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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A taxonomy of epithelial human cancer and their metastases.
PMID 20017941 · PMC2806369 · BMC medical genomics · 2009 · 8 claims · 6 setups
Unsupervised hierarchical clustering of 1566 primary epithelial tumors yields large tissue-enriched clusters (breast, colon/GI, lung, ovary, kidney) plus smaller prostate, thyroid-kidney, and mixed clusters
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Has reproduction · 73
A gene signature related to programmed cell death to predict immunotherapy response and prognosis in colon adenocarcinoma.
PMID 39950044 · PMC11823652 · PeerJ · 2025 · 8 claims · 8 setups
COAD patients can be divided into two molecular subtypes (S1, S2) based on 21 prognostic PCD-related genes, with S1 showing worse prognosis and immunosuppressive microenvironment, S2 showing better prognosis and stronger anti-tumor immunity
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PURE-seq integrates FACS and PIP-seq for single-cell genomics of ultra-rare cells.
PMID 41565684 · PMC12881479 · Nature communications · 2026 · 8 claims · 8 setups
PURE-seq integrates FACS sorting directly into PIP-seq barcoding reaction tubes, minimizing manual handling and cell loss for rare-cell single-cell sequencing.
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Has reproduction · 74
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.
PMID 27583132 · PMC4972086 · F1000Research · 2016 · 6 claims · 6 setups
An open-source, reproducible RNA-seq pipeline delivered as an IPython notebook and Docker image can process raw RNA-seq data into interactive PCA/HC plots, enrichment results, and small-molecule predictions with minimal setup overhead
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Has reproduction · 57
Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod.
PMID 33782539 · PMC8007741 · Communications biology · 2021 · 8 claims · 7 setups
t-SNE clustering of all-gene expression data groups field-collected (diapause program) samples into one cluster while early and late culture (reproductive program) samples separate into two distinct phenotypes
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Antigen specificity of clonally enriched CD8(+) T cells in multiple sclerosis.
PMID 41644766 · PMC12956596 · Nature immunology · 2026 · 8 claims · 7 setups
A subset of 23 highly expanded, CSF-enriched CD8+ T cell clonotypes exists predominantly in the CSF of the MS/CIS cohort.
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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 · 8 claims · 8 setups
A three-class WSI cluster (C0/C1/C2) derived via mini batch K-means clustering on Inception V3-extracted image features is significantly associated with overall survival and is an independent prognostic predictor in BLCA.
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WebGestalt: an integrated system for exploring gene sets in various biological contexts.
PMID 15980575 · PMC1160236 · Nucleic acids research · 2005 · 8 claims · 6 setups
WebGestalt is an integrated web-based system composed of four modules: gene set management, information retrieval, organization/visualization, and statistics.
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DeCAF defines clinical fibroblast subtypes and multidimensional tumor-stroma crosstalk shaping prognosis and immunotherapy response.
PMID 41707654 · PMC12923980 · Cell reports. Medicine · 2026 · 8 claims · 8 setups
DeCAF is a single-sample kTSP classifier using 9 TSP gene pairs that predicts proCAF vs restCAF subtypes from bulk expression data
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Construction of a SEMA3 family-based model to predict prognosis and molecular subtypes in pancreatic ductal adenocarcinoma.
PMID 41792569 · PMC13079247 · Discover oncology · 2026 · 8 claims · 8 setups
SEMA3 family expression defines two molecular subtypes (A and B) of PDAC with significantly different overall survival
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Highly efficient chromatin conformation capture with post-enrichment in single cells by HiChew.
PMID 42036683 · PMC13112749 · Genome biology · 2026 · 8 claims · 8 setups
HiChew achieves approximately 50% valid pair ratios compared to about 8% for unenriched methods like Dip-C
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SGCRNA: spectral clustering-guided co-expression network analysis without scale-free constraints for multi-omic data.
PMID 41615289 · PMC12856952 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups
WGCNA's reliance on a scale-free topology assumption is problematic because real co-expression networks do not consistently exhibit scale-free properties
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Has reproduction · 54
Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.
PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups
Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes
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Has reproduction
Using random walks to identify cancer-associated modules in expression data.
PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups
Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.
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Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.
PMID 18366609 · PMC2386062 · BMC genomics · 2008 · 8 claims · 7 setups
The mapping algorithm identified 5,647 candidate bidirectional promoter regions in the mouse genome, similar in number to those previously found in human.
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Lactate metabolism-related interaction perturbation network enables robust stratification of hepatocellular carcinoma.
PMID 41689750 · PMC13009326 · Discover oncology · 2026 · 8 claims · 8 setups
An LM-related gene interaction perturbation network can stratify HCC into four robust molecular subtypes (Cluster1-4)
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High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND.
PMID 41887797 · PMC13138010 · Genome research · 2026 · 7 claims · 6 setups
scBOND is a bidirectional dual-channel VAE framework for cross-modality translation between scRNA-seq and scDNAm that outperforms existing baseline methods (scCross, MAPLE) in both translation directions
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Has reproduction · 81
CCL8 as a promising prognostic factor in diffuse large B-cell lymphoma via M2 macrophage interactions: A bioinformatic analysis of the tumor microenvironment.
PMID 36072582 · PMC9441746 · Frontiers in immunology · 2022 · 8 claims · 8 setups
Higher stromal and ESTIMATE scores are associated with favorable prognosis in DLBCL
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Has reproduction · 75
Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.
PMID 34680427 · PMC8533098 · Biomedicines · 2021 · 8 claims · 7 setups
AD and PD patients can be stratified by transcriptomic clustering into three subclasses with distinct gene expression and metabolic profiles
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Has reproduction · 71
Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer.
PMID 30993001 · PMC6459838 · NPJ systems biology and applications · 2019 · 8 claims · 7 setups
Retaining only the top ~3 most correlated edges per gene (EPG3) combined with FastUnfold clustering (termed PGCNA) produces gene co-expression modules with significantly better separation and enrichment of known biology than using all edges or other clustering methods.