#30 · Systems biology

Automated tools link genomic variants and expression data to regulatory interpretation

The dominant thread is software that automates the steps between genomic or expression data and biological interpretation. SNPannotator, an R package, identifies LD proxies for post-GWAS variants and queries Ensembl, GTEx, eQTL Catalog and STRING for functional and eQTL annotation. SignifiKANTE computes approximate permutation-based P-values for edges in gene regulatory networks from any regression-based GRN, while BLOBFISH extracts compact subnetworks linking a predefined gene set across regulatory and eQTL bipartite graphs. GAMclust, also an R package, identifies transcriptionally regulated metabolic modules in bulk, single-cell and spatial expression data. DNABERT-Enhancer is a sequence-level model that applies a genomic language model to predict human enhancers and allele-specific activity, releasing genome-wide annotations. What is new is packaged, automated coverage spanning post-association annotation, network-level inference and module identification, with DNABERT-Enhancer extending the scope to sequence-level prediction.