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).
-
Full-text index only
Identification of gene interactions associated with disease from gene expression data using synergy networks.
PMID 18234101 · PMC2258206 · BMC systems biology · 2008 · 8 claims · 4 setups
Synergy of a gene pair with respect to disease, defined as I(G1,G2;C) - [I(G1;C)+I(G2;C)], identifies gene pairs that interact cooperatively with respect to a phenotype rather than independently.
-
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.
-
Full-text index only
Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.
PMID 17166053 · PMC1664705 · PLoS computational biology · 2006 · 8 claims · 8 setups
Integrating interactome and transcriptome data reveals a pair of transcriptionally anticorrelated network modules (P and D) each comprising hundreds of genes, present across individuals and species.
-
Full-text index only
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.