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 · 69
A blood-based DNA damage signature in patients with Parkinson's disease is associated with disease progression.
PMID 40913219 · PMC12443628 · Nature aging · 2025 · 8 claims · 2 setups
A blood-based DNA damage signature is present in PD patients and is associated with disease progression.
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Has reproduction · 85
Integration of multi-omics and machine learning strategies identifies immune related candidate biomarkers in inflammation-associated hypertrophic cardiomyopathy.
PMID 41080564 · PMC12510942 · Frontiers in immunology · 2025 · 8 claims · 8 setups
Seven key immune-related genes (RNF165, SNCA, SRGN, MARCO, STEAP4, SIGLEC9, TKT) are associated with HCM by intersecting DEGs with MR-identified eQTLs
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Has reproduction · 64
Integrated multi-omics analysis combined with clinical validation reveals that HLA-DRB5 and ODAPH are causal risk genes for keratoconus.
PMID 41803193 · PMC13179358 · Scientific reports · 2026 · 8 claims · 8 setups
2,884 differentially expressed genes (DEGs) were identified as the union of upregulated genes from two independent KC transcriptome datasets (GSE151631, GSE77938), enriched in cell adhesion, immune response, and TNF/IL-17 signaling pathways.
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Has reproduction · 72
Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.
PMID 33138797 · PMC7607642 · BMC cancer · 2020 · 8 claims · 8 setups
edgeR-based DEG selection is more appropriate for feature selection than Elastic Net when sample sizes are small.
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Has reproduction · 62
Predicting Bone Metastasis Using Gene Expression-Based Machine Learning Models.
PMID 34858485 · PMC8631472 · Frontiers in genetics · 2021 · 7 claims · 5 setups
A DNN model using the top 34 betweenness-centrality-ranked hub genes predicts bone metastasis with AUC of 92.11% on the GEO validation data.
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Has reproduction · 93
Integrated bioinformatics analysis screened the key genes and pathways of idiopathic pulmonary fibrosis.
PMID 40280949 · PMC12032202 · Scientific reports · 2025 · 8 claims · 8 setups
5328 differentially expressed transcripts (4083 genes) were identified in GSE173355 by limma, with 4012 transcripts (3206 genes) confirmed by both limma and edgeR (logFC>1, FDR<0.05)
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Has reproduction · 77
Representing and querying disease networks using graph databases.
PMID 27462371 · PMC4960687 · BioData mining · 2016 · 7 claims · 8 setups
Graph databases are well suited for representing biological information because it is typically highly connected, semi-structured and unpredictable, unlike relational databases which require rigid schemas.
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Has reproduction · 50
SMAC, a computational system to link literature, biomedical and expression data.
PMID 31324861 · PMC6642118 · Scientific reports · 2019 · 8 claims · 8 setups
SMAC is a tool that extracts, prioritises, integrates and analyses biomedical and molecular data according to user-defined terms
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Has reproduction · 100
Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility.
PMID 33707641 · PMC7970949 · Scientific reports · 2021 · 8 claims · 8 setups
WGCNA on control human cervical spinal cord RNA-seq identifies 13 co-expression modules (SC.M1-M13), each representing distinct biological processes or cell types.