genomation: a toolkit to summarize, annotate and visualize genomic intervals. - Altuna Akalin; Vedran Franke; Kristian Vlahovicek; Christopher E. Mason; Dirk Schübeler (Bioinform., 2015)

Compass: A Comprehensive Tool for Accurate and Efficient Molecular Docking in Inference and Fine-Tuning. - Ahmet Sarigün; Vedran Franke; Altuna Akalin (CoRR, 2024)

Evaluating large language model workflows in clinical decision support for triage and referral and diagnosis. - Farieda Gaber; Maqsood Shaik; Fabio Allega; Agnes Julia Bilecz; Felix Busch; Kelsey Goon; Vedran Franke; Altuna Akalin (npj Digit. Medicine, 2025)

PocketVina Enables Scalable and Highly Accurate Physically Valid Docking through Multi-Pocket Conditioning. - Ahmet Sarigün; Bora Uyar; Vedran Franke; Altuna Akalin (CoRR, 2025)