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).
-
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.
-
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 15-gene immune infiltration-related signature (IRS) predicts overall survival in breast cancer, with higher IRS indicating worse prognosis
-
Has reproduction · 85
Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.
PMID 38254989 · PMC10815467 · Genes · 2024 · 8 claims · 8 setups
Combining scRNA-seq and spatial transcriptomics enables inference of malignant cells at the invasive front of the ER+ breast cancer TME and dissection of events at the tumor infiltration forefront
-
Has reproduction · 71
IRSN-23 gene diagnosis enhances breast cancer subtype classification and predicts response to neoadjuvant chemotherapy: new validation analyses.
PMID 40128415 · PMC11993443 · Breast cancer (Tokyo, Japan) · 2025 · 8 claims · 8 setups
IRSN-23 Gp-R patients have significantly higher pCR rates than Gp-NR patients without anti-HER2 therapy, across the OUH cohort and multiple independent public datasets
-
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 divided into 4 m6A subtypes (quiescent, m6A methylation, protein-binding, mixed) based on expression of m6A-related genes, with consistent proportions across datasets
-
Has reproduction · 94
Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.
PMID 36681937 · PMC10025442 · Briefings in bioinformatics · 2023 · 8 claims · 8 setups
HiCAT is a hierarchical, marker-based cell-type identifier that uses gene set analysis (GSA) scoring with markers structured in a three-level taxonomy tree (major-type, minor-type, subset)
-
Has reproduction · 84
Elucidating the Prognostic and Therapeutic Implications of Insulin Resistance Genes in Breast Cancer: A Machine Learning-Powered Analysis.
PMID 40427728 · PMC12109394 · Biology · 2025 · 8 claims · 8 setups
A seven-gene IRG prognostic signature (LIFR, EZR, TBC1D4, NSF, RPL5, SAA1, PGK1) predicts overall survival in breast cancer across training and four validation cohorts
-
Has reproduction · 83
Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.
PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups
Twenty-two genes lie at the intersection of AFB1-predicted targets and breast cancer-associated co-expression modules/DEGs
-
Has reproduction · 64
Characterizing Neutrophil Subtypes in Cancer Using scRNA Sequencing Demonstrates the Importance of IL1β/CXCR2 Axis in Generation of Metastasis-specific Neutrophils.
PMID 38358352 · PMC10903300 · Cancer research communications · 2024 · 8 claims · 7 setups
Two main neutrophil subtypes exist in primary tumors: an activated subtype sharing transcriptomic signatures with healthy neutrophils, and a tumor-specific subtype.
-
Full-text index only
Direct resequencing of the complete ERBB2 coding sequence reveals an absence of activating mutations in ERBB2 amplified breast cancer.
PMID 18418848 · PMC6668724 · Genes, chromosomes & cancer · 2008 · 6 claims · 5 setups
Emulsion PCR combined with picotiter plate pyrosequencing (454 sequencing) enables high-resolution, high-throughput detection of low-frequency sequence variants among the many individual copies of an amplified gene.
-
Full-text index only
Social and ethical implications of genomics, race, ethnicity, and health inequities.
PMID 19000599 · PMC2892396 · Seminars in oncology nursing · 2008 · 8 claims · 5 setups
Race and ethnicity are increasingly viewed as genetic surrogates for predicting disease risk and treatment response, though directly assessing genomic and environmental factors is more accurate.
-
Has reproduction · 50
SMAC, a computational system to link literature, biomedical and expression data.
PMID 31324861 · PMC6642118 · Scientific reports · 2019 · 7 claims · 6 setups
SMAC is a tool that extracts, prioritises, integrates and analyses biomedical literature and molecular data according to user-defined terms, linking PubMed and GEO.