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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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
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Inferring combinatorial regulation of transcription in silico.
PMID 15647509 · PMC546154 · Nucleic acids research · 2005 · 8 claims · 5 setups
Combining Cluster-Buster (TFBS cluster prediction) with GOSSIP (rigorous GO enrichment statistics with multiple-testing/FDR correction) predicts biological functions controlled by combinatorial transcription factor action, without prior knowledge of factor targets
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Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).
PMID 17601345 · PMC1929076 · BMC genomics · 2007 · 8 claims · 8 setups
MPSS detected 10,279 UniGene clusters, representing 7,475 known genes, in human hepatocytes
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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