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 · 65
A urine extracellular vesicle lncRNA classifier for high-grade prostate cancer and increased risk of progression: A multi-center study.
PMID 37852185 · PMC10591064 · Cell reports. Medicine · 2023 · 8 claims · 8 setups
A 3-lncRNA urine extracellular vesicle classifier (Clnc: AC015987.1, CTD-2589M5.4, RP11-363E6.3) detects high-grade PCa with higher accuracy than PCA3, mpMRI, PCPT-RC 2.0, and ERSPC-RC
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Has reproduction · 50
Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.
PMID 37076665 · PMC10115855 · NPJ precision oncology · 2023 · 8 claims · 8 setups
A convergent-phenotype-based seed gene/co-expression method can extract consensus gene expression signatures predictive of response to chemotherapeutic drugs in the GDSC database
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Has reproduction · 51
Construction and Validation of an Immune Infiltration-Related Gene Signature for the Prediction of Prognosis and Therapeutic Response in Breast Cancer.
PMID 33986754 · PMC8110914 · Frontiers in immunology · 2021 · 7 claims · 8 setups
A higher immune infiltration-related risk score (IRS) indicates worse prognosis and lower sensitivity to immunotherapy in breast cancer patients
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Has reproduction · 100
Proneural-mesenchymal antagonism dominates the patterns of phenotypic heterogeneity in glioblastoma.
PMID 38433919 · PMC10905000 · iScience · 2024 · 8 claims · 8 setups
The four proposed GBM molecular subtypes (Proneural, Neural, Classical, Mesenchymal / NPC-like, OPC-like, AC-like, MES-like) are not mutually exclusive or independent of one another
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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 · 100
Genomic insight into the influence of selection, crossbreeding, and geography on population structure in poultry.
PMID 36670351 · PMC9854048 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups
Dutch traditional chicken breeds show a complex and admixed subdivided population structure that partly matches historical management-based clustering (past-productive, ornamental, country fowl, Lakenvelder).
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Has reproduction · 48
Comparative analysis of molecular signatures reveals a hybrid approach in breast cancer: Combining the Nottingham Prognostic Index with gene expressions into a hybrid signature.
PMID 35143511 · PMC8830616 · PloS one · 2022 · 8 claims · 6 setups
A Hybrid signature combining the NPI with 14 SIS-selected genes was constructed from METABRIC training data
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Has reproduction · 53
Molecular Biomarker of Drug Resistance Developed From Patient-Derived Organoids Predicts Survival of Colorectal Cancer Patients.
PMID 35425715 · PMC9004628 · Frontiers in oncology · 2022 · 8 claims · 7 setups
Patient-derived colorectal cancer organoids (CRCOs) can be established from surgical CRC tissue with an 82% success rate (41/50)
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Has reproduction
Comprehensive analysis of m(6)A methylome alterations after azacytidine plus venetoclax treatment for acute myeloid leukemia by nanopore sequencing.
PMID 38510975 · PMC10950754 · Computational and structural biotechnology journal · 2024 · 8 claims · 6 setups
m6A site number and m6A levels are significantly lower in post-treatment complete remission (CR) bone marrow than in pre-treatment AML bone marrow
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Has reproduction · 78
Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.
PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 6 claims · 8 setups
A consensus WGCNA approach combining matched tumor-organoid and independent organoid drug-response expression data identifies gene modules and hub genes predictive of 5-FU chemotherapy response
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Has reproduction · 81
Deubiquitination enzyme USP35 negatively regulates MAVS signaling to inhibit anti-tumor immunity.
PMID 40016186 · PMC11868397 · Cell death & disease · 2025 · 8 claims · 8 setups
USP35 interacts with MAVS and removes its K63-linked polyubiquitin chains, inhibiting viral-induced MAVS-TBK1-IRF3 activation and downstream inflammatory gene expression
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Has reproduction · 74
Identification and validation of a metabolic-related gene risk model predicting the prognosis of lung, colon, and breast cancers.
PMID 39779736 · PMC11711664 · Scientific reports · 2025 · 8 claims · 8 setups
540 DEGs overlap across breast, colorectal, and lung cancers out of 11,384 DEGs analyzed
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Has reproduction · 75
Revealing the critical state and identifying individualized dynamic network biomarker for type 2 diabetes through advanced analysis methods on individual basis.
PMID 39890881 · PMC11785715 · Scientific reports · 2025 · 8 claims · 5 setups
sJSD, NIG, and TNFE methods can detect critical states/tipping points before disease deterioration using only a single sample
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Has reproduction · 71
Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma.
PMID 41048340 · PMC12491262 · Frontiers in bioinformatics · 2025 · 8 claims · 8 setups
IRG expression pattern clusters LUAD patients into groups with significantly different survival outcomes and immune cell infiltration
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Has reproduction · 48
Bioinformatics Analysis of the Characteristics and Correlation of m6A Methylation in Breast Cancer Progression.
PMID 35655723 · PMC9148239 · Contrast media & molecular imaging · 2022 · 8 claims · 8 setups
Breast cancer samples can be classified into 4 m6A subtypes (quiescent, m6A methylation, protein-binding, mixed) based on Z-score median of Set1 (writer+reader) and Set2 (eraser) gene expression
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Has reproduction · 62
Specific Marker Gene Analysis for Primary Central Nervous System Lymphoma Based on Methylation Difference and Development of Detection Primers.
PMID 41097902 · PMC12528802 · Brain and behavior · 2025 · 7 claims · 5 setups
450K microarray analysis identified 26 overlapping differential methylation sites distinguishing PCNSL from CNS and non-CNS groups
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Has reproduction · 53
Gene Dosage Analysis on the Single-Cell Transcriptomes Linking Cotranslational Protein Targeting to Metastatic Triple-Negative Breast Cancer.
PMID 34577617 · PMC8472593 · Pharmaceuticals (Basel, Switzerland) · 2021 · 8 claims · 7 setups
A computational framework mapping single-cell Z-score expression to matched patient-level CNV data can identify recurrent, cross-cell-type copy-number-driven expression (dosage) events.
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Has reproduction · 67
binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.
PMID 36239393 · PMC9677464 · Briefings in bioinformatics · 2022 · 8 claims · 8 setups
binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods (MetaBAT2, MaxBin2, CONCOCT, VAMB, SemiBin, MetaDecoder)
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Has reproduction · 80
Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity.
PMID 36928603 · PMC10101853 · Nature genetics · 2023 · 8 claims · 6 setups
The WHO histopathological classification of MPM accounts for only up to ~10% of interpatient molecular differences
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Has reproduction · 78
Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.
PMID 33674593 · PMC7935900 · Nature communications · 2021 · 8 claims · 8 setups
A transcriptome-derived T-cell exhaustion score (ES) is prognostic for HCC patient survival independent of known clinical/molecular factors