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 · 48
Bioinformatics Analysis of the Characteristics and Correlation of m6A Methylation in Breast Cancer Progression.
PMID 35655723 · PMC9148239 · Contrast media & molecular imaging · 2022 · 8 claims · 8 setups
Breast cancer samples can be divided into 4 m6A subtypes (quiescent, m6A methylation, protein-binding, mixed) based on expression of m6A-related genes, with consistent proportions across datasets
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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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Bayesian survival analysis in genetic association studies.
PMID 18617538 · PMC2530885 · Bioinformatics (Oxford, England) · 2008 · 7 claims · 5 setups
A novel Bayesian method (BETA-Surv) extends prior case-control haplotype-clustering work to censored survival outcomes by clustering haplotypes via gene tree/perfect phylogeny topology and relative mutation age.
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Has reproduction · 83
Multimodal data integration for biologically-relevant artificial intelligence to guide adjuvant chemotherapy in stage II colorectal cancer.
PMID 40472802 · PMC12171563 · EBioMedicine · 2025 · 6 claims · 7 setups
AI-derived radiological clustering identifies stage II CRC patients with significantly different survival benefit from adjuvant chemotherapy
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Has reproduction · 76
Intrinsic suppression of type I interferon production underlies the therapeutic efficacy of IL-15-producing natural killer cells in B-cell acute lymphoblastic leukemia.
PMID 37217248 · PMC10231005 · Journal for immunotherapy of cancer · 2023 · 8 claims · 8 setups
High expression of IFN-I signaling/response genes predicts favorable clinical outcome (longer relapse-free survival) in B-ALL patients
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Has reproduction · 48
Indoleamine 2, 3-Dioxygenase 1 and CD8 Expression Profiling Revealed an Immunological Subtype of Colon Cancer With a Poor Prognosis.
PMID 33425745 · PMC7793995 · Frontiers in oncology · 2020 · 7 claims · 6 setups
The CD8A-high/IDO1-high colon cancer subtype (group IV*) has the worst survival despite high CD8 infiltrates.
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Has reproduction · 71
Developing a novel immune infiltration-associated mitophagy prediction model for amyotrophic lateral sclerosis using bioinformatics strategies.
PMID 38601155 · PMC11005030 · Frontiers in immunology · 2024 · 7 claims · 6 setups
An 18-gene mitophagy-related prognostic signature was identified by machine learning and used to build a prognostic risk score model for ALS.
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Indirect genomic effects on survival from gene expression data.
PMID 18358079 · PMC2397510 · Genome biology · 2008 · 7 claims · 6 setups
A novel methodology (dynamic path analysis combined with additive hazard survival regression) can detect and quantify indirect effects of gene expression on survival mediated through transcription factor target genes.
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Association of p53 gene mutations with short survival in pancreatic adenocarcinoma.
PMID 7730141 · PMC5920762 · Japanese journal of cancer research : Gann · 1995 · 8 claims · 4 setups
p53 gene mutations were detected in 16 of 37 (43%) pancreatic adenocarcinomas by SSCP and direct sequencing
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Predicting survival outcomes using subsets of significant genes in prognostic marker studies with microarrays.
PMID 16549007 · PMC1544357 · BMC bioinformatics · 2006 · 7 claims · 2 setups
A methodology combining Cox proportional hazards models with a compound covariate, cross-validated log partial likelihood (ACVL) for predictive accuracy, and permutation-based significance testing can identify an optimal subset of significant genes for survival prediction
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Has reproduction · 59
Downregulation of Splicing Factor PTBP1 Curtails FBXO5 Expression to Promote Cellular Senescence in Lung Adenocarcinoma.
PMID 39057099 · PMC11276454 · Current issues in molecular biology · 2024 · 8 claims · 8 setups
PTBP1 is significantly upregulated across multiple cancer types including LUAD, and higher PTBP1 levels are associated with worse LUAD patient survival
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Has reproduction · 88
Constructing an APOBEC-related gene signature with predictive value in the overall survival and therapeutic sensitivity in lung adenocarcinoma.
PMID 37954334 · PMC10637964 · Heliyon · 2023 · 8 claims · 8 setups
APOBEC family genes are aberrantly expressed across cancers, with APOBEC3B the most consistently upregulated, and APOBEC3B/APOBEC3A are markedly altered in LUAD
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Has reproduction · 89
What's Genetic Variation Got to Do with It? Starvation-Induced Self-Fertilization Enhances Survival in Paramecium.
PMID 32163147 · PMC7239694 · Genome biology and evolution · 2020 · 8 claims · 5 setups
Self-fertilization enhances heat shock resistance in P. tetraurelia in the absence of new genetic variation
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Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development.
PMID 16800721 · PMC1483910 · PLoS medicine · 2006 · 8 claims · 8 setups
Multi-scale genomic similarities exist between four human lung cancer subtypes and the developing mouse lung, and these similarities are prognostically meaningful.
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Has reproduction · 71
Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.
PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 7 claims · 7 setups
AML patients can be categorized into two distinct PANRG-based clusters with differing prognosis and immune characteristics
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Has reproduction · 48
Comparative analysis of molecular signatures reveals a hybrid approach in breast cancer: Combining the Nottingham Prognostic Index with gene expressions into a hybrid signature.
PMID 35143511 · PMC8830616 · PloS one · 2022 · 8 claims · 6 setups
A hybrid signature combining the Nottingham Prognostic Index with SIS-selected gene expressions can be built in a data-driven fashion (NPI treated as a gene expression during feature selection).
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Has reproduction · 81
Deubiquitination enzyme USP35 negatively regulates MAVS signaling to inhibit anti-tumor immunity.
PMID 40016186 · PMC11868397 · Cell death & disease · 2025 · 8 claims · 8 setups
USP35 interacts with MAVS and removes its K63-linked polyubiquitin chains, inhibiting viral-induced MAVS-TBK1-IRF3 activation and downstream inflammatory gene expression
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Has reproduction · 62
Specific Marker Gene Analysis for Primary Central Nervous System Lymphoma Based on Methylation Difference and Development of Detection Primers.
PMID 41097902 · PMC12528802 · Brain and behavior · 2025 · 6 claims · 6 setups
RHEB promoter hypermethylation is a PCNSL-specific biomarker distinguishing PCNSL from other CNS diseases.
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Has reproduction · 80
Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity.
PMID 36928603 · PMC10101853 · Nature genetics · 2023 · 8 claims · 6 setups
The WHO histopathological classification of MPM accounts for only up to ~10% of interpatient molecular differences
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Allelotype of squamous cell carcinoma of the head and neck: fractional allele loss correlates with survival.
PMID 7577465 · PMC2033926 · British journal of cancer · 1995 · 7 claims · 4 setups
Allelic imbalance/LOH occurs most frequently on chromosome arms 3p, 9p, 17p and 18q (>45% LOH) in SCCHN