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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Inparanoid: a comprehensive database of eukaryotic orthologs.
PMID 15608241 · PMC540061 · Nucleic acids research · 2005 · 8 claims · 4 setups
The Inparanoid algorithm identifies true ortholog clusters by seeding on reciprocal best-matching pairs, gathering inparalogs (post-speciation duplicates) while excluding outparalogs (pre-speciation duplicates)
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Pseudofam: the pseudogene families database.
PMID 18957444 · PMC2686518 · Nucleic acids research · 2009 · 8 claims · 7 setups
Pseudofam is an online database of pseudogene families built by mapping pseudogenes to Pfam protein families, providing query tools, statistics, and sequence alignments
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SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.
PMID 18174224 · PMC2238826 · Nucleic acids research · 2008 · 6 claims · 5 setups
Standard genome annotation pipelines misannotate selenoprotein genes because they rely on UGA as a universal stop codon, failing to recognize its dual role as the selenocysteine-recoding codon.
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Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.
PMID 16849434 · PMC1524920 · Nucleic acids research · 2006 · 8 claims · 7 setups
A fast integrative in silico pipeline combining UniGene mRNA/EST mapping to GoldenPath genomes with CDS, poly(A) signal, poly(A) tail and splicing site evidence can reliably identify cis-NATs genome-wide across multiple species