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 identification of specific oligonucleotides using artificial neural network and computational genomic analysis.
PMID 17518996 · PMC1892811 · BMC bioinformatics · 2007 · 7 claims · 4 setups
The IAB algorithm (integration of ANN and BLAST) identifies genome-wide specific oligos much faster than pure BLAST search while maintaining comparable success rate and cross homology
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JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions.
PMID 16925843 · PMC1810558 · Genome biology · 2006 · 8 claims · 4 setups
Adding model states for specific biological features (signal peptides, CpG islands, etc.) to non-comparative GHMM gene finders did little or nothing to enhance predictive accuracy, sometimes reducing it.
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Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle.
PMID 17362520 · PMC1839098 · BMC genomics · 2007 · 8 claims · 8 setups
The bovine BPI-like locus spans 470 kbp and contains 14 contiguous genes (13 intact + 1 pseudogene); 9 are orthologous to human/mouse BPI-like genes and 4 (named BSP30A, BSP30B, BSP30C, BSP30D) arose through cattle-specific duplication of the PSP gene
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Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.
PMID 16569258 · PMC1557760 · Genome biology · 2006 · 8 claims · 7 setups
An exon-gene-union (EGU) algorithm followed by an open-reading-frame-selection algorithm can synthesize ab initio (GENSCAN, GeneMark, SNAP) and comparative (Ensembl/Genewise) predictions into a single, more complete CDS set