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).

Publications 1.3k Datasets 392.5k Experiments 4

System / cell line: protein-protein ✕ Assay: leave-one-out ✕ Clear

Analysis of protein sequence and interaction data for candidate disease gene prediction.

PMID 17020920 · PMC1636487 · Nucleic acids research · 2006 · 8 claims · 7 setups

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Combining CPS and CMP using known disease genes as input achieves sensitivity 0.52 and specificity 0.97, reducing candidate lists 13-fold

ophid biocarta kegg pfam-annotated common benchmarking multiple-interval
VIRGO: computational prediction of gene functions.

PMID 16845022 · PMC1538839 · Nucleic acids research · 2006 · 8 claims · 6 setups

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VIRGO constructs a functional linkage network (FLN) from gene expression and molecular interaction data, labels genes with GO annotations, and propagates these labels to predict functions of unlabelled genes

cerevisiae sapiens leave-one-out gene protein-protein
PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data.

PMID 18925948 · PMC2605471 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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Gonna, a supervised k-nearest-neighbor Guilt-By-Association predictor, proposes GO annotations for a gene based on similarity of its transcriptome, proteome, or interactome profile to genes already annotated by GeneDB

plasmodium genedb-annotated k-nn leave-one-out
Identification of a pediatric acute hypoxemic respiratory failure signature in peripheral blood leukocytes at 24 hours post-ICU admission with machine learning.

PMID 37009294 · PMC10063855 · Frontiers in pediatrics · 2023 · 7 claims · 5 setups

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A machine learning stability selection approach (bootstrapped logistic regression, 100 simulations) can identify genes associated with PaO2/FiO2 < 200 vs ≥200 when standard differential expression with FDR correction shows no overlap between cohorts.

pediatric combined top-ranked whole-blood machine pathway

Experiments

Analysis of protein sequence and interaction data for candidate disease gene prediction.

VIRGO: computational prediction of gene functions.

PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data.

Identification of a pediatric acute hypoxemic respiratory failure signature in peripheral blood leukocytes at 24 hours post-ICU admission with machine learning.