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 · 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
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Has reproduction · 40
DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data.
PMID 38950178 · PMC11236288 · Bioinformatics (Oxford, England) · 2024 · 8 claims · 2 setups
DeepGSEA is an explainable deep gene set enrichment analysis method built on interpretable, prototype-based neural networks.
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Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.
PMID 18828907 · PMC2760872 · Genome biology · 2008 · 8 claims · 8 setups
A combinatorial bioinformatics pipeline (evolutionary double filtering comparative genomics, GXD/ZFIN database queries, MEDLINE text mining) can rapidly and specifically identify PAX2/5/8 direct downstream targets in the otic vesicle
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Hit selection with false discovery rate control in genome-scale RNAi screens.
PMID 18628291 · PMC2504311 · Nucleic acids research · 2008 · 8 claims · 3 setups
A Bayesian FDR-controlling methodology for hit selection in genome-scale RNAi HTS is proposed, using a direct posterior probability approach analogous to Newton et al.