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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On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve.
PMID 18076765 · PMC2211327 · BMC bioinformatics · 2007 · 8 claims · 4 setups
The TGDR-AUC algorithm regularizes the empirical AUC by replacing the non-differentiable 0-1 loss with a smooth sigmoid surrogate function and applies constrained threshold gradient descent regularization
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Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics.
PMID 18788775 · PMC3744223 · Journal of proteome research · 2008 · 7 claims · 4 setups
PeptideProphet's fixed LDA coefficients for combining search scores (Xcorr', ΔCn, SpRank) may not be optimal under all search/instrument conditions.
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An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results.
PMID 15005801 · PMC341449 · BMC bioinformatics · 2004 · 7 claims · 3 setups
An XML schema called Annotated Gel Markup Language (AGML) is proposed to manage, analyze, and disseminate annotated 2D gel electrophoresis and MS results.
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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