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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Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals.
PMID 15882449 · PMC1134656 · BMC genomics · 2005 · 8 claims · 4 setups
A predictive computational screen covering ~40% of annotated protein-coding genes identified 21 co-expressed gene clusters with statistically supported sharing of cis-regulatory motifs.
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The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.
PMID 15608292 · PMC540057 · Nucleic acids research · 2005 · 8 claims · 6 setups
Built a library of 1134 HMM models (359 matrix-derived, 718 factor-derived, 57 JASPAR-derived), corresponding to 863 distinct TF names, from TRANSFAC and JASPAR binding site data
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QuadBase: genome-wide database of G4 DNA--occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes.
PMID 17962308 · PMC2238983 · Nucleic acids research · 2008 · 8 claims · 3 setups
QuadBase is a compendium of G4 DNA (quadruplex) motifs focused on their occurrence and conservation in promoters, composed of EuQuad and ProQuad
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Comparative genomics of the neglected human malaria parasite Plasmodium vivax.
PMID 18843361 · PMC2651158 · Nature · 2008 · 8 claims · 8 setups
P. vivax resembles other sequenced malaria parasites (P. falciparum, P. knowlesi, P. yoelii) in gene content and metabolic potential