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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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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The EH1 motif in metazoan transcription factors.
PMID 16309560 · PMC1310626 · BMC genomics · 2005 · 8 claims · 5 setups
There is a statistically significant association between EH1hox motif HMM score and transcription factor function across human, Drosophila and C. elegans proteomes.
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Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.
PMID 16912992 · PMC1538848 · Nucleic acids research · 2006 · 7 claims · 8 setups
PANTHER HMMs built from family/subfamily multiple sequence alignments can classify novel protein sequences into functional groups based on statistically significant HMM match scores
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Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint.
PMID 17349043 · PMC1829165 · BMC bioinformatics · 2007 · 8 claims · 6 setups
A combined target-selection approach — pursuing both structurally uncharacterised domain families and additional targets from large structurally characterised superfamilies — is essential for comprehensive structural coverage of the genomes.