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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Peptide bioinformatics: peptide classification using peptide machines.
PMID 19065810 · PMC7122642 · Methods in molecular biology (Clifton, N.J.) · 2008 · 8 claims · 4 setups
The bio-basis function, which converts peptides into numerical vectors using nongapped pairwise homology alignment scores against indicator peptides, can statistically quantify peptide similarity for classification.
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Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.
PMID 19903485 · PMC2836169 · Journal of immunological methods · 2010 · 7 claims · 7 setups
PS mutations V7I and I34L (p17) and K403R (p7) in HIV-1 gag significantly correlate with HLA-A*0301
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Non-linear mapping for exploratory data analysis in functional genomics.
PMID 15661072 · PMC548129 · BMC bioinformatics · 2005 · 8 claims · 8 setups
A relaxation method for non-linear mapping adapts one pair of points per step rather than all points at once, and was originally shown by Chang and Lee to outperform Sammon's mapping in cluster detection effectiveness and computational efficiency.
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Has reproduction · 61
A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.
PMID 25392735 · PMC4228822 · 8 claims · 8 setups
T. melanosporum shows a high rate of cytosine methylation (>44%) that selectively targets transposable elements rather than genes, with a strong preference for CpG sites.