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 · 49
Integration of Transcriptomics With Interpretable Artificial Intelligence for Identifying Molecular Signatures of Physiological Stress in Sleep Deprivation.
PMID 42216239 · PMC13240488 · Journal of cellular and molecular medicine · 2026 · 8 claims · 8 setups
S100A3 is a robust candidate biomarker showing consistent discriminatory performance across the acute sleep deprivation training cohort, an independent sleep deprivation cohort, and a chronic insomnia cohort.
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Has reproduction · 50
Integrated drug resistance and leukemic stemness gene-expression scores predict outcomes in large cohort of over 3500 AML patients from 10 trials.
PMID 39090192 · PMC11294346 · NPJ precision oncology · 2024 · 7 claims · 6 setups
A 5-gene ADE-Resistance Score (ADE-RS5), derived via LASSO regression from 67 pharmacologically relevant genes, predicts MRD positivity, EFS and OS in pediatric AML.
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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 · 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
Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma.
PMID 34654806 · PMC8519947 · Nature communications · 2021 · 7 claims · 4 setups
Pathway-based signatures derived from on-treatment tumor specimens (PASS-ON) are highly predictive of response to anti-PD1 blockade in metastatic melanoma, achieving validation AUCs of 0.85–0.89.
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Has reproduction · 85
Integration of multi-omics and machine learning strategies identifies immune related candidate biomarkers in inflammation-associated hypertrophic cardiomyopathy.
PMID 41080564 · PMC12510942 · Frontiers in immunology · 2025 · 8 claims · 8 setups
Seven key immune-related genes (RNF165, SNCA, SRGN, MARCO, STEAP4, SIGLEC9, TKT) were identified for HCM by intersecting DEGs with MR-derived HCM-associated eQTLs.
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Has reproduction · 50
Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.
PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 5 setups
A 186-gene signature derived from six GEO transcriptomic datasets predicts nCRT response in LARC with AUC 0.80 in cross-validation
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Has reproduction · 100
Computational modeling demonstrates that glioblastoma cells can survive spatial environmental challenges through exploratory adaptation.
PMID 31836713 · PMC6911112 · Nature communications · 2019 · 8 claims · 6 setups
Stochastic exploration of the gene-regulatory network structure confers enhanced adaptive capacity, enabling GBM cells to converge to new target phenotypes in novel environments.
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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 · 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 · 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 · 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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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 · 100
Identification of a PRDM1-regulated T cell network to regulate atherosclerotic plaque inflammation.
PMID 41039608 · PMC12490039 · Genome medicine · 2025 · 6 claims · 7 setups
A distinct gene co-expression module with a prominent T cell signature is enriched in unstable plaques and distinguishes high-risk from low-risk lesions.
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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 · 50
Heterogeneity of cancer-associated fibroblasts in head and neck squamous cell carcinoma.
PMID 37320872 · PMC10277597 · Translational oncology · 2023 · 8 claims · 9 setups
Seven distinct CAF subsets exist in HNSCC, identified via integration of scRNA-seq, bulk transcriptomic, and spatial transcriptomic data.
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Has reproduction · 75
PD-1 and TIGIT coexpression identifies a circulating CD8 T cell subset predictive of response to anti-PD-1 therapy.
PMID 33188038 · PMC7668369 · Journal for immunotherapy of cancer · 2020 · 6 claims · 6 setups
The frequency of circulating PD-1+TIGIT+ (DPOS) CD8+ T cells after 1 month of anti-PD-1 therapy is associated with clinical response and overall survival across three independent cohorts.
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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 · 4 setups
Adding PD-1 blockade to neoadjuvant chemotherapy (NAPC) increases tumor infiltration of CD20+ B cells, CD4+ T cells, CD4+CD127+ T cells, CD8+ T cells, CD8+CD127+ and CD8+KLRG1+ T cells, whereas NAC alone increases only CD20+ B 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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Has reproduction
Differential Infiltration of Key Immune T-Cell Populations Across Malignancies Varying by Immunogenic Potential and the Likelihood of Response to Immunotherapy.
PMID 39682743 · PMC11640164 · Cells · 2024 · 7 claims · 4 setups
Immune-activation-related T-cell populations (APA, TRM, stem-like, early/late dysfunctional T-cells) are more heavily infiltrated in ICI-responsive malignancies (melanoma, bladder) than in poorly responsive ones (ovarian, pancreatic).