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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Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.
PMID 15693947 · PMC551538 · Genome biology · 2005 · 7 claims · 8 setups
FastCompare, a non-alignment-based, linear-time algorithm, computes a genome-wide conservation score for all k-mers (7-9 nt) between two genomes to identify conserved regulatory elements
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Ab initio identification of putative human transcription factor binding sites by comparative genomics.
PMID 15865625 · PMC1097714 · BMC bioinformatics · 2005 · 8 claims · 5 setups
An integrated algorithm combining human-mouse genomic comparison, motif overrepresentation, and coregulation filters (GO annotation and microarray coexpression) can identify candidate transcription factor binding sites genome-wide
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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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Inference of transcriptional regulation using gene expression data from the bovine and human genomes.
PMID 17683551 · PMC1978505 · BMC genomics · 2007 · 7 claims · 8 setups
Using human reference promoter sequences is a useful approach for studying gene expression regulation in species with limited or non-existing genomic sequence, such as cattle.