QUASAR - scoring and ranking of sequence-structure alignments. - Fabian Birzele; Jan E. Gewehr; Ralf Zimmer (Bioinform., 2005)

A new representation for protein secondary structure prediction based on frequent patterns. - Fabian Birzele; Stefan Kramer 001 (Bioinform., 2006)

Vorolign - fast structural alignment using Voronoi contacts. - Fabian Birzele; Jan E. Gewehr; Gergely Csaba; Ralf Zimmer (Bioinform., 2007)

Protein structure alignment considering phenotypic plasticity. - Gergely Csaba; Fabian Birzele; Ralf Zimmer (ECCB, 2008)

AutoPSI: a database for automatic structural classification of protein sequences and structures. - Fabian Birzele; Jan E. Gewehr; Ralf Zimmer (Nucleic Acids Res., 2008)

ProSAS: a database for analyzing alternative splicing in the context of protein structures. - Fabian Birzele; Robert Küffner; Franziska Meier; Florian Oefinger; Christian Potthast; Ralf Zimmer (Nucleic Acids Res., 2008)

Algorithmische Systembiologie mit Petrinetzen - Von qualitativen zu quantitativen Systemmodellen. - Fabian Birzele; Gergely Csaba; Florian Erhard; Caroline C. Friedel; Robert Küffner; Tobias Petri; Lukas Windhager; Ralf Zimmer (Inform. Spektrum, 2009)

Improving structure alignment-based prediction of SCOP families using Vorolign Kernels. - Tobias Hamp; Fabian Birzele; Fabian Buchwald; Stefan Kramer 001 (Bioinform., 2011)

Manananggal - a novel viewer for alternative splicing events. - Matthias Barann; Ralf Zimmer; Fabian Birzele (BMC Bioinform., 2017)