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 UCSC Genome Browser Database: 2008 update.

  PMID 18086701 · PMC2238835 · Nucleic acids research · 2008 · 8 claims · 8 setups

  Full-text index only

  The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes.

  zebrafish yale vertebrate non-human sage expression snp

• 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

  Full-text index only

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

  european tmd gwas gtex gwas gwas-by-subtraction bayesian

• Mapping Genetic Regulation of Transcription to Identify Functional Variants and Genes Associated with Pancreatic Cancer Risk.

  PMID 41824785 · PMC13205582 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Full-text index only

  A genome-wide cis-eQTL meta-analysis of 482 pancreatic tissues (177 TCGA tumor + 305 GTEx normal) identified 1,123,483 significant SNP-gene pairs, 709,720 unique eQTLs, and 13,758 eGenes (FDR<0.05)

  tcga chinese significant egenes cis-eqtl gwas variant

• GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.

  PMID 40208796 · PMC11984350 · GigaScience · 2025 · 8 claims · 8 setups

  Has reproduction · 76

  GeneSetCart is a web-based platform that lets users assemble, augment, combine, visualize, and analyze gene sets from multiple sources in one place

  user-assembled archs4 generif-derived aggregated gene gene-gene literature

• The gene expression landscape of disease genes.

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

  Full-text index only

  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

• Analyzing biomarker discovery: Estimating the reproducibility of biomarker sets.

  PMID 35901020 · PMC9333302 · PloS one · 2022 · 8 claims · 6 setups

  Has reproduction · 83

  Non-reproducibility is a common problem in biomarker discovery: independently derived biomarker sets for the same phenotype frequently share very few features across studies

  gse7390 geo ega tcga-brca t-test-based reproducibility genome-wide

• Differentially expressed genes reflect disease-induced rather than disease-causing changes in the transcriptome.

  PMID 34561431 · PMC8463674 · Nature communications · 2021 · 8 claims · 7 setups

  Has reproduction · 100

  revTWMR, a reverse transcriptome-wide Mendelian Randomization approach integrating GWAS and whole-blood trans-eQTL summary statistics, is proposed to estimate the causal effect of a phenotype on gene expression.

  blood ra-associated genome-wide revtwmr transcriptome-wide reverse functional

• Reactive astrocytes acquire neuroprotective as well as deleterious signatures in response to Tau and Aß pathology.

  PMID 35013236 · PMC8748982 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 84

  Aβ (APP/PS1) and Tau (MAPT P301S) pathology induce distinct but overlapping astrocyte translatome signatures

  astrocytes aldh1l1_egfp-rpl10a astrocyte ageing trap-seq immunofluorescence ribosome

• Genomic regions and candidate genes selected during the breeding of rice in Vietnam.

  PMID 35899250 · PMC9309459 · Evolutionary applications · 2022 · 8 claims · 7 setups

  Has reproduction · 75

  XP-CLR and FST scans identify genomic regions with distorted allele frequency/differentiation patterns resulting from differential selective pressures between Vietnamese rice subpopulations

  vietnamese indica subpopulation whole-genome whole-genome xp-clr fst

• 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

• A HML6 endogenous retrovirus on chromosome 3 is upregulated in amyotrophic lateral sclerosis motor cortex.

  PMID 34253796 · PMC8275748 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction · 84

  The ERV locus HML6_3p21.31c is significantly upregulated in ALS post-mortem motor cortex after multiple-testing correction

  post-mortem als bulk cell-type weighted

• Transcriptome analysis reveals differential splicing events in IPF lung tissue.

  PMID 24647608 · PMC3960165 · PloS one · 2014 · 8 claims · 6 setups

  Has reproduction · 81

  873 genes are differentially expressed in IPF lung tissue versus healthy controls at FDR<5%, with more up-regulated than down-regulated genes.

  lung discovery gene gse24206 sequencing rna-seq real-time