The HHpred interactive server for protein homology detection and structure prediction. - Johannes Söding; Andreas Biegert; Andrei N. Lupas (Nucleic Acids Res., 2005)

The MPI Bioinformatics Toolkit for protein sequence analysis. - Andreas Biegert; Christian E. Mayer; Michael Remmert; Johannes Söding; Andrei N. Lupas (Nucleic Acids Res., 2006)

HHrep: de novo protein repeat detection and the origin of TIM barrels. - Johannes Söding; Michael Remmert; Andreas Biegert (Nucleic Acids Res., 2006)

HHsenser: exhaustive transitive profile search using HMM-HMM comparison. - Johannes Söding; Michael Remmert; Andreas Biegert; Andrei N. Lupas (Nucleic Acids Res., 2006)

De novo identification of highly diverged protein repeats by probabilistic consistency. - Andreas Biegert; Johannes Söding (Bioinform., 2008)

Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors. - Alex Bateman; Robert D. Finn; Peter J. Sims; Therese Wiedmer; Andreas Biegert; Johannes Söding (Bioinform., 2009)

Discriminative modelling of context-specific amino acid substitution probabilities. - Christof Angermüller; Andreas Biegert; Johannes Söding (Bioinform., 2012)