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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Network inference and network response identification: moving genome-scale data to the next level of biological discovery.
PMID 20174676 · PMC3087299 · Molecular bioSystems · 2010 · 8 claims · 8 setups
Cellular response to a signal is assumed to involve only specific TRN modules (conditionally active subnetworks) rather than the entire network, providing quantitative tractability
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Environmental genome project: focusing on differences to understand the whole.
PMID 12460813 · PMC1241127 · Environmental health perspectives · 2002 · 8 claims · 4 setups
The EGP has generated a working list of more than 550 environmentally responsive genes involved in pathways such as metabolism, DNA repair, and cell cycle control as candidates for SNP resequencing.
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Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.
PMID 16912992 · PMC1538848 · Nucleic acids research · 2006 · 7 claims · 8 setups
PANTHER HMMs built from family/subfamily multiple sequence alignments can classify novel protein sequences into functional groups based on statistically significant HMM match scores
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Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments.
PMID 15850479 · PMC1127068 · BMC bioinformatics · 2005 · 8 claims · 8 setups
A step-down quadratic regression method (fitting quadratic, then linear, then null models per gene) identifies differentially expressed genes and classifies them into 9 temporal expression patterns using continuous time information.