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 · 90
Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer.
PMID 40216980 · PMC12117045 · EMBO reports · 2025 · 8 claims · 11 setups
MYC eRNAs (notably MYC-490-kb) are transcribed from the MYC super-enhancer and are upregulated by chronic TNF-α stimulation specifically in pancreatic cancer cells, not normal pancreatic epithelial cells
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Has reproduction · 22
Machine learning-based DNA microarray analysis for disease detection using the MICRO-AI framework.
PMID 41925147 · PMC13051084 · Science progress · 2026 · 8 claims · 1 setups
MICRO-AI's attention-weighted feature fusion reduces dimensionality by over 99% (from ~20,000 to ~127 genes) without loss of biological significance
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Has reproduction · 73
Detecting aberrant DNA methylation in Illumina DNA methylation arrays: a toolbox and recommendations for its use.
PMID 37218167 · PMC10208159 · Epigenetics · 2023 · 8 claims · 8 setups
Developed OutlierMeth, an R package that computes probe-specific thresholds and flags DNA methylation outliers from array data
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Has reproduction · 51
Unveiling prognostics biomarkers of tyrosine metabolism reprogramming in liver cancer by cross-platform gene expression analyses.
PMID 32542016 · PMC7295234 · PloS one · 2020 · 7 claims · 8 setups
Five tyrosine catabolic enzymes (TAT, HPD, HGD, GSTZ1, FAH) are downregulated in HCC compared to normal liver at mRNA and/or protein level
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Has reproduction · 35
Molecular and Clinical Relevance of ZBTB38 Expression Levels in Prostate Cancer.
PMID 32365491 · PMC7281456 · Cancers · 2020 · 8 claims · 8 setups
ZBTB38 mRNA expression is significantly lower in prostate cancer than in normal/benign prostate tissue, and further reduced in metastatic versus localised tumours
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Full-text index only
Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer.
PMID 39018396 · PMC466953 · Science advances · 2024 · 8 claims · 8 setups
Primate-specific ERVs are a rich source of enhancers displaying cancer-specific activity across multiple tumor types
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Has reproduction · 61
miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems.
PMID 32374865 · PMC7319446 · Nucleic acids research · 2020 · 8 claims · 3 setups
miEAA 2.0 supports miRNA/precursor enrichment input from ten frequently investigated organisms, expanding beyond the human-only first release.
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Has reproduction · 62
Predicting Bone Metastasis Using Gene Expression-Based Machine Learning Models.
PMID 34858485 · PMC8631472 · Frontiers in genetics · 2021 · 8 claims · 5 setups
A DNN model built on 34 top-ranked hub genes achieves the highest prediction accuracy (AUC 92.11%) for distinguishing primary from bone-metastasized tumors
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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 · 77
PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines.
PMID 34093998 · PMC8142020 · Computational and structural biotechnology journal · 2021 · 6 claims · 8 setups
PredTAD, a Gradient Boosting Machine model using epigenomic and genomic ChIP-seq-derived features plus neighboring-bin information, classifies 10 kb genomic bins as TAD boundary or non-boundary
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Has reproduction · 89
Inference of Subpathway Activity Profiles Reveals Metabolism Abnormal Subpathway Regions in Glioblastoma Multiforme.
PMID 33072547 · PMC7533644 · Frontiers in oncology · 2020 · 8 claims · 7 setups
A GSVA-based method for constructing a metabolic subpathway activity score matrix accurately identifies abnormal GBM metabolic targets
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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 · 84
AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas.
PMID 36134663 · PMC9675486 · JCI insight · 2022 · 8 claims · 8 setups
An AI-guided Boolean network approach (BoNE) models transcriptomic continuum states of normal esophagus, BE, and EAC to derive classifier gene signatures
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Full-text index only
Migratory Tumor Cells Cooperate with Cancer Associated Fibroblasts in Hormone Receptor-Positive and HER2-Negative Breast Cancer.
PMID 38892065 · PMC11172245 · International journal of molecular sciences · 2024 · 8 claims · 8 setups
HR+/HER2-BC tumor epithelial cells comprise four single-cell-defined functional (SC-f) subtypes: migratory, secretory, proliferating, and dysfunctional.
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Has reproduction · 89
mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations.
PMID 31799603 · PMC6954439 · Nucleic acids research · 2020 · 5 claims · 5 setups
mitoXplorer integrates transcriptome, proteome, and mutation data with a manually curated mitochondrial interactome of ~1200 genes grouped into 38 mitochondrial processes across four model species.