Thermodynamics of RNA-RNA binding. - Ulrike Mückstein; Hakim Tafer; Jörg Hackermüller; Stephan H. Bernhart; Peter F. Stadler; Ivo L. Hofacker (Bioinform., 2006)

Duplicated RNA genes in teleost Fish genomes. - Dominic Rose; Julian Jöris; Jörg Hackermüller; Kristin Reiche; Qiang Li; Peter F. Stadler (J. Bioinform. Comput. Biol., 2008)

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures. - Steve Hoffmann; Christian Otto; Stefan Kurtz; Cynthia M. Sharma; Philipp Khaitovich; Jörg Vogel 002; Peter F. Stadler; Jörg Hackermüller (PLoS Comput. Biol., 2009)

The primary transcriptome of the major human pathogen Helicobacter pylori. - Cynthia M. Sharma; Steve Hoffmann; Fabien Darfeuille; Jérémy Reignier; Sven Findeiß; Alexandra Sittka; Sandrine Chabas; Kristin Reiche; Jörg Hackermüller; Richard Reinhardt; Peter F. Stadler; Jörg Vogel 002 (Nat., 2010)

Computational discovery of human coding and non-coding transcripts with conserved splice sites. - Dominic Rose; Michael Hiller; Katharina Schutt; Jörg Hackermüller; Rolf Backofen; Peter F. Stadler (Bioinform., 2011)

Detection of differentially expressed segments in tiling array data. - Christian Otto; Kristin Reiche; Jörg Hackermüller (Bioinform., 2012)

uap: reproducible and robust HTS data analysis. - Christoph Kämpf; Michael Specht; Alexander Scholz; Sven-Holger Puppel; Gero Doose; Kristin Reiche; Jana Schor; Jörg Hackermüller (BMC Bioinform., 2019)

multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data. - Sebastian Canzler; Jörg Hackermüller (BMC Bioinform., 2020)

Preserving Cluster Features in Imputing High Dimensional Data with Extensive Missing Rate. - Chih Lai; Carolin Poschen; Lisa Maria Steinheuer; Jörg Hackermüller (IEEE Big Data, 2022)

AI for predicting chemical-effect associations at the chemical universe level - deepFPlearn. - Jana Schor; Patrick Scheibe; Matthias Bernt; Wibke Busch; Chih Lai; Jörg Hackermüller (Briefings Bioinform., 2022)

deepFPlearn +: enhancing toxicity prediction across the chemical universe using graph neural networks. - Kyriakos Soulios; Patrick Scheibe; Matthias Bernt; Jörg Hackermüller; Jana Schor (Bioinform., 2023)

Automated curation of spatial metadata in environmental monitoring data. - Ilhan Mutlu; Jörg Hackermüller; Jana Schor (Ecol. Informatics, 2025)

An extended miRNA repertoire in Rattus norvegicus. - Julienne Lehmann; Ali Yazbeck; Jörg Hackermüller; Sebastian Canzler (Frontiers Bioinform., 2025)