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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Assessing the genomic evidence for conserved transcribed pseudogenes under selection.
PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups
1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.
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Has reproduction · 76
Transcriptional landscape of repetitive elements in normal and cancer human cells.
PMID 25012247 · PMC4122776 · BMC genomics · 2014 · 8 claims · 8 setups
RepEnrich, a computational method that uses all mapping reads (uniquely mapping plus multi-mapping reads assigned to repetitive element subfamily assemblies/pseudogenomes), quantifies genome-wide repetitive element enrichment
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A third approach to gene prediction suggests thousands of additional human transcribed regions.
PMID 16543943 · PMC1391917 · PLoS computational biology · 2006 · 8 claims · 7 setups
A third basic concept for gene prediction exists, based on detecting strand-specific 'transcription footprints' (mutational and selectional biases) rather than gene structure or sequence similarity.
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Detecting transcriptionally active regions using genomic tiling arrays.
PMID 16859498 · PMC1779562 · Genome biology · 2006 · 8 claims · 4 setups
A non-parametric method (TranscriptionDetector) integrates single-channel p-values from multiple replicate arrays into a multi-channel p-value (MCPV) to identify transcribed probed loci without assumptions about intensity distributions.