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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Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.
PMID 15941473 · PMC1164402 · BMC bioinformatics · 2005 · 8 claims · 5 setups
A combined linguistic+statistical+rule-based method achieves precision 0.61 and recall 0.97 (f=0.74) detecting yeast protein-protein interactions across 12,300 Medline abstracts.
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Ontological visualization of protein-protein interactions.
PMID 15707487 · PMC550656 · BMC bioinformatics · 2005 · 8 claims · 8 setups
Aggregating independently made GO 'protein binding' (IPI) annotations reveals larger, previously undescribed mouse protein-protein interaction networks
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Indirect genomic effects on survival from gene expression data.
PMID 18358079 · PMC2397510 · Genome biology · 2008 · 7 claims · 6 setups
A novel methodology (dynamic path analysis combined with additive hazard survival regression) can detect and quantify indirect effects of gene expression on survival mediated through transcription factor target genes.
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VIRGO: computational prediction of gene functions.
PMID 16845022 · PMC1538839 · Nucleic acids research · 2006 · 8 claims · 6 setups
VIRGO constructs a functional linkage network (FLN) from gene expression and molecular interaction data, labels genes with GO annotations, and propagates these labels to predict functions of unlabelled genes