Protein

Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction

The expansion of protein-ligand annotation databases has enabled large-scale networking of proteins by ligand similarity. These ligand-based protein networks, which implicitly predict the ability of neighboring proteins to bind related ligands, may …

Measuring the wisdom of the crowds in network-based gene function inference

MOTIVATION: Network-based gene function inference methods have proliferated in recent years, but measurable progress remains elusive. We wished to better explore performance trends by controlling data and algorithm implementation, with a particular …

Bias tradeoffs in the creation and analysis of protein-protein interaction networks

Networks constructed from aggregated protein-protein interaction data are commonplace in biology. But the studies these data are derived from were conducted with their own hypotheses and foci. Focusing on data from budding yeast present in BioGRID, …

Analysis of genome-wide association study data using the protein knowledge base

BACKGROUND: Genome-wide association studies (GWAS) aim to identify causal variants and genes for complex disease by independently testing a large number of SNP markers for disease association. Although genes have been implicated in these studies, few …