NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis. - Anna Wierczeiko; Stefan Pastore; Stefan Mündnich; Anne M. Busch; Vincent Dietrich; Mark Helm; Tamer Butto; Susanne Gerber (Bioinform., 2023)

Cortexa: a comprehensive resource for studying gene expression and alternative splicing in the murine brain. - Stephan Weißbach; Jonas Milkovits; Stefan Pastore; Martin Heine; Susanne Gerber; Hristo Todorov (BMC Bioinform., 2024)

ClearFinder: a Python GUI for annotating cells in cleared mouse brain. - Stefan Pastore; Philipp Hillenbrand; Nils Molnar; Irina Kovlyagina; Monika Chanu Chongtham; Stanislav Sys; Beat Lutz; Margarita Tevosian; Susanne Gerber (BMC Bioinform., 2025)