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 · 82
Landscape of allele-specific transcription factor binding in the human genome.
PMID 33980847 · PMC8115691 · Nature communications · 2021 · 8 claims · 6 setups
A novel statistical framework (ADASTRA) calls allele-specific TF binding from existing ChIP-Seq alignments by jointly correcting for background allelic dosage (BAD, from aneuploidy/CNVs) and reference mapping bias.
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Has reproduction · 49
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
LRP1 is the top hub gene with the highest diagnostic performance for distinguishing ectopic from eutopic endometrium in EMS
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Has reproduction · 85
Digital sorting of complex tissues for cell type-specific gene expression profiles.
PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups
The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.
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Has reproduction · 55
Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.
PMID 37691920 · PMC10485775 · Frontiers in immunology · 2023 · 8 claims · 8 setups
352 DEGs (198 up-regulated, 154 down-regulated) were identified between RPL and control endometrial samples
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Has reproduction · 42
Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.
PMID 39152432 · PMC11328457 · Journal of translational medicine · 2024 · 7 claims · 8 setups
PAAD tumors can be consensus-clustered into immunologically hot and cold subtypes based on CIBERSORT-derived immune cell fractions, with significantly different survival outcomes.
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Has reproduction · 80
Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.
PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 7 claims · 8 setups
Six genes (CST7, HSP90AB1, PADI4, PLBD1, RAB32, SLAMF6) are signature diagnostic biomarkers for aSAH identified by LASSO and SVM-RFE.
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Has reproduction · 79
TGF-β-mediated activation of fibroblasts in cervical cancer: implications for tumor microenvironment and prognosis.
PMID 40124621 · PMC11929507 · PeerJ · 2025 · 8 claims · 8 setups
TGF-β signaling pathway activity is significantly increased in fibroblasts from cervical cancer samples compared to normal samples and correlates with tumor proliferation and differentiation.
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Has reproduction · 68
Machine learning algorithm predicts fibrosis-related blood diagnosis markers of intervertebral disc degeneration.
PMID 37915003 · PMC10619283 · BMC medical genomics · 2023 · 7 claims · 7 setups
CEP120 and SPDL1 are fibrosis-related diagnostic genes for IDD, identified via a random forest model from 29 differentially expressed fibrosis-related genes
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Has reproduction · 71
Identification of the shared hub gene signatures and molecular mechanisms between HIV-1 and pulmonary arterial hypertension.
PMID 38528047 · PMC10963360 · Scientific reports · 2024 · 7 claims · 7 setups
HIV-1 and PAH share 109 co-expressed genes primarily enriched in type I interferon (IFN) pathways.
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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 · 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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Full-text index only
High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.
PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups
Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse
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Has reproduction · 76
M6A-mediated molecular patterns and tumor microenvironment infiltration characterization in nasopharyngeal carcinoma.
PMID 38532632 · PMC10978033 · Cancer biology & therapy · 2024 · 8 claims · 8 setups
NPC samples can be divided into two distinct m6A-related molecular subclasses based on prognostic m6A regulators
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Has reproduction · 73
Comprehensive analysis of mitophagy in HPV-related head and neck squamous cell carcinoma.
PMID 37161060 · PMC10170109 · Scientific reports · 2023 · 8 claims · 8 setups
In HPV-associated HNSCC, the mitophagy process affects tumour development, immune cell infiltration and prognosis.
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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 · 7 setups
TAA/TAV pathogenesis is more associated with immune-related gene expression than TAA/BAV, with two WGCNA gene modules (brown and blue) enriched for immune functions.