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 · 79
Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx.
PMID 34254998 · PMC8575036 · Briefings in bioinformatics · 2021 · 6 claims · 4 setups
ParProx implements latent group lasso penalized regression (overlapping and non-overlapping groups) for survival (Cox) and classification (logistic) analysis of omics data.
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Family history of breast cancer and all-cause mortality after breast cancer diagnosis in the Breast Cancer Family Registry.
PMID 19034644 · PMC2728159 · Breast cancer research and treatment · 2009 · 7 claims · 5 setups
Family history of breast cancer is not associated with all-cause mortality after breast cancer diagnosis in women without a known germline BRCA1/BRCA2 mutation.
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An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer.
PMID 18676830 · PMC2680495 · Cancer research · 2008 · 8 claims · 5 setups
PIK3CA mutations are more common in hormone receptor-positive and HER2-positive tumors than in basal-like breast cancers
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Has reproduction · 72
Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.
PMID 33138797 · PMC7607642 · BMC cancer · 2020 · 8 claims · 8 setups
edgeR-based DEG selection is more appropriate for feature selection than Elastic Net when sample sizes are small.
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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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TP53 mutations in ovarian carcinomas from sporadic cases and carriers of two distinct BRCA1 founder mutations; relation to age at diagnosis and survival.
PMID 16229746 · PMC1276789 · BMC cancer · 2005 · 8 claims · 4 setups
Survival for BRCA1-familial ovarian cancer cases with TP53 mutations was not significantly different from familial cases without TP53 mutations (p=0.25, RR=1.64)
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Risk of pancreatic cancer in families with Lynch syndrome.
PMID 19861671 · PMC4091624 · JAMA · 2009 · 7 claims · 3 setups
Families with germline MMR gene mutations (Lynch Syndrome) have an 8.6-fold increased risk of pancreatic cancer compared to the general U.S. population.
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Has reproduction · 73
Expression Patterns of Immune Genes Reveal Heterogeneous Subtypes of High-Risk Neuroblastoma.
PMID 32629858 · PMC7408437 · Cancers · 2020 · 8 claims · 8 setups
Unsupervised biclustering of 283 NB-specific immune genes stratifies HR-NB into two reproducible subtypes: ultra-high-risk (UHR-NB) and (revised) HR-NB.
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Joint association of polymorphism of the FGFR4 gene and mutation TP53 gene with bladder cancer prognosis.
PMID 17088904 · PMC2360734 · British journal of cancer · 2006 · 8 claims · 5 setups
No clear correlation was found between the FGFR4 Gly388Arg genotype and risk of developing bladder cancer.
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Expression and mutation analysis of the discoidin domain receptors 1 and 2 in non-small cell lung carcinoma.
PMID 17299390 · PMC2360060 · British journal of cancer · 2007 · 8 claims · 6 setups
DDR1 is significantly upregulated in NSCLC tumour tissue compared with matched normal lung tissue
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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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Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development.
PMID 16800721 · PMC1483910 · PLoS medicine · 2006 · 8 claims · 8 setups
Multi-scale genomic similarities exist between four human lung cancer subtypes and the developing mouse lung, and these similarities are prognostically meaningful.
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Comparison of prognostic gene expression signatures for breast cancer.
PMID 18717985 · PMC2533026 · BMC genomics · 2008 · 8 claims · 5 setups
The three prognostic signatures (70-gene, 76-gene, GGI) show similar prognostic performance for predicting DMFS despite differing gene identity and development approach
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Has reproduction · 68
Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.
PMID 35012625 · PMC8743438 · Genome biology · 2022 · 8 claims · 9 setups
GENEVA (Gene Expression Variance Analysis) is a semi-automated framework that mines large-scale public RNA-seq datasets to identify conditions associated with a gene's expression variance
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Has reproduction · 49
Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity.
PMID 23326238 · PMC3542081 · PLoS genetics · 2013 · 8 claims · 8 setups
B-cell non-Hodgkin lymphomas display striking intra-tumor (intra-sample) and inter-patient (inter-sample) cytosine methylation heterogeneity that increases progressively with disease aggressiveness (NBC<NGC<FL<GCB<ABC).