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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fREDUCE: detection of degenerate regulatory elements using correlation with expression.
PMID 17941998 · PMC2174516 · BMC bioinformatics · 2007 · 6 claims · 5 setups
fREDUCE is a computational method that detects weak or degenerate binding motifs from gene expression or ChIP-chip data by exhaustive search of degenerate IUPAC oligonucleotides
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Decision tree-driven tandem mass spectrometry for shotgun proteomics.
PMID 18931669 · PMC2597439 · Nature methods · 2008 · 8 claims · 5 setups
A decision tree (DT) algorithm that selects CAD or ETD per precursor based on z and m/z yields more peptide identifications than either CAD or ETD alone
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Evolutionary origins of human apoptosis and genome-stability gene networks.
PMID 18832373 · PMC2577361 · Nucleic acids research · 2008 · 8 claims · 8 setups
The entanglement of DNA repair, chromosome stability and apoptosis gene networks appears with the caspase gene family and the antiapoptotic gene BCL2.
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Has reproduction · 30
Minimal metabolic pathway structure is consistent with associated biomolecular interactions.
PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups
MinSpan, a mixed-integer linear optimization algorithm, computes the shortest, linearly independent pathways (sparsest basis of the null space of the stoichiometric matrix S) for genome-scale metabolic networks, which convex approaches (extreme pathways, elementary flux modes) cannot do at genome scale.