HyPaLib: a database of RNAs and RNA structural elements defined by hybrid patterns. - Stefan Gräf; Dirk Strothmann; Stefan Kurtz; Gerhard Steger (Nucleic Acids Res., 2001)

PoSSuMsearch: Fast and Sensitive Matching of Position Specific Scoring Matrices using Enhanced Suffix Arrays. - Michael Beckstette; Dirk Strothmann; Robert Homann; Robert Giegerich; Stefan Kurtz (German Conference on Bioinformatics, 2004)

The affix array data structure and its applications to RNA secondary structure analysis. - Dirk Strothmann (Theor. Comput. Sci., 2007)