MolSurfer: a macromolecular interface navigator. - Razif R. Gabdoulline; Rebecca C. Wade; Dirk Walther 001 (Nucleic Acids Res., 2003)

pcaMethods - a bioconductor package providing PCA methods for incomplete data. - Wolfram Stacklies; Henning Redestig; Matthias Scholz; Dirk Walther 001; Joachim Selbig (Bioinform., 2007)

ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites. - Jan Hummel; Michaela Niemann; Stefanie Wienkoop; Waltraud X. Schulze; Dirk Steinhauser; Joachim Selbig; Dirk Walther 001; Wolfram Weckwerth (BMC Bioinform., 2007)

The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles. - Pawel Durek; Dirk Walther 001 (BMC Syst. Biol., 2008)

PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. - Joshua L. Heazlewood; Pawel Durek; Jan Hummel; Joachim Selbig; Wolfram Weckwerth; Dirk Walther 001; Waltraud X. Schulze (Nucleic Acids Res., 2008)

Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins. - Pawel Durek; Christian Schudoma; Wolfram Weckwerth; Joachim Selbig; Dirk Walther 001 (BMC Bioinform., 2009)

Modeling RNA loops using sequence homology and geometric constraints. - Christian Schudoma; Patrick May; Dirk Walther 001 (Bioinform., 2010)

The complexity of gene expression dynamics revealed by permutation entropy. - Xiaoliang Sun; Yong Zou 002; Victoria J. Nikiforova; Jürgen Kurths; Dirk Walther 001 (BMC Bioinform., 2010)

The Roles of Post-translational Modifications in the Context of Protein Interaction Networks. - Guangyou Duan; Dirk Walther 001 (PLoS Comput. Biol., 2015)

A perspective on genetic and polygenic risk scores - advances and limitations and overview of associated tools. - Jana Schwarzerova; Martin Hurta; Vojtech Barton; Matej Lexa; Dirk Walther 001; Valentine Provazník; Wolfram Weckwerth (Briefings Bioinform., 2024)