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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Non-EST based prediction of exon skipping and intron retention events using Pfam information.
PMID 16204458 · PMC1243800 · Nucleic acids research · 2005 · 7 claims · 5 setups
A novel ab initio method predicts exon skipping and intron retention events using only Pfam domain annotation, via a Viterbi-like dynamic programming algorithm applied to the Pfam alignment.
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PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.
PMID 17202160 · PMC1899096 · Nucleic acids research · 2007 · 7 claims · 5 setups
PolyA_DB 2 catalogs poly(A) sites for genes in human, mouse, rat, chicken and zebrafish, identified by aligning cDNA/ESTs with genome sequences
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Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.
PMID 16925837 · PMC1810552 · Genome biology · 2006 · 6 claims · 3 setups
Promoter predictors that combine promoter prediction with gene prediction (N-SCAN, Fprom) achieve better performance than pure ab initio promoter predictors, mainly by reducing the promoter search space and false positives
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Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes.
PMID 16840528 · PMC1524903 · Nucleic acids research · 2006 · 7 claims · 5 setups
MS-PET, which dimerizes PETs prior to 454 multiplex sequencing, achieves an approximate 100-fold efficiency increase over standard Sanger-based PET analysis