Fast accessibility-based prediction of RNA-RNA interactions. - Hakim Tafer; Fabian Amman; Florian Eggenhofer; Peter F. Stadler; Ivo L. Hofacker (Bioinform., 2011)

RNApredator: fast accessibility-based prediction of sRNA targets. - Florian Eggenhofer; Hakim Tafer; Peter F. Stadler; Ivo L. Hofacker (Nucleic Acids Res., 2011)

CMCompare webserver: comparing RNA families via covariance models. - Florian Eggenhofer; Ivo L. Hofacker; Christian Höner zu Siederdissen (Nucleic Acids Res., 2013)

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)

CMV: visualization for RNA and protein family models and their comparisons. - Florian Eggenhofer; Ivo L. Hofacker; Rolf Backofen; Christian Höner zu Siederdissen (Bioinform., 2018)

Freiburg RNA tools: a central online resource for RNA-focused research and teaching. - Martin Raden; Syed M. Ali; Omer S. Alkhnbashi; Anke Busch; Fabrizio Costa; Jason A. Davis; Florian Eggenhofer; Rick Gelhausen; Jens Georg; Steffen Heyne; Michael Hiller; Kousik Kundu; et al. (Nucleic Acids Res., 2018)

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)

CRISPRloci: comprehensive and accurate annotation of CRISPR-Cas systems. - Omer S. Alkhnbashi; Alexander Mitrofanov; Robson Bonidia; Martin Raden; Van Dinh Tran; Florian Eggenhofer; Shiraz A. Shah; Ekrem Öztürk; Victor Alexandre Padilha; Danilo Sipoli Sanches; André C. P. L. F. de Carvalho; Rolf Backofen (Nucleic Acids Res., 2021)

RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria. - Rick Gelhausen; Teresa Müller; Sarah L. Svensson; Omer S. Alkhnbashi; Cynthia M. Sharma; Florian Eggenhofer; Rolf Backofen (Briefings Bioinform., 2022)

Peakhood: individual site context extraction for CLIP-seq peak regions. - Michael Uhl; Dominik Rabsch; Florian Eggenhofer; Rolf Backofen (Bioinform., 2022)