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).

Publications 1.3k Datasets 392.5k Experiments 9

System / cell line: gene ✕ Assay: single-sample ✕ Clear

Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

Has reproduction · 95

Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

breast-cancer-specific tcga ccle four single-sample survival genome-wide
Detecting tipping points of complex diseases by network information entropy.

PMID 38960408 · PMC11221888 · Briefings in bioinformatics · 2024 · 8 claims · 4 setups

Has reproduction · 78

NIEE can detect critical states or tipping points in diverse data types, including bulk and single-sample expression data

real stringdb individual genes network background sample-specific
SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.

PMID 18840289 · PMC2571113 · BMC bioinformatics · 2008 · 8 claims · 6 setups

Full-text index only

SIGMA2 is a Java-based software system that integrates and visualizes genomic, epigenomic, and transcriptomic cancer data.

single hcc2218 nsclc array gene multi-omics
Exploration of the shared diagnostic genes and molecular mechanism between obesity and atherosclerosis via bioinformatic analysis.

PMID 39825072 · PMC11742665 · Scientific reports · 2025 · 8 claims · 8 setups

Has reproduction · 76

56 shared genes with consistent expression trend were identified between OB and AS by intersecting WGCNA key module genes with DEGs

obesity atherosclerosis differential wgcna lasso
Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma.

PMID 38230570 · PMC10795782 · Cancer biology & therapy · 2024 · 8 claims · 6 setups

Has reproduction · 87

NOR-specific and MES-specific gene expression patterns are largely mutually exclusive, exhibiting a teams-like behavior across multiple bulk NB transcriptomic datasets

lines bulk single-cell housekeeping bulk pca single-sample
A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.

PMID 34316714 · PMC8271219 · NAR cancer · 2021 · 7 claims · 8 setups

Has reproduction · 85

EMT and tamoxifen-resistance (TamR) regulatory axes can drive one another, enabling non-genetic heterogeneity via six co-existing phenotypes (ES, ER, HS, HR, MS, MR)

gene same randomized publicly racipe stochastic randomized
Computational modeling demonstrates that glioblastoma cells can survive spatial environmental challenges through exploratory adaptation.

PMID 31836713 · PMC6911112 · Nature communications · 2019 · 8 claims · 6 setups

Has reproduction · 100

Stochastic exploration of the gene-regulatory network structure confers enhanced adaptive capacity, enabling GBM cells to converge to new target phenotypes in novel environments.

gbm glioma gbm-focused glioma-related transcriptomic differential gene-regulatory
High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

PMID 17925008 · PMC2246289 · Genome biology · 2007 · 7 claims · 8 setups

Full-text index only

A novel subtype of high-grade ER-negative breast cancer exists, characterized by a low genomic instability index (GII)

breast computational array-cgh gene bac
iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.

PMID 37023414 · PMC10236149 · Cancer immunology research · 2023 · 8 claims · 8 setups

Has reproduction · 94

Malignant cells cluster by patient in scRNA-seq data while immune and stromal cells cluster by cell type, making malignant cells uniquely suited to carry patient-level inflamed/cold signal

nsclc coad brca tcga scrna-seq bulk rna-seq

Experiments

Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

Detecting tipping points of complex diseases by network information entropy.

SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.

Exploration of the shared diagnostic genes and molecular mechanism between obesity and atherosclerosis via bioinformatic analysis.

Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma.

A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.

Computational modeling demonstrates that glioblastoma cells can survive spatial environmental challenges through exploratory adaptation.

High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.