A spectrum of nonsense-mediated mRNA decay efficiency along the degree of mutational constraint.

Despite its importance for regulating gene expression, nonsense-mediated mRNA decay (NMD) remains poorly understood. Here, we extend the findings of a previous landmark study that proposed several factors associated with NMD efficiency using matched genome and transcriptome data from The Cancer Genome Atlas Program (TCGA) by incorporating additional data including Genotype-Tissue Expression (GTEx), gnomAD, and metrics for mutational constraints. Factors affecting NMD efficiency are analyzed using an allele-specific expression (ASE)-based measure to reduce noise caused by random variations.

Generating post-hoc explanations for Skip-gram-based node embeddings by identifying important nodes with bridgeness.

Node representation learning in a network is an important machine learning technique for encoding relational information in a continuous vector space while preserving the inherent properties and structures of the network. Recently, unsupervised node embedding methods such as DeepWalk (Perozzi et al., 2014), LINE (Tang et al.