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 · 40
Machine learning developed an intratumor heterogeneity signature for predicting clinical outcome and immunotherapy benefit in bladder cancer.
PMID 39100839 · PMC11291408 · Translational andrology and urology · 2024 · 8 claims · 8 setups
An integrative machine learning procedure (10 methods, 101 algorithm combinations) identified an Enet (alpha=0.2)-based intratumor heterogeneity-related signature (IRS) with the highest average C-index (0.69) across TCGA and GEO cohorts
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Has reproduction · 95
A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity.
PMID 37963558 · PMC10645512 · Journal of the Royal Society, Interface · 2023 · 8 claims · 7 setups
RKIP and BACH1 are negatively correlated with each other across most cancer types in TCGA
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Has reproduction · 59
Advances in genomic and pharmacokinetic profiling for clinical stratification of metastatic breast cancer.
PMID 41369820 · PMC12799884 · Discover oncology · 2025 · 7 claims · 8 setups
Eight gene modules linked to metastasis were identified via scored network analysis and validated through pathway databases.
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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 · 83
Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.
PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups
Twenty-two genes lie at the intersection of AFB1-predicted targets and breast cancer-associated co-expression modules/DEGs
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Has reproduction · 64
Characterizing Neutrophil Subtypes in Cancer Using scRNA Sequencing Demonstrates the Importance of IL1β/CXCR2 Axis in Generation of Metastasis-specific Neutrophils.
PMID 38358352 · PMC10903300 · Cancer research communications · 2024 · 8 claims · 7 setups
Two main neutrophil subtypes exist in primary tumors: an activated subtype sharing transcriptomic signatures with healthy neutrophils, and a tumor-specific subtype.
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Has reproduction · 78
Identification of succinylation-related genes in bladder cancer: integration of single-cell and transcriptomic data.
PMID 42220482 · PMC13218921 · Frontiers in immunology · 2026 · 8 claims · 8 setups
KCTD16, CD3D and GSDMB are succinylation-related prognostic genes in BLCA
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Has reproduction · 100
Transcriptomic-Based Quantification of the Epithelial-Hybrid-Mesenchymal Spectrum across Biological Contexts.
PMID 35053177 · PMC8773604 · Biomolecules · 2021 · 8 claims · 8 setups
The 76GS, KS, and MLR EMT scoring metrics show concordant trends in quantifying EMP across bulk RNA-seq datasets spanning multiple cancer types
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Has reproduction · 67
Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility.
PMID 26969729 · PMC4812528 · Molecular systems biology · 2016 · 7 claims · 6 setups
Cell adhesion (cell-cell and cell-ECM) pathways are significantly and consistently dysregulated in women who develop familial breast cancer across multiple omic data types and tissues.
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Has reproduction · 95
Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.
PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups
Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature
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Has reproduction · 77
Metabolic reprogramming and prognostic insights in molecular landscapes driven by glycolysis in ovarian cancer.
PMID 40707588 · PMC12290113 · Scientific reports · 2025 · 7 claims · 8 setups
457 differentially expressed GRGs were identified between OC and normal ovarian tissue, of which 30 were significantly associated with prognosis
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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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Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.
PMID 19763266 · PMC2740864 · PloS one · 2009 · 8 claims · 8 setups
Androgen treatment alters the whole-cell proteome of LNCaP prostate cancer cells
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Has reproduction · 78
Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.
PMID 36851919 · PMC9957767 · Computational and structural biotechnology journal · 2023 · 8 claims · 7 setups
Simulations of the EMT-AR crosstalk network reveal four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR), and mesenchymal-sensitive (MS), with MS occurring rarely
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Network-assisted protein identification and data interpretation in shotgun proteomics.
PMID 19690572 · PMC2736651 · Molecular systems biology · 2009 · 7 claims · 7 setups
Confidently identified proteins in a sample form tightly connected sub-networks in the protein interaction network, with significantly higher clustering coefficients than random or topology-matched random sub-networks.