Dynamic Programming Algorithm for the Density of States of RNA Secondary Structures. - Jan Cupal; Ivo L. Hofacker; Peter F. Stadler (German Conference on Bioinformatics, 1996)

Density of States, Metastable States, and Saddle Points: Exploring the Energy Landscape of an RNA Molecule. - Jan Cupal; Christoph Flamm; Alexander Renner; Peter F. Stadler (ISMB, 1997)

Topology in Phenotype Space. - Jan Cupal (German Conference on Bioinformatics, 1999)

RNA Shape Space Topology. - Jan Cupal; Stephan Kopp; Peter F. Stadler (Artif. Life, 2000)