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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Transcription network construction for large-scale microarray datasets using a high-performance computing approach.
PMID 18366618 · PMC2386070 · BMC genomics · 2008 · 8 claims · 7 setups
RMT removes the random noise component of the gene expression correlation matrix by testing its eigenvalue statistics against a null hypothesis derived from a truly random correlation matrix
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Has reproduction · 81
Ribosome A and P sites revealed by length analysis of ribosome profiling data.
PMID 25805170 · PMC4402525 · Nucleic acids research · 2015 · 7 claims · 8 setups
Accounting for variation in ribosome footprint lengths, by aligning footprints to the correct end, reveals the ribosome A and P site locations.
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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.
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Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.
PMID 20003344 · PMC2801700 · BMC genomics · 2009 · 7 claims · 8 setups
Meta-analysis of 16 microarray datasets across human, mouse, rat and yeast identifies 164 genes (MDEGs) consistently differentially expressed in response to high fat diet or PPAR signaling perturbation.