Gene Regulatory Networks

Predictability of human differential gene expression
Differential expression (DE) is commonly used to explore molecular mechanisms of biological conditions. While many studies report …
Cite DOI
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 …
Cite DOI
EGAD: ultra-fast functional analysis of gene networks
Exploiting single-cell expression to characterize co-expression replicability
BACKGROUND: Co-expression networks have been a useful tool for functional genomics, providing important clues about the cellular and …
Cite DOI
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 …
Cite DOI
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 …
Cite DOI
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 …
Cite DOI
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. …
Cite DOI
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 …
Cite DOI