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 · 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
Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.
PMID 41758938 · PMC12947870 · Science advances · 2026 · 7 claims · 8 setups
MYOD1 L122R-mutant SRMS comprises three coexisting tumor cell states (MYOD1-enriched progenitor-like, proliferative transition, and partially differentiated with reduced MYOD1 activity) reflecting disrupted myogenic differentiation.
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Has reproduction · 48
Indoleamine 2, 3-Dioxygenase 1 and CD8 Expression Profiling Revealed an Immunological Subtype of Colon Cancer With a Poor Prognosis.
PMID 33425745 · PMC7793995 · Frontiers in oncology · 2020 · 7 claims · 6 setups
The CD8A-high/IDO1-high colon cancer subtype (group IV*) has the worst survival despite high CD8 infiltrates.
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Has reproduction · 50
Wx: a neural network-based feature selection algorithm for transcriptomic data.
PMID 31324856 · PMC6642261 · Scientific reports · 2019 · 8 claims · 8 setups
The Wx algorithm ranks genes by a discriminative index (DI) score representing classification power for distinguishing given groups, enabling intuitive selection of optimal biomarker genes.
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Has reproduction · 76
Correcting scale distortion in RNA sequencing data.
PMID 39875825 · PMC11776150 · BMC bioinformatics · 2025 · 8 claims · 8 setups
Local averaging reveals expression-level-dependent biases that differ from sample to sample across all RNA-seq datasets studied, and are not corrected by conventional normalization (TPM/FPKM)
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Has reproduction · 71
Assessment tool based on fatty acid metabolic signatures for predicting the prognosis and treatment response in bladder cancer.
PMID 38076064 · PMC10703629 · Heliyon · 2023 · 8 claims · 8 setups
Consensus clustering of prognosis-related fatty acid metabolism genes (FAMGs) identifies three molecular subtypes of BLCA (FAMC1, FAMC2, FAMC3) with distinct prognoses and tumor microenvironments
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Has reproduction · 23
Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals.
PMID 39418301 · PMC11521246 · PLoS computational biology · 2024 · 7 claims · 4 setups
COPD GWAS loci are more spatially clustered across the genome than expected by chance, with significant enrichment on chromosome 4q.
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Has reproduction · 84
A HML6 endogenous retrovirus on chromosome 3 is upregulated in amyotrophic lateral sclerosis motor cortex.
PMID 34253796 · PMC8275748 · Scientific reports · 2021 · 8 claims · 8 setups
The ERV locus HML6_3p21.31c is significantly upregulated in ALS post-mortem motor cortex after multiple-testing correction
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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 · 73
Design of a targeted blood transcriptional panel for monitoring immunological changes accompanying pregnancy.
PMID 38352867 · PMC10861739 · Frontiers in immunology · 2024 · 6 claims · 3 setups
A targeted panel of 176 transcripts plus 8 housekeeping genes was identified for monitoring immunological changes during pregnancy
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Has reproduction · 69
A blood-based DNA damage signature in patients with Parkinson's disease is associated with disease progression.
PMID 40913219 · PMC12443628 · Nature aging · 2025 · 8 claims · 2 setups
A blood-based DNA damage signature is present in PD patients and is associated with disease progression.
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Has reproduction · 85
A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.
PMID 38157249 · PMC10781479 · Aging · 2023 · 6 claims · 7 setups
A nine-gene oxidative stress-related scoring (OSRS) model (AREG, CES1, CSTA, FDCSP, JCHAIN, IFFO2, PGLYRP4, SPOCK2, SPINK6) predicts overall survival in HNSCC.
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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 Nottingham Prognostic Index with SIS-selected gene expressions can be built in a data-driven fashion (NPI treated as a gene expression during feature selection).
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Has reproduction · 71
Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.
PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 7 claims · 8 setups
Two distinct RNA modification patterns exist among BCa samples with radically different clinical outcomes and biological characteristics.
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Has reproduction · 73
RSK1 is an exploitable dependency in myeloproliferative neoplasms and secondary acute myeloid leukemia.
PMID 39820365 · PMC11739599 · Nature communications · 2025 · 8 claims · 8 setups
RSK1 is a conserved, exploitable therapeutic dependency across MPN and secondary AML
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Has reproduction · 79
The relationship between PLOD1 expression level and glioma prognosis investigated using public databases.
PMID 34040895 · PMC8127981 · PeerJ · 2021 · 8 claims · 8 setups
PLOD1 mRNA expression is significantly higher in glioma tissue than in normal brain tissue
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Has reproduction · 55
Gene module regulation in dilated cardiomyopathy and the role of Na/K-ATPase.
PMID 35901050 · PMC9333241 · PloS one · 2022 · 5 claims · 8 setups
Several co-expressed gene modules are significantly associated with left ventricle ejection fraction (LVEF) and the DCM phenotype, enriched in fibrosis-related, small molecule transporting-related, and immune response-related pathways.
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Has reproduction · 73
Comprehensive analysis of mitophagy in HPV-related head and neck squamous cell carcinoma.
PMID 37161060 · PMC10170109 · Scientific reports · 2023 · 8 claims · 8 setups
In HPV-associated HNSCC, the mitophagy process affects tumour development, immune cell infiltration and prognosis.
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Has reproduction · 71
Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma.
PMID 40458122 · PMC12127311 · Frontiers in cell and developmental biology · 2025 · 8 claims · 8 setups
DKC1 mRNA and protein expression are significantly upregulated in UCEC tumors compared with non-tumorous endometrial tissue
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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