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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Designating eukaryotic orthology via processed transcription units.
PMID 18445630 · PMC2425467 · Nucleic acids research · 2008 · 8 claims · 5 setups
Existing ortholog databases discard/ignore alternative splicing via all-against-all protein comparisons, causing ambiguous ortholog calls and misclassification of AS isoforms as in-paralogs
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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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A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.
PMID 19043541 · PMC2580819 · PLoS computational biology · 2008 · 8 claims · 5 setups
A general model-free methodological framework is proposed for reconstructing Contiguous Ancestral Regions (CARs) from conserved syntenies, generalizing prior computational and cytogenetic approaches
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CLEAN: CLustering Enrichment ANalysis.
PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups
The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).