| Bioconda: sustainable and comprehensive software distribution for the life sciences B Grüning, R Dale, A Sjödin, BA Chapman, J Rowe, CH Tomkins-Tinch, ... Nature methods 15 (7), 475-476, 2018 | 1564 | 2018 |
| LocARNA-P: accurate boundary prediction and improved detection of structural RNAs S Will, T Joshi, IL Hofacker, PF Stadler, R Backofen Rna 18 (5), 900-914, 2012 | 446 | 2012 |
| Freiburg RNA tools: a central online resource for RNA-focused research and teaching M Raden, SM Ali, OS Alkhnbashi, A Busch, F Costa, JA Davis, ... Nucleic acids research 46 (W1), W25-W29, 2018 | 170 | 2018 |
| RNApredator: fast accessibility-based prediction of sRNA targets F Eggenhofer, H Tafer, PF Stadler, IL Hofacker Nucleic acids research 39 (suppl_2), W149-W154, 2011 | 167 | 2011 |
| Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells M Hölzer, V Krähling, F Amman, E Barth, SH Bernhart, VAO Carmelo, ... Scientific reports 6 (1), 34589, 2016 | 73 | 2016 |
| Fast accessibility-based prediction of RNA–RNA interactions H Tafer, F Amman, F Eggenhofer, PF Stadler, IL Hofacker Bioinformatics 27 (14), 1934-1940, 2011 | 62 | 2011 |
| A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence E Venturini, SL Svensson, S Maaß, R Gelhausen, F Eggenhofer, L Li, ... Microlife 1 (1), uqaa002, 2020 | 54 | 2020 |
| The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy BA Grüning, J Fallmann, D Yusuf, S Will, A Erxleben, F Eggenhofer, ... Nucleic acids research 45 (W1), W560-W566, 2017 | 54 | 2017 |
| ViennaNGS: A toolbox for building efficient next-generation sequencing analysis pipelines MT Wolfinger, J Fallmann, F Eggenhofer, F Amman F1000Research 4, 50, 2015 | 43 | 2015 |
| CRISPRloci: comprehensive and accurate annotation of CRISPR–Cas systems OS Alkhnbashi, A Mitrofanov, R Bonidia, M Raden, VD Tran, ... Nucleic acids research 49 (W1), W125-W130, 2021 | 41 | 2021 |
| Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimized mass spectrometry L Hadjeras, J Bartel, LK Maier, S Maaß, V Vogel, SL Svensson, ... Microlife 4, uqad001, 2023 | 33 | 2023 |
| RNAlien – Unsupervised RNA family model construction F Eggenhofer, IL Hofacker, CH zu Siederdissen Nucleic Acids Research 44 (17), 9, 2016 | 33 | 2016 |
| RiboReport-benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria R Gelhausen, T Müller, SL Svensson, OS Alkhnbashi, CM Sharma, ... Briefings in Bioinformatics 23 (2), bbab549, 2022 | 27 | 2022 |
| HRIBO: high-throughput analysis of bacterial ribosome profiling data R Gelhausen, SL Svensson, K Froschauer, F Heyl, L Hadjeras, ... Bioinformatics 37 (14), 2061-2063, 2021 | 22 | 2021 |
| A global data-driven census of E Venturini, SL Svensson, S Maaß, R Gelhausen, F Eggenhofer, L Li, ... Salmonella, 2020 | 20 | 2020 |
| Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni K Froschauer, SL Svensson, R Gelhausen, E Fiore, P Kible, A Klaude, ... Nature Communications 16 (1), 3078, 2025 | 17 | 2025 |
| The long noncoding RNA mimi scaffolds neuronal granules to maintain nervous system maturity D Grzejda, J Mach, JA Schweizer, B Hummel, AM Rezansoff, ... Science Advances 8 (39), eabo5578, 2022 | 15 | 2022 |
| The RNA workbench 2.0: next generation RNA data analysis J Fallmann, P Videm, A Bagnacani, B Batut, MA Doyle, T Klingstrom, ... Nucleic acids research 47 (W1), W511-W515, 2019 | 14 | 2019 |
| CMCompare webserver: comparing RNA families via covariance models F Eggenhofer, IL Hofacker, C Höner zu Siederdissen Nucleic acids research 41 (W1), W499-W503, 2013 | 14 | 2013 |
| uORF-Tools—Workflow for the determination of translation-regulatory upstream open reading frames A Scholz, F Eggenhofer, R Gelhausen, B Grüning, K Zarnack, B Brüne, ... PLoS One 14 (9), e0222459, 2019 | 12 | 2019 |
Rolf BackofenProfessor für Bioinformatik, Universität FreiburgVerified email at informatik.uni-freiburg.de
