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
Developing a novel immune infiltration-associated mitophagy prediction model for amyotrophic lateral sclerosis using bioinformatics strategies.
PMID 38601155 · PMC11005030 · Frontiers in immunology · 2024 · 7 claims · 6 setups
An 18-gene mitophagy-related prognostic signature was identified by machine learning and used to build a prognostic risk score model for ALS.
-
Has reproduction · 77
SurvConvMixer: robust and interpretable cancer survival prediction based on ConvMixer using pathway-level gene expression images.
PMID 38539106 · PMC10967213 · BMC bioinformatics · 2024 · 7 claims · 6 setups
SurvConvMixer reformats KEGG Pathways-in-Cancer gene expression values into pathway-level 2D gene expression images and applies a ConvMixer-based model for overall survival prediction
-
Has reproduction · 63
Community assessment of methods to deconvolve cellular composition from bulk gene expression.
PMID 39191725 · PMC11350143 · Nature communications · 2024 · 8 claims · 4 setups
Most deconvolution methods accurately predict coarse-grained immune/stromal cell populations from bulk expression.
-
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 · 49
Integration of Transcriptomics With Interpretable Artificial Intelligence for Identifying Molecular Signatures of Physiological Stress in Sleep Deprivation.
PMID 42216239 · PMC13240488 · Journal of cellular and molecular medicine · 2026 · 8 claims · 8 setups
S100A3 is a robust candidate biomarker showing consistent discriminatory performance across the acute sleep deprivation training cohort, an independent sleep deprivation cohort, and a chronic insomnia cohort.
-
Has reproduction · 44
Dynamic Gene Attention Focus (DyGAF): Enhancing Biomarker Identification Through Dual-Model Attention Networks.
PMID 40160891 · PMC11951896 · Bioinformatics and biology insights · 2025 · 6 claims · 5 setups
DyGAF, a dual-model attention neural network (independent Model A + dependent Model B), identifies and ranks genes by significance for COVID-19 biomarker discovery more effectively than differential expression analysis (DEA) and random forest (RF) feature selection
-
Has reproduction · 90
Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits.
PMID 33461502 · PMC7812657 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 6 setups
Many significant cis-eQTL (geQTL, eeQTL, sQTL) were detected in sheep liver and muscle at FDR < 0.01.
-
Has reproduction · 92
Similarities and Differences in Gene Expression Networks Between the Breast Cancer Cell Line Michigan Cancer Foundation-7 and Invasive Human Breast Cancer Tissues.
PMID 34056582 · PMC8155268 · Frontiers in artificial intelligence · 2021 · 8 claims · 8 setups
MCF-7 cell lines and human breast cancer tissues share only minimal similarity in biological processes, though fundamental functions such as cell cycle are conserved
-
Has reproduction · 83
A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients.
PMID 36694043 · PMC9873918 · Communications biology · 2023 · 8 claims · 7 setups
The DSS phenotype-by-time interaction defines parsimonious temporal (dynamic) expression and splicing signatures of acute and chronic colitis distinct from time-specific differential expression.
-
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.
-
Has reproduction · 75
Integrative analysis reveals chemokines CCL2 and CXCL5 mediated shear stress-induced aortic dissection formation.
PMID 38163105 · PMC10757018 · Heliyon · 2024 · 7 claims · 8 setups
Chemokines CCL2 and CXCL5 mediate a shear stress-induced 'Endothelial-Monocyte-Neutrophil' axis that contributes to aortic dissection development.
-
Has reproduction
Differential Infiltration of Key Immune T-Cell Populations Across Malignancies Varying by Immunogenic Potential and the Likelihood of Response to Immunotherapy.
PMID 39682743 · PMC11640164 · Cells · 2024 · 7 claims · 4 setups
Immune-activation-related T-cell populations (APA, TRM, stem-like, early/late dysfunctional T-cells) are more heavily infiltrated in ICI-responsive malignancies (melanoma, bladder) than in poorly responsive ones (ovarian, pancreatic).
-
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 · 96
Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis.
PMID 34079055 · PMC8172904 · Communications biology · 2021 · 8 claims · 8 setups
An integrated 50K mouse and 24K human mammary epithelial cell atlas (scRNA-seq) captures mammary epithelium reorganization across most lifetime stages.
-
Has reproduction · 71
Comprehensive comparison of gene expression diversity among a variety of human stem cells.
PMID 36458020 · PMC9706419 · NAR genomics and bioinformatics · 2022 · 6 claims · 7 setups
iPSC gene expression is more strongly influenced by tissue origin than other stem cell types, whereas ESCs and somatic stem cells (MSCs, HSCs) are more strongly impacted by culture condition.
-
Has reproduction · 59
Application of Machine Learning in Predicting Hepatic Metastasis or Primary Site in Gastroenteropancreatic Neuroendocrine Tumors.
PMID 37887568 · PMC10605255 · Current oncology (Toronto, Ont.) · 2023 · 8 claims · 7 setups
Multi-gene random forest models classify primary tumor vs. liver metastasis samples with 100% accuracy in training/test cohorts and >90% accuracy in an independent validation cohort
-
Has reproduction · 94
A four-gene signature from blood to exclude bacterial etiology of lower respiratory tract infection in adults.
PMID 41285807 · PMC12644739 · Nature communications · 2025 · 8 claims · 8 setups
A 4-gene whole-blood signature (ITGB4, ITGA7, IFI27, FAM20A) discriminates any bacterial from nonbacterial ARI with cross-validated AUC = 0.90
-
Has reproduction · 50
Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.
PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 5 setups
A 186-gene signature derived from six GEO transcriptomic datasets predicts nCRT response in LARC with AUC 0.80 in cross-validation
-
Has reproduction · 53
Blood RNA signature RISK4LEP predicts leprosy years before clinical onset.
PMID 34090257 · PMC8182229 · EBioMedicine · 2021 · 7 claims · 5 setups
A 4-gene blood RNA signature (RISK4LEP: MT-ND2, REX1BD, TPGS1, UBC) predicts leprosy development 4–61 months before clinical diagnosis
-
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.