Models

Strength of functional signature correlates with effect size in autism
BACKGROUND: Disagreements over genetic signatures associated with disease have been particularly prominent in the field of psychiatric …
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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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Positive and negative forms of replicability in gene network analysis
MOTIVATION: Gene networks have become a central tool in the analysis of genomic data but are widely regarded as hard to interpret. This …
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Guidance for RNA-seq co-expression network construction and analysis: safety in numbers
MOTIVATION: RNA-seq co-expression analysis is in its infancy and reasonable practices remain poorly defined. We assessed a variety of …
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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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Conditions for the evolution of gene clusters in bacterial genomes
Genes encoding proteins in a common pathway are often found near each other along bacterial chromosomes. Several explanations have been …
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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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