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).
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Has reproduction · 78
Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.
PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 6 claims · 8 setups
A consensus WGCNA approach combining matched tumor-organoid and independent organoid drug-response expression data identifies gene modules and hub genes predictive of 5-FU chemotherapy response
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Has reproduction · 83
Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients.
PMID 38650649 · PMC11034498 · PeerJ · 2024 · 8 claims · 8 setups
188 differentially expressed genes (DEGs) between IS and control blood samples were identified and enriched in immune-related biological pathways
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Has reproduction · 77
SurvConvMixer: robust and interpretable cancer survival prediction based on ConvMixer using pathway-level gene expression images.
PMID 38539106 · PMC10967213 · BMC bioinformatics · 2024 · 6 claims · 5 setups
SurvConvMixer, using pathway-level gene expression images and ConvMixer, achieves strong internal validation AUC for overall survival prediction, especially on larger datasets like LUAD
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Has reproduction · 97
Identification of immune-related signatures and pathogenesis differences between thoracic aortic aneurysm patients with bicuspid versus tricuspid valves via weighted gene co-expression network analysis.
PMID 37883426 · PMC10602290 · PloS one · 2023 · 6 claims · 8 setups
TAA/TAV pathogenesis is more strongly associated with immune-related gene expression than TAA/BAV.
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Has reproduction · 73
A gene signature related to programmed cell death to predict immunotherapy response and prognosis in colon adenocarcinoma.
PMID 39950044 · PMC11823652 · PeerJ · 2025 · 8 claims · 8 setups
COAD patients can be divided into two molecular subtypes (S1, S2) based on 21 prognostic PCD-related genes, with S1 showing worse prognosis and immunosuppressive microenvironment, S2 showing better prognosis and stronger anti-tumor immunity
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Has reproduction · 71
Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma.
PMID 41048340 · PMC12491262 · Frontiers in bioinformatics · 2025 · 8 claims · 8 setups
IRG expression pattern clusters LUAD patients into groups with significantly different survival outcomes and immune cell infiltration
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Has reproduction · 76
Exploration of the shared diagnostic genes and molecular mechanism between obesity and atherosclerosis via bioinformatic analysis.
PMID 39825072 · PMC11742665 · Scientific reports · 2025 · 8 claims · 8 setups
56 shared genes with consistent expression trend were identified between OB and AS by intersecting WGCNA key module genes with DEGs
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Has reproduction · 80
Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma.
PMID 39553728 · PMC11569783 · PeerJ · 2024 · 8 claims · 8 setups
WGCNA identified 214 key genes in the blue module most correlated with LUAD
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Has reproduction · 50
STAT1 and IL-7 as potential diagnostic biomarkers for distinguishing high-grade from low-grade serous ovarian cancer: a multi-cohort analysis.
PMID 42058211 · PMC13120972 · Frontiers in immunology · 2026 · 8 claims · 7 setups
STAT1 and IL-7 are differentially expressed immune-related genes that can distinguish HGSOC from LGSOC with strong diagnostic performance in the training cohort (AUC 0.908 and 0.842).
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Has reproduction
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
Differential DNA methylation occurs predominantly in intergenic regions and low methylated regions (LMRs), highlighting the role of distal regulatory elements in COVID-19 severity.
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Has reproduction · 75
geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response.
PMID 33952321 · PMC8097837 · Genome biology · 2021 · 8 claims · 6 setups
geneshot identifies microbial genomic islands consistently associated with ICI response across independent cohorts
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Has reproduction · 65
Estimating biodiversity across the tree of life on Mount Everest's southern flank with environmental DNA.
PMID 36148432 · PMC9486557 · iScience · 2022 · 8 claims · 6 setups
eDNA from ten high-alpine ponds and streams (4,500-5,500 m) on Mt. Everest's southern flank revealed 187 potential orders from 36 phyla across the Tree of Life.
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Has reproduction · 56
DESE: estimating driver tissues by selective expression of genes associated with complex diseases or traits.
PMID 31694669 · PMC6836538 · Genome biology · 2019 · 8 claims · 8 setups
DESE is a unified iterative framework that estimates driver tissues of complex diseases/traits from tissue-selective expression of GWAS-associated genes, and outputs prioritized susceptibility genes as a byproduct
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Expression of p73, a novel protein related to the p53 tumour suppressor p53, and apoptosis in cholangiocellular carcinoma of the liver.
PMID 10362118 · PMC2363034 · British journal of cancer · 1999 · 7 claims · 6 setups
p73 protein is expressed (nuclear immunostaining) in a substantial subset of cholangiocellular carcinomas
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Multiple molecular marker testing (p53, C-Ki-ras, c-erbB-2) improves estimation of prognosis in potentially curative resected non-small cell lung cancer.
PMID 10945494 · PMC2374666 · British journal of cancer · 2000 · 6 claims · 4 setups
Testing 3 molecular markers (c-Ki-ras, p53, c-erbB-2) together improves estimation of prognosis compared to single marker testing and defines low- and high-risk groups for treatment failure in R0-resected NSCLC.
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p53 mutations in urinary bladder cancer.
PMID 11384101 · PMC2363660 · British journal of cancer · 2001 · 6 claims · 5 setups
p53 mutations are strongly associated with high-grade/high-stage bladder tumors and are nearly absent in lowly malignant tumors (Ta, G1-G2a)
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Inactivation of O6-methylguanine-DNA methyltransferase by promoter CpG island hypermethylation in gastric cancers.
PMID 12085181 · PMC2375420 · British journal of cancer · 2002 · 6 claims · 8 setups
Loss of MGMT expression in gastric carcinomas frequently results from promoter CpG island hypermethylation.
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Polymorphism at the C-reactive protein locus influences gene expression and predisposes to systemic lupus erythematosus.
PMID 14645206 · PMC3707088 · Human molecular genetics · 2004 · 8 claims · 5 setups
The minor (rare) allele of CRP SNP 'CRP 4' is associated/linked with development of SLE in family-based transmission studies.
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CHEK2 variants associate with hereditary prostate cancer.
PMID 14612911 · PMC2394451 · British journal of cancer · 2003 · 8 claims · 6 setups
CHEK2 1100delC frameshift mutation is significantly more frequent in Finnish HPC patients than in population controls
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Association between telomere length and V(H) gene mutation status in chronic lymphocytic leukaemia: clinical and biological implications.
PMID 12592375 · PMC2377180 · British journal of cancer · 2003 · 7 claims · 5 setups
Unmutated VH gene CLL cases have significantly shorter telomeres than mutated VH gene CLL cases