identification of potential therapeutic targets for nonischemic cardiomyopathy in European ancestry: an integrated multiomics analysis.

  PMID 39267096 · PMC11396958 · Cardiovascular diabetology · 2024 · 8 claims · 7 setups

  Has reproduction · 89

  Two-sample MR analysis identified 255 circulating plasma proteins associated with NISCM

  european cis-pqtl myocardial geo mendelian bayesian differential

• Integrating human plasma proteomes with genome-wide association data implicates novel proteins and drug targets for rheumatoid arthritis.

  PMID 41540382 · PMC12892679 · Clinical proteomics · 2026 · 8 claims · 8 setups

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  PWAS integrating RA GWAS with ARIC and INTERVAL plasma pQTL data identified 35 genetically regulated proteins (42 associations) significantly associated with RA risk.

  plasma shared gtex blood proteome-wide two-sample bayesian

• scTWAS: a powerful statistical framework for single-cell transcriptome-wide association studies.

  PMID 41820391 · PMC13121454 · Nature communications · 2026 · 8 claims · 5 setups

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  scTWAS uses a latent-variable expression-measurement model combined with a moment-based regression to more accurately estimate genetic regulation of gene expression from single-cell data, improving GReX prediction across cell types and datasets

  onek1k-derived onek1k-based immune brain simulated two-sample stage

• Genetics and environment distinctively shape the human immune cell epigenome.

  PMID 41593234 · PMC12900638 · Nature genetics · 2026 · 8 claims · 6 setups

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  Exposure-associated differentially methylated regions (eDMRs) and genotype-associated DMRs (gDMRs) show distinct genomic distributions: eDMRs are enriched at enhancers/regulatory regions, while gDMRs are predominantly found in gene bodies.

  pbmcs pbmc edmrs differentially single-nucleus fluorescence-activated motif

• 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

• SLC25A37 as a novel therapeutic target for benign prostatic hyperplasia: integrative analyses of single-cell RNA sequencing and genome-wide association studies.

  PMID 41726128 · PMC12917586 · Open medicine (Warsaw, Poland) · 2026 · 8 claims · 8 setups

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  SLC25A37 is causally associated with increased BPH risk, supported by MR, Bayesian colocalization, and reverse MR analyses

  prostate gwas eqtl bph single-cell mendelian bayesian

• Rare variant analyses provide insights into the genetic architecture of endometriosis.

  PMID 41736152 · PMC13001359 · Human genomics · 2026 · 7 claims · 8 setups

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  Gene-based burden testing of rare LoF and deleterious missense variants identifies SOGA1 as significantly associated with endometriosis after Bonferroni correction

  unrelated finngen biobank soga1 exome gene-based protein-protein

• Context-specific regulatory genetic variation in MTOR dampens neutrophil-T cell crosstalk in pneumonia-associated sepsis.

  PMID 41741465 · PMC13057173 · Nature communications · 2026 · 8 claims · 7 setups

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  The MTOR eQTL variant rs4845987 has context-specific, opposite effects on MTOR expression: decreasing it in activated T cells and increasing it in neutrophils.

  blood bulk eqtl sepsis bulk cell-type colocalisation

• Integration of multi-omics and machine learning strategies identifies immune related candidate biomarkers in inflammation-associated hypertrophic cardiomyopathy.

  PMID 41080564 · PMC12510942 · Frontiers in immunology · 2025 · 8 claims · 8 setups

  Has reproduction · 85

  Seven key immune-related genes (RNF165, SNCA, SRGN, MARCO, STEAP4, SIGLEC9, TKT) are associated with HCM by intersecting DEGs with MR-identified eQTLs

  left eqtl degs merged bulk two-sample functional

• LRP1 as a potential diagnostic and immunomodulatory target in endometriosis: evidence from multi-omics and single-cell analyses.

  PMID 42064072 · PMC13124487 · Frontiers in immunology · 2026 · 8 claims · 8 setups

  Has reproduction · 49

  LRP1 is a hub gene with the highest diagnostic performance among 30 candidate hub genes identified by machine learning

  ectopic geo gse5108 training microarray wgcna machine