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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PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization.
PMID 15608166 · PMC540074 · Nucleic acids research · 2005 · 7 claims · 4 setups
PA-GOSUB significantly extends the coverage of GO molecular function and subcellular localization annotations for 10 model organism proteomes compared with existing databases (GOA, Swiss-Prot).
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Empirical Bayes analysis of quantitative proteomics experiments.
PMID 19829701 · PMC2759080 · PloS one · 2009 · 8 claims · 4 setups
Developed a new empirical Bayes framework that models log2 SILAC protein ratios and is robust to non-Gaussian tails and data sparsity, unlike Gaussian mixture models or Efron's original spline-based approach
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A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.
PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups
A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types
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Has reproduction · 40
On the holobiont 'predictome' of immunocompetence in pigs.
PMID 37127575 · PMC10150480 · Genetics, selection, evolution : GSE · 2023 · 8 claims · 8 setups
Holobiont (combined genotype + microbiome) models performed better than partial models (genotype-only or microbiome-only) overall