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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Inferring combinatorial regulation of transcription in silico.
PMID 15647509 · PMC546154 · Nucleic acids research · 2005 · 8 claims · 5 setups
Combining Cluster-Buster (TFBS cluster prediction) with GOSSIP (rigorous GO enrichment statistics with multiple-testing/FDR correction) predicts biological functions controlled by combinatorial transcription factor action, without prior knowledge of factor targets
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Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs.
PMID 17217514 · PMC1780116 · BMC bioinformatics · 2006 · 6 claims · 4 setups
A novel method combining 8-species comparative genomics with de novo motif discovery identifies human TF DNA-binding motifs overrepresented and conserved in upstream regions of co-regulated genes
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Automatic annotation of eukaryotic genes, pseudogenes and promoters.
PMID 16925832 · PMC1810547 · Genome biology · 2006 · 8 claims · 6 setups
Fgenesh++ gene prediction pipeline identifies 91% of coding nucleotides with 90% specificity
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Does distance matter? Variations in alternative 3' splicing regulation.
PMID 17704130 · PMC2018619 · Nucleic acids research · 2007 · 8 claims · 7 setups
Alternative 3' splice sites can be distinguished from constitutive splice sites by a combination of sequence/conservation properties that vary depending on the distance between the splice sites.