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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Adaptation to different human populations by HIV-1 revealed by codon-based analyses.
PMID 16789820 · PMC1480537 · PLoS computational biology · 2006 · 8 claims · 8 setups
Developed two fixed effects maximum likelihood methods: one to detect selection that persists in a population (internal vs. terminal branches) and one to detect differential selection on codons between two populations.
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CLEAN: CLustering Enrichment ANalysis.
PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups
The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).
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Bayesian coestimation of phylogeny and sequence alignment.
PMID 15804354 · PMC1087833 · BMC bioinformatics · 2005 · 7 claims · 3 setups
Alignment and phylogenetic inference are mutually dependent, and treating them as separate sequential steps (align then infer tree) is fundamentally flawed and produces biased, overconfident estimates.
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Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs.
PMID 15380029 · PMC521075 · BMC genomics · 2004 · 8 claims · 6 setups
Cell-cycle related CDKs (orthologs of CDK1-6) are present in all sampled eukaryotic organisms, including the most ancestral protists.