An enhanced RNA alignment benchmark for sequence alignment programs. - Andreas Wilm; Indra Mainz; Gerhard Steger (Algorithms Mol. Biol., 2006)

StrAl: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time. - Deniz Dalli; Andreas Wilm; Indra Mainz; Gerhard Steger (Bioinform., 2006)

Knowledge Acquisition Focused Cooperative Development of Bio-ontologies - A Case Study with BIO2Me. - Dominic Mainz; Ingo Paulsen; Indra Mainz; Katrin Weller; Jochen Kohl; Arndt von Haeseler (BIRD, 2008)

Development and implementation of techniques for ontology engineering and an ontology-based search for bioinformatics tools and methods. - Indra Mainz (2008)