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 · 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 · 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 · 8 claims · 7 setups
STAT1 and IL-7 are differentially expressed immune-related genes that can distinguish HGSOC from LGSOC with strong diagnostic performance in the training cohort (AUC 0.908 and 0.842).
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Urinary proteomic profiling for diagnostic bladder cancer biomarkers.
PMID 19811072 · PMC3422861 · Expert review of proteomics · 2009 · 8 claims · 8 setups
Single protein biomarkers (e.g., NMP-22, BTA) suffer from high false-positive rates and none have replaced cystoscopy or cytology for bladder cancer detection.
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Discovery and identification of potential biomarkers of papillary thyroid carcinoma.
PMID 19785722 · PMC2761863 · Molecular cancer · 2009 · 8 claims · 7 setups
A 3-peak (m/z 9190, 6631, 8697 Da) SVM classification model discriminates PTC from non-cancer controls with high sensitivity and specificity
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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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Applying proteomics to the diagnosis and treatment of ALS and related diseases.
PMID 19670321 · PMC2836583 · Muscle & nerve · 2009 · 8 claims · 8 setups
Protein-based biomarkers for ALS/MND require further verification and large-scale validation/qualification studies, including disease mimics, before clinical use
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Has reproduction · 62
scATD: a high-throughput and interpretable framework for single-cell cancer drug resistance prediction and biomarker identification.
PMID 40501071 · PMC12159290 · Briefings in bioinformatics · 2025 · 8 claims · 6 setups
scATD enables high-throughput single-cell drug sensitivity prediction for new patients without model parameter retraining via bidirectional Bi-AdaIN style transfer
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Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.
PMID 15258335 · PMC3851082 · Disease markers · 2003 · 8 claims · 8 setups
Proteomic pattern analysis of serum mass spectra, without identifying the underlying proteins, can distinguish cancer patients from healthy controls with high sensitivity and specificity.
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Identification and validation of key PANoptosis-related genes via integrative machine learning and single-cell sequencing in AILI.
PMID 41858622 · PMC12995703 · iScience · 2026 · 8 claims · 8 setups
Cdkn1a and Pdk1 are key PANoptosis-related genes with high diagnostic potential for AILI
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Radiogenomics predicts immune microenvironment heterogeneity and response to combination immunotherapy in hepatocellular carcinoma.
PMID 41555384 · PMC12895822 · Journal of translational medicine · 2026 · 8 claims · 8 setups
A parsimonious 2-gene immune-related signature (IRS = 0.425×KPNA2 + 0.302×SMG5) is significantly associated with immune heterogeneity and response to ICI plus anti-angiogenic combination therapy in HCC
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Single-cell sequencing analysis and machine learning model reveal aberrant TIM-3 expression in microglia during Alzheimer's disease progression.
PMID 41580850 · PMC12911240 · Journal of translational medicine · 2026 · 7 claims · 8 setups
A TIM-3+ microglial subset drives AD pathogenesis through a dual mechanism: sustained neuroinflammation via TNF-α/NF-κB and IL-6/JAK/STAT3 signaling, and impaired amyloid-β clearance linked to PI3K-AKT and FcγR pathways
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Limitations in SELDI-TOF MS whole serum proteomic profiling with IMAC surface to specifically detect colorectal cancer.
PMID 19689818 · PMC2743709 · BMC cancer · 2009 · 7 claims · 3 setups
The previously reported classifier (m/z 8,132 and 4,002) failed to discriminate CRC patients from healthy volunteers in this independent validation cohort
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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 · 80
Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.
PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 8 claims · 8 setups
A neutrophil-related co-expression gene module (blue module) is significantly associated with aSAH occurrence