Computational Design of a Circular RNA with Prionlike Behavior. - Stefan Badelt; Christoph Flamm; Ivo L. Hofacker (Artif. Life, 2016)

A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities. - Stefan Badelt; Seung Woo Shin; Robert F. Johnson; Qing Dong; Chris Thachuk; Erik Winfree (DNA, 2017)

Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction. - Christoph Flamm; Julia Wielach; Michael T. Wolfinger; Stefan Badelt; Ronny Lorenz; Ivo L. Hofacker (Frontiers Bioinform., 2022)

DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model. - Stefan Badelt; Ronny Lorenz; Ivo L. Hofacker (Bioinform., 2023)

DrForna: visualization of cotranscriptional folding. - Anda Ramona Tanasie; Peter Kerpedjiev; Stefan Hammer; Stefan Badelt (Bioinform., 2023)