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
D2H2: diabetes data and hypothesis hub.
PMID 38107655 · PMC10723036 · Bioinformatics advances · 2023 · 6 claims · 5 setups
D2H2 is a web portal hosting hundreds of curated, uniformly reprocessed diabetes-relevant transcriptomics datasets from GEO with per-study visualization, differential expression, and single-gene queries.
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Has reproduction · 80
Curation of over 10 000 transcriptomic studies to enable data reuse.
PMID 33599246 · PMC7904053 · Database : the journal of biological databases and curation · 2021 · 8 claims · 6 setups
Gemma is a curated database and bioinformatics system that addresses metadata, probe annotation, and expression data inconsistencies in GEO to enable transcriptomic data reuse
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Has reproduction · 53
PulmonDB: a curated lung disease gene expression database.
PMID 31949184 · PMC6965635 · Scientific reports · 2020 · 7 claims · 6 setups
PulmonDB is a curated, web-based relational database (plus R package) integrating microarray and RNA-seq gene expression data with controlled-vocabulary annotation for COPD and IPF.
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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
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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 · 89
MirDIP 5.2: tissue context annotation and novel microRNA curation.
PMID 36453996 · PMC9825511 · Nucleic acids research · 2023 · 7 claims · 6 setups
mirDIP 5.2 removed eight outdated resources, added miRNATIP, and ran five prediction algorithms against miRBase and mirGeneDB miRNAs to expand and improve interaction coverage
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Has reproduction · 59
Advances in genomic and pharmacokinetic profiling for clinical stratification of metastatic breast cancer.
PMID 41369820 · PMC12799884 · Discover oncology · 2025 · 8 claims · 8 setups
Key genes AR, AKT1, UBC, CDH1, SMAD3, ROR1, and ROR2 are associated with chemotherapy resistance and poor prognosis in metastatic breast cancer
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Has reproduction · 70
Spatial transcriptomics reveals the molecular signatures of prodromal and advanced α-synucleinopathy.
PMID 41736854 · PMC12927100 · iScience · 2026 · 7 claims · 6 setups
Early-stage (prodromal) aSyn pathology in M83+/+ mouse brainstem is associated with upregulation of ATP/energy metabolism pathways (glycolysis, oxidative phosphorylation, fatty acid metabolism)
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Has reproduction
Using random walks to identify cancer-associated modules in expression data.
PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups
Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.