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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CoMoDis: composite motif discovery in mammalian genomes.
PMID 17130158 · PMC1702496 · Nucleic acids research · 2007 · 7 claims · 4 setups
CoMoDis is a new bioinformatics tool that streamlines computational identification of novel regulatory modules starting from a single seed motif
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InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.
PMID 17868464 · PMC2375030 · Genome biology · 2007 · 8 claims · 8 setups
InSite predicts protein-pair-specific binding motifs ('Motif M on protein A binds to protein B') by integrating heterogeneous PPI and motif-motif interaction evidence within a Bayesian network trained by EM
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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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Has reproduction · 65
High-throughput sequencing SELEX for the determination of DNA-binding protein specificities in vitro.
PMID 35776646 · PMC9243297 · STAR protocols · 2022 · 8 claims · 8 setups
HT-SELEX enables unbiased, in vitro determination of preferred DNA target motifs for DNA-binding proteins by iterative selection and PCR amplification of bound oligonucleotides