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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Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.
PMID 16925842 · PMC1810557 · Genome biology · 2006 · 8 claims · 4 setups
MARS, an extension of the Twinscan algorithm, uses multiple pairwise informant genomes to predict human alternatively spliced transcripts de novo without expressed sequence information.
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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
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Transcriptome annotation using tandem SAGE tags.
PMID 17709346 · PMC2034470 · Nucleic acids research · 2007 · 8 claims · 7 setups
A novel algorithm pairs tandem SAGE tags anchored on two different restriction sites (CATG and GATC) to define tag-delimited genomic sequences (TDGS)