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 · 64
GeMI: interactive interface for transformer-based Genomic Metadata Integration.
PMID 35657113 · PMC9216561 · Database : the journal of biological databases and curation · 2022 · 8 claims · 5 setups
GeMI is a web tool that uses a fine-tuned GPT2 model to extract 15 structured key-value attributes from free-text GEO sample metadata.
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Has reproduction · 75
An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries.
PMID 33247935 · PMC7698665 · Database : the journal of biological databases and curation · 2020 · 8 claims · 6 setups
GETc enables discovery and visualization of time-course gene expression data and analytical results from GEO
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Has reproduction · 74
Wide-Open: Accelerating public data release by automating detection of overdue datasets.
PMID 28594819 · PMC5464523 · PLoS biology · 2017 · 6 claims · 5 setups
A general text-mining + API-query approach (Wide-Open) can automatically identify datasets that are overdue for public release in a repository
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Has reproduction · 99
The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression Omnibus data repository.
PMID 40926267 · PMC12421755 · Genome biology · 2025 · 8 claims · 3 setups
Across 253 manually curated studies (164,000+ samples), over 25% of critical metadata are omitted, with only 74.8% of relevant phenotypes available overall.
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Has reproduction
D2H2: diabetes data and hypothesis hub.
PMID 38107655 · PMC10723036 · Bioinformatics advances · 2023 · 6 claims · 6 setups
D2H2 is a web-based portal integrating hundreds of curated diabetes-relevant transcriptomics datasets with bioinformatics tools for gene/gene set queries
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Has reproduction · 62
Gbdmr: identifying differentially methylated CpG regions in the human genome via generalized beta regressions.
PMID 38443825 · PMC10916021 · BMC bioinformatics · 2024 · 8 claims · 4 setups
gbdmr models DNA methylation levels of CpG sites using a generalized beta distribution instead of assuming normality as in linear-regression-based methods
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Has reproduction · 67
Reducing language barriers, promoting information absorption, and communication using fanyi.
PMID 39039634 · PMC11332769 · Chinese medical journal · 2024 · 7 claims · 3 setups
The fanyi R package retrieves gene information from NCBI and translates it into multiple languages using AI-driven online translation services
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Has reproduction · 89
Graph Random Forest: A Graph Embedded Algorithm for Identifying Highly Connected Important Features.
PMID 37509188 · PMC10377046 · Biomolecules · 2023 · 8 claims · 6 setups
GRF identifies effective features that form highly connected sub-graphs on the underlying biological network