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 · 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 · 75
Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight.
PMID 35028613 · PMC8714941 · Cell reports. Medicine · 2021 · 8 claims · 8 setups
Stage-stratified molecular subclassification (analyzing Ta and T1 separately) is more biologically and clinically informative than subtypes derived from all NMIBC combined, especially for T1 tumors.
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Has reproduction · 40
PD-1 blockade potentiates neoadjuvant chemotherapy in NSCLC via increasing CD127(+) and KLRG1(+) CD8 T cells.
PMID 37231145 · PMC10213055 · NPJ precision oncology · 2023 · 8 claims · 5 setups
NAPC produces higher major pathological response (MPR) and pathological complete response (pCR) rates and longer DFS/OS than NAC alone
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Has reproduction · 44
Phased differentiation of γδ T and T CD8 tumor-infiltrating lymphocytes revealed by single-cell transcriptomics of human cancers.
PMID 34721945 · PMC8555559 · Oncoimmunology · 2021 · 7 claims · 6 setups
In tumors, TCRVγnon9 γδ T cells (the majority γδ TIL subset) are quantitatively correlated and aligned with T CD8 cells for differentiation, exhaustion, gene expression profile, and response to immune checkpoint therapy
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Has reproduction · 67
An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.
PMID 36548438 · PMC9822106 · PLoS computational biology · 2022 · 8 claims · 6 setups
An individualized Bayesian causal discovery framework can learn tumor-specific intercellular communication networks (ICNs) by combining single-cell gene expression module (GEM) discovery, bulk tumor deconvolution, and individualized causal network learning.
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Has reproduction · 76
High DNA methylation age deceleration defines an aggressive phenotype with immunoexclusion environments in endometrial carcinoma.
PMID 37388735 · PMC10303802 · Frontiers in immunology · 2023 · 8 claims · 8 setups
Almost 90% of TCGA EC tumors exhibit DNA methylation age deceleration (DNAmad) relative to patient chronological age as assessed by the Horvath clock
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Has reproduction · 84
Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.
PMID 41758938 · PMC12947870 · Science advances · 2026 · 8 claims · 8 setups
MYOD1 L122R-mutant SRMS tumors contain three coexisting, conserved cell states (progenitor, transition, differentiated) reflecting aberrant myogenic differentiation
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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 · 8 claims · 8 setups
A colon cancer subtype with CD8Ahigh IDO1high tumors shows the worst survival despite high CD8 T cell infiltrates
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Has reproduction
Developing a thyroid cancer differentiation state classification system using deep residual networks and metabolic signature profiling.
PMID 40993300 · PMC12460824 · NPJ digital medicine · 2025 · 8 claims · 8 setups
Metabolic status is closely tied to tumor differentiation state, with distinct metabolic reprogramming occurring during thyroid cancer dedifferentiation
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Has reproduction · 85
A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.
PMID 38157249 · PMC10781479 · Aging · 2023 · 7 claims · 8 setups
Consensus clustering of 74 oxidative stress-related genes identifies three distinct HNSCC molecular subgroups (Cluster1-3) with significantly different overall survival and tumor stage distribution
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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 · 66
Liver-specific paraoxonase-1 alleviates regulatory T cell-driven immunosuppression via metabolic reprogramming in hepatocellular carcinoma.
PMID 41387425 · PMC12701056 · Nature communications · 2025 · 8 claims · 8 setups
PON1 expression is downregulated in HCC tumor tissue and low PON1 is associated with worse prognosis
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Has reproduction · 50
Patient-Derived Meningioma Organoids: A Reliable Model for Studying Human Tumor Pathophysiology.
PMID 39941893 · PMC11817449 · Cancers · 2025 · 8 claims · 7 setups
A standardized, reproducible protocol can establish meningioma organoids (MEN-Os) from patient-resected tumor tissue without mechanical/enzymatic dissociation, using serum-free medium lacking growth factors or exogenous ECM.
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Social and ethical implications of genomics, race, ethnicity, and health inequities.
PMID 19000599 · PMC2892396 · Seminars in oncology nursing · 2008 · 8 claims · 5 setups
Race and ethnicity are increasingly viewed as genetic surrogates for predicting disease risk and treatment response, though directly assessing genomic and environmental factors is more accurate.