AREsite: a database for the comprehensive investigation of AU-rich elements. - Andreas R. Gruber; Jörg Fallmann; Franz Kratochvill; Pavel Kovarik; Ivo L. Hofacker (Nucleic Acids Res., 2011)

AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements. - Jörg Fallmann; Vitaly Sedlyarov; Andrea Tanzer; Pavel Kovarik; Ivo L. Hofacker (Nucleic Acids Res., 2016)

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. - Björn A. Grüning; Jörg Fallmann; Dilmurat Yusuf; Sebastian Will; Anika Erxleben; Florian Eggenhofer; Torsten Houwaart; Bérénice Batut; Pavankumar Videm; Andrea Bagnacani; Markus Wolfien; Steffen Lott; et al. (Nucleic Acids Res., 2017)

Accurate mapping of tRNA reads. - Anne Hoffmann 002; Jörg Fallmann; Elisa Vilardo; Mario Mörl; Peter F. Stadler; Fabian Amman (Bioinform., 2018)

Automatic curation of large comparative animal MicroRNA datasets. - Ali M. Yazbeck; Peter F. Stadler; Kifah Tout; Jörg Fallmann (Bioinform., 2019)

The RNA workbench 2.0: next generation RNA data analysis. - Jörg Fallmann; Pavankumar Videm; Andrea Bagnacani; Bérénice Batut; Maria A. Doyle; Tomas Klingström; Florian Eggenhofer; Peter F. Stadler; Rolf Backofen; Björn A. Grüning (Nucleic Acids Res., 2019)

Are spliced ncRNA host genes distinct classes of lncRNAs? - Rituparno Sen; Jörg Fallmann; Maria Emília M. T. Walter; Peter F. Stadler (Theory Biosci., 2020)

Machine Learning Studies of Non-coding RNAs based on Artificially Constructed Training Data. - Mirele C. S. F. Costa; João Victor de Araújo Oliveira; Waldeyr M. C. Silva; Rituparno Sen; Jörg Fallmann; Peter F. Stadler; Maria Emília M. T. Walter (BIOINFORMATICS, 2021)

LazyB: fast and cheap genome assembly. - Thomas Gatter; Sarah von Löhneysen; Jörg Fallmann; Polina Drozdova; Tom Hartmann; Peter F. Stadler (Algorithms Mol. Biol., 2021)

Weighted Consensus Segmentations. - Halima Saker; Rainer Machné; Jörg Fallmann; Douglas B. Murray; Ahmad M. Shahin; Peter F. Stadler (Comput., 2021)

Tailored machine learning models for functional RNA detection in genome-wide screens. - Christopher Klapproth; Siegfried Zöztsche; Felix Kühnl; Jörg Fallmann; Peter F. Stadler; Sven Findeiß (Zenodo, 2023)

RNA interaction format: a general data format for RNA interactions. - Richard A. Schäfer; Dominik Rabsch; Guillaume E. Scholz; Peter F. Stadler; Wolfgang R. Hess; Rolf Backofen; Jörg Fallmann; Björn Voß (Bioinform., 2023)