Humans

Predictability of human differential gene expression
Differential expression (DE) is commonly used to explore molecular mechanisms of biological conditions. While many studies report …
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Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor
Single-cell RNA-sequencing (scRNA-seq) technology provides a new avenue to discover and characterize cell types; however, the …
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Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor
EGAD: ultra-fast functional analysis of gene networks
Summary: Evaluating gene networks with respect to known biology is a common task but often a computationally costly one. Many …
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EGAD: ultra-fast functional analysis of gene networks
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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Using predictive specificity to determine when gene set analysis is biologically meaningful
Gene set analysis, which translates gene lists into enriched functions, is among the most common bioinformatic methods. Yet few would …
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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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Novel therapeutics for coronary artery disease from genome-wide association study data
BACKGROUND: Coronary artery disease (CAD), one of the leading causes of death globally, is influenced by both environmental and genetic …
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