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 · 50
STAT1 and IL-7 as potential diagnostic biomarkers for distinguishing high-grade from low-grade serous ovarian cancer: a multi-cohort analysis.
PMID 42058211 · PMC13120972 · Frontiers in immunology · 2026 · 7 claims · 6 setups
STAT1 and IL-7 are differentially expressed immune-related genes that can distinguish HGSOC from LGSOC and may serve as ancillary diagnostic biomarkers.
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Has reproduction · 66
Integrative bioinformatics and artificial intelligence analyses of transcriptomics data identified genes associated with major depressive disorders including NRG1.
PMID 37583471 · PMC10423927 · Neurobiology of stress · 2023 · 7 claims · 5 setups
Differentially expressed genes in MDD patients are enriched in immune response, inflammatory response, neurodegeneration, and cerebellar atrophy pathways.
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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
Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.
PMID 36245985 · PMC9553530 · Journal of oncology · 2022 · 6 claims · 8 setups
A deep learning WSI cluster (three-class mini batch K-means on Inception V3 features) is associated with overall survival (P<0.001) and is an independent prognostic predictor (P=0.031) in BLCA.
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Has reproduction · 86
Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.
PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 6 claims · 4 setups
A training gene set of 719 unique upregulated DEGs (subtype-specific) can be used to build ML models that classify TNBC into BLIA, BLIS, MES, and LAR subtypes.
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Has reproduction · 59
Refining breast cancer biomarker discovery and drug targeting through an advanced data-driven approach.
PMID 38253993 · PMC10810249 · BMC bioinformatics · 2024 · 8 claims · 8 setups
The BGWO_SA_Ens algorithm (hybrid BGWO + simulated annealing with an ensemble classifier objective function) selects predictive breast cancer biomarker genes with high classification performance
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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 · 80
Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.
PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 7 claims · 8 setups
Six genes (CST7, HSP90AB1, PADI4, PLBD1, RAB32, SLAMF6) are signature diagnostic biomarkers for aSAH identified by LASSO and SVM-RFE.
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Has reproduction · 49
Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.
PMID 40520228 · PMC12162626 · Frontiers in genetics · 2025 · 8 claims · 8 setups
ENTPD1, SERPINA1, and TACSTD2 are potential transcriptomic biomarkers for PTC
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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 · 44
Dynamic Gene Attention Focus (DyGAF): Enhancing Biomarker Identification Through Dual-Model Attention Networks.
PMID 40160891 · PMC11951896 · Bioinformatics and biology insights · 2025 · 6 claims · 5 setups
DyGAF, a dual-model attention neural network (independent Model A + dependent Model B), identifies and ranks genes by significance for COVID-19 biomarker discovery more effectively than differential expression analysis (DEA) and random forest (RF) feature selection
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Has reproduction · 80
Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma.
PMID 39553728 · PMC11569783 · PeerJ · 2024 · 8 claims · 8 setups
WGCNA identified 214 key genes in the blue module most correlated with LUAD
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Has reproduction · 78
Machine learning and free energy clustering reveal PAH protein binding linked to AD risk.
PMID 41953002 · PMC13053772 · iScience · 2026 · 7 claims · 8 setups
An integrated framework of bioinformatics, machine learning, and ΔG clustering can prioritize PAHs for AD-associated neurotoxicity.
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Has reproduction · 100
Betacoronavirus-specific alternate splicing.
PMID 35074468 · PMC8782732 · Genomics · 2022 · 8 claims · 8 setups
Genes showing differential alternative splicing in SARS-CoV-2 have a similar functional profile to those in SARS-CoV and MERS, affecting a diverse set of genes and biological functions related to virus biology.
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Has reproduction · 100
Shared and unique phosphoproteomics responses in skeletal muscle from exercise models and in hyperammonemic myotubes.
PMID 36345342 · PMC9636548 · iScience · 2022 · 8 claims · 7 setups
Comparative phosphoproteomics of hyperammonemic myotubes and exercise-model muscle identifies shared enriched pathways: PKA, calcium signaling, MAPK signaling, and protein homeostasis.
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Full-text index only
Proteomics as a tool for biomarker discovery.
PMID 18057524 · PMC3851415 · Disease markers · 2007 · 8 claims · 7 setups
A useful clinical biomarker must be easily attainable, have adequate sensitivity, have adequate specificity, and lead to patient benefit through intervention
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Has reproduction · 67
Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.
PMID 37847658 · PMC10628388 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 3 setups
PSPred-ALE, a deep learning predictor using a self-adaptive learning embedding algorithm, automatically extracts contextual sequence features and identifies SARS-CoV-2 phosphorylation sites without feature engineering.
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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 · 58
Identification of common genetic characteristics of rheumatoid arthritis and major depressive disorder by bioinformatics analysis and machine learning.
PMID 37415981 · PMC10320004 · Frontiers in immunology · 2023 · 7 claims · 8 setups
EAF1, SDCBP and RNF19B are common genetic characteristics (hub genes) shared by RA and MDD
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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