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 · 80
Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.
PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 7 claims · 8 setups
Six genes (CST7, HSP90AB1, PADI4, PLBD1, RAB32, SLAMF6) are signature diagnostic biomarkers for aSAH identified by LASSO and SVM-RFE.
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Has reproduction · 50
Genetic parallels in biomineralization of the calcareous sponge Sycon ciliatum and stony corals.
PMID 40922549 · PMC12419799 · eLife · 2025 · 8 claims · 8 setups
829 genes are overexpressed in the oscular region of increased calcite spicule formation in S. ciliatum
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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 Nottingham Prognostic Index with SIS-selected gene expressions can be built in a data-driven fashion (NPI treated as a gene expression during feature selection).
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Has reproduction · 55
Gene module regulation in dilated cardiomyopathy and the role of Na/K-ATPase.
PMID 35901050 · PMC9333241 · PloS one · 2022 · 5 claims · 8 setups
Several co-expressed gene modules are significantly associated with left ventricle ejection fraction (LVEF) and the DCM phenotype, enriched in fibrosis-related, small molecule transporting-related, and immune response-related pathways.
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Has reproduction · 100
Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.
PMID 37138775 · PMC10149407 · iScience · 2023 · 8 claims · 7 setups
Hsp90-dependent gene expression varies among different yeast strains
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Has reproduction · 78
Disrupted PGR-B and ESR1 signaling underlies defective decidualization linked to severe preeclampsia.
PMID 34709177 · PMC8553341 · eLife · 2021 · 8 claims · 5 setups
A 120-gene endometrial transcriptomic fingerprint encodes defective decidualization associated with severe preeclampsia.
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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
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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.
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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.
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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
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Has reproduction · 100
Identification of a PRDM1-regulated T cell network to regulate atherosclerotic plaque inflammation.
PMID 41039608 · PMC12490039 · Genome medicine · 2025 · 6 claims · 7 setups
A distinct gene co-expression module with a prominent T cell signature is enriched in unstable plaques and distinguishes high-risk from low-risk lesions.
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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
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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
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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
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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
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Has reproduction · 94
Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0.
PMID 31343654 · PMC6660187 · Investigative ophthalmology & visual science · 2019 · 8 claims · 6 setups
EiaD is a reproducible, versioned pan-eye and body RNA-seq transcriptome dataset built from 916 eye and 1375 GTEx samples via a Snakemake pipeline output as a single SQLite database.
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Has reproduction · 92
Synergism between IL7R and CXCR4 drives BCR-ABL induced transformation in Philadelphia chromosome-positive acute lymphoblastic leukemia.
PMID 32581241 · PMC7314847 · Nature communications · 2020 · 8 claims · 8 setups
IL7R interacts/colocalizes with CXCR4 on the cell surface, recruiting BCR-ABL1 and JAK kinases into close proximity to form a platform for transformation
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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.
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Has reproduction · 100
Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.
PMID 35197309 · PMC8997347 · Genome research · 2022 · 8 claims · 5 setups
A network-based approach integrating RNA-seq and cell-shape imaging data identifies data-derived signaling networks specific to cell-shape regulation in breast cancer.
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Has reproduction · 63
RummaGEO: Automatic mining of human and mouse gene sets from GEO.
PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups
RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO