Databases

AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression
In addition to detecting novel transcripts and higher dynamic range, a principal claim for RNA-sequencing has been greater …
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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 …
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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. …
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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 …
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Identification of novel therapeutics for complex diseases from genome-wide association data
BACKGROUND: Human genome sequencing has enabled the association of phenotypes with genetic loci, but our ability to effectively …
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Gentrepid V2.0: a web server for candidate disease gene prediction
BACKGROUND: Candidate disease gene prediction is a rapidly developing area of bioinformatics research with the potential to deliver …
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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 …
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Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies
BACKGROUND: Automated candidate gene prediction systems allow geneticists to hone in on disease genes more rapidly by identifying the …
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