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).

• Deep-learning prediction of gene expression from personal genomes.

  PMID 41495833 · PMC12869966 · Genome biology · 2026 · 8 claims · 8 setups

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  Fine-tuning Enformer on paired personal WGS and RNA-seq data (Variformer) corrects Enformer's failure to predict inter-individual gene expression differences across held-out people.

  gtex rosmap same monocyte paired mutagenesis chromhmm

• NGSTroubleFinder: a tool for detection and quantification of contamination and kinship across human NGS data.

  PMID 41608734 · PMC12838523 · NAR genomics and bioinformatics · 2026 · 8 claims · 8 setups

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  NGSTroubleFinder detects cross-sample contamination, sample swaps, kinship, and sex mismatches from BAM/CRAM files without requiring additional variant-calling steps

  genomes 1000gp internal whole-genome whole-transcriptome wgs

• Single-cell spatial transcriptomic analysis of human skin anatomy.

  PMID 41872488 · PMC13083264 · Nature genetics · 2026 · 8 claims · 6 setups

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  MERFISH-based spatial atlas of ~1.2 million cells resolves 45 cell types across 114 samples and 15 anatomic sites in normal human skin

  normal skin gtex matched merfish scrna-seq bulk

• pmid-41880523

  PMID 41880523 · PMC13154832 · 7 claims · 8 setups

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  Hallmarks of malignancy and cell cycle regulatory pathways are consistently enriched across single-cell, bulk, and spatial transcriptomic modalities, promoting tumor cell proliferation and progression.

  tumor gbm normal wild-type single-cell bulk microarray

• Hypoxia-associated genes as predictors of outcomes in gastric cancer: a genomic approach.

  PMID 40129974 · PMC11931070 · Frontiers in immunology · 2025 · 8 claims · 8 setups

  Has reproduction · 96

  A prognostic model built from five H1-specific hypoxia-associated transcription factors (EHF, EIF1AD, GLA, KEAP1, MAGED2) predicts overall survival in STAD, with high-risk patients showing significantly worse OS.

  gastric gene scrna-seq tcga single-cell wgcna cell-cell

• Genetic subtraction reveals divergent pathways and targets in anxiety-related and anxiety-independent TMD.

  PMID 41796324 · PMC13081294 · The journal of headache and pain · 2026 · 8 claims · 8 setups

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  Anxiety shows significant genetic correlation with TMD (rg=0.4417, p=1.98x10^-19)

  european tmd gwas gtex gwas gwas-by-subtraction bayesian

• 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

• Involvement of N4BP2L1, PLEKHA4, and BEGAIN genes in breast cancer and muscle cell development.

  PMID 38859961 · PMC11163233 · Frontiers in cell and developmental biology · 2024 · 8 claims · 8 setups

  Has reproduction · 73

  N4BP2L1, PLEKHA4, and BEGAIN, normally highly expressed in breast myoepithelial and smooth muscle cells, are significantly downregulated in breast tumor tissue of a 50-patient cohort

  breast paired embryonic hesc-derived bulk rt-qpcr immunofluorescence