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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Dissecting microregulation of a master regulatory network.
PMID 18294391 · PMC2289817 · BMC genomics · 2008 · 8 claims · 6 setups
143 human miRNAs (termed p53-miRs) each contain at least one putative p53 binding site within 10 kb flanking sequence and are predicted to target at least one known gene
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Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.
PMID 19756158 · PMC2742196 · PLoS computational biology · 2009 · 8 claims · 4 setups
MIP active learning is a novel active learning method that preferentially seeks informative Positive (functionally active) examples rather than only maximizing classifier accuracy.
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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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A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.
PMID 16670430 · PMC1456330 · Nucleic acids research · 2006 · 8 claims · 7 setups
Highly-degenerate RE1 sites are significantly enriched in promoters of validated and putative REST target genes compared to control promoters