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).

• 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

• 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

• 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) were identified for HCM by intersecting DEGs with MR-derived HCM-associated eQTLs.

  left european merged degs bulk two-sample machine

• Identification and analysis of co-occurrence networks with NetCutter.

  PMID 18781200 · PMC2526157 · PloS one · 2008 · 8 claims · 4 setups

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  Random sampling from a complete permutation set of the bipartite graph permits co-occurrence analysis with optimal stringency, and the edge-swapping (ES) model closely approximates this and is the preferred null-model among six tested.

  publime bipartite randomized co-occurrence null-model signal-to-noise

• 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

• Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.

  PMID 17166053 · PMC1664705 · PLoS computational biology · 2006 · 8 claims · 8 setups

  Full-text index only

  Integrating interactome and transcriptome data reveals a pair of transcriptionally anticorrelated network modules (P and D) each comprising hundreds of genes, present across individuals and species.

  postmortem genes gene proteins microarray protein-protein hierarchical

• Reusable building blocks in biological systems.

  PMID 30958230 · PMC6303794 · Journal of the Royal Society, Interface · 2018 · 8 claims · 4 setups

  Has reproduction · 82

  Biological systems can be decomposed into phenotypic building blocks (PBBs) via k-maximally reusable decompositions (k-MRD) that maximize average reusability across conditions.

  tissues conditions randomized est-based mirna randomization

• Integrated multi-omics analysis combined with clinical validation reveals that HLA-DRB5 and ODAPH are causal risk genes for keratoconus.

  PMID 41803193 · PMC13179358 · Scientific reports · 2026 · 7 claims · 8 setups

  Has reproduction · 64

  HLA-DRB5 and ODAPH are causal risk genes for keratoconus, supported by SMR and Bayesian colocalization (HLA-DRB5 PP4=0.844, SMR p=0.001, OR=1.768; ODAPH PP4=1.0, SMR p=0.013, OR=202.851).

  corneal gwas string bulk summary-data two-sample

• Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

  PMID 17683551 · PMC1978505 · BMC genomics · 2007 · 7 claims · 8 setups

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  Using human reference promoter sequences is a useful approach for studying gene expression regulation in species with limited or non-existing genomic sequence, such as cattle.

  muscle-specific bovine refseq cardiac novo est blastn

• 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 · 7 claims · 8 setups

  Has reproduction · 49

  LRP1 is the top hub gene with the highest diagnostic performance for distinguishing ectopic from eutopic endometrium in EMS

  ectopic geo training gwas microarray wgcna machine

• Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome.

  PMID 16277660 · PMC1309615 · BMC evolutionary biology · 2005 · 8 claims · 5 setups

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  Ligands are not more closely linked (shorter physical distance) to their cognate receptors than expected by chance

  genome genomic chromosome randomization

• Positive Relationships between Intraocular Pressure and Thyroid Function in Graves' Ophthalmopathy: A Three-Aspect Evidence Analysis.

  PMID 40992768 · PMC12479196 · Yonsei medical journal · 2025 · 6 claims · 4 setups

  Has reproduction · 68

  Increased thyroid function is a risk factor for elevated IOP in patients with Graves' ophthalmopathy.

  patients nhanes gtex geo retrospective cross-sectional summary-data-based

• An analysis of human microRNA and disease associations.

  PMID 18923704 · PMC2559869 · PloS one · 2008 · 8 claims · 8 setups

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  MicroRNAs tend to show similar dysfunctional evidence (both up- or both down-regulated) for diseases within the same disease cluster, and different dysfunctional evidence between different disease clusters.

  literature-derived diseases mirnas mirna literature bipartite mirna

• Topological signatures in regulatory network enable phenotypic heterogeneity in small cell lung cancer.

  PMID 33729159 · PMC8012062 · eLife · 2021 · 7 claims · 6 setups

  Has reproduction · 94

  Discrete (Boolean/Ising) and continuous (RACIPE) simulations of the SCLC regulatory network yield similar multistable phenotypic distributions, with four dominant steady states (X1-X4) that map onto experimentally observed SCLC molecular subtypes.

  sclc randomized mutant boolean racipe network

• 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 pQTLs (59 cis, 121 trans).

  plasma blood tissues pqtl genome-wide pqtl cis-eqtl

• Decoding and reconstructing disease relations between dry eye and depression: a multimodal investigation comprising meta-analysis, genetic pathways and Mendelian randomization.

  PMID 38548265 · PMC11954816 · Journal of advanced research · 2025 · 7 claims · 8 setups

  Has reproduction · 79

  Meta-analysis confirms a positive bidirectional association between DED and DEP (DED patients have increased DEP prevalence and vice versa).

  studies taiwan twb ded meta-analysis genome-wide conditional

• A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.

  PMID 34316714 · PMC8271219 · NAR cancer · 2021 · 7 claims · 8 setups

  Has reproduction · 85

  EMT and tamoxifen-resistance (TamR) regulatory axes can drive one another, enabling non-genetic heterogeneity via six co-existing phenotypes (ES, ER, HS, HR, MS, MR)

  gene same randomized publicly racipe stochastic randomized

• A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity.

  PMID 37963558 · PMC10645512 · Journal of the Royal Society, Interface · 2023 · 8 claims · 7 setups

  Has reproduction · 95

  RKIP and BACH1 are negatively correlated with each other across most cancer types in TCGA

  tcga er+ ccle computational spearman correlation gene

• Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites.

  PMID 17003057 · PMC1635253 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  Stepwise directed evolution using chimeric FLRT (FRT/genomic hybrid) intermediate sites can generate Flp variants capable of recombining native genomic FRT-like sequences from the human IL10 gene (FL-IL10A, FL-IL10B).

  coli flp il10 flp-holliday recombination site-specific computational

• Genome-wide associations of aortic distensibility suggest causality for aortic aneurysms and brain white matter hyperintensities.

  PMID 35922433 · PMC9349177 · Nature communications · 2022 · 8 claims · 7 setups

  Has reproduction

  Genome-wide association of six CMR-derived aortic traits in up to 32,590 UK Biobank participants identifies 102 loci (including 27 novel associations) for aortic distensibility and area.

  biobank arterial aortic genome-wide multi-trait cardiac