Erik L. L. Sonnhammer

Comprehensive analysis of the RBP regulome reveals functional modules and drug candidates in liver cancer

The paper identifies key RBP regulatory interactions in liver cancer and suggests potential drug candidates through GRN analysis and enrichment studies.

GeneSNAKE: a Python package for benchmarking and simulation of gene regulatory networks and perturbation-induced expression data

GeneSNAKE is a Python package that simulates gene regulatory networks and perturbation-induced expression data for benchmarking, offering control over network properties and noise models.

The FunCoup Cytoscape App: multi-species network analysis and visualization

The FunCoup Cytoscape App integrates FunCoup network data with Cytoscape for multi-species gene interaction analysis and visualization.

FunCoup 6: advancing functional association networks across species with directed links and improved user experience

FunCoup 6 enhances functional association networks with directed links, expanded coverage, and improved tools for analyzing protein interactions across species.

Benchmarking enrichment analysis methods with the disease pathway network

The paper benchmarks enrichment analysis methods using a disease pathway network and finds Network Enrichment Analysis methods perform best.

Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms

The paper infers a gene regulatory network (GRN) from perturbation experiments in cancer cells, identifying both known and novel regulatory interactions that contribute to oncogenic processes.