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Mag. Florian Eggenhofer, PhD Bioinformatics Group Department of Computer Science Albert-Ludwigs-University Freiburg Georges-Köhler-Allee 106 79110 Freiburg Germany Fax: +49 (0) 761 / 203 - 7462 Phone: +49 (0) 761 / 203 - 8246 Email: egg@cs.uni-freiburg.de GitHub: github.com/eggzilla ORCID: orcid.org/0000-0001-9564-7525 Twitter: twitter.com/eggzilla |
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14. A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence. Elisa Venturini, Sarah L Svensson, Sandra Maaß, Rick Gelhausen, Florian Eggenhofer, Lei Li, Amy K Cain, Julian Parkhill, Dörte Becher, Rolf Backofen, Lars Barquist, Cynthia M Sharma, Alexander J Westermann, and Jörg Vogel. microLife, 1 no. 1, 10 2020 [ www | bib ] |
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13. HRIBO: high-throughput analysis of bacterial ribosome profiling data Rick Gelhausen, Sarah L Svensson, Kathrin Froschauer, Florian Heyl, Lydia Hadjeras, Cynthia M Sharma, Florian Eggenhofer, and Rolf Backofen Bioinformatics, 11 2020 [ www | bib ] |
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12. uORF-Tools-Workflow for the determination of translation-regulatory upstream open reading frames Anica Scholz, Florian Eggenhofer, Rick Gelhausen, Björn Grüning, Kathi Zarnack, Bernhard Brülne, Rolf Backofen, Tobias Schmid Plos One, 2019 [ www | bib ] |
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11. The RNA workbench 2.0: next generation RNA data analysis Jörg Fallmann, Pavankumar Videm, Andrea Bagnacani, Bérénice Batut, Maria A Doyle, Tomas Klingstrom, Florian Eggenhofer, Peter F Stadler, Rolf Backofen, Björn Grüning Nucleic Acid Research, 2019 [ www | bib ] |
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10. Bioconda: sustainable and comprehensive software distribution for the life sciences. Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A Chapman, Jillian Rowe, Christopher H Tomkins-Tinch, Renan Valieris, Johannes Köster, Team Bioconda Nature Method 15, 475-476, 2018 [ www | ris ] |
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9. 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, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, Rolf Backofen Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W25-W29 [ www | bib ] |
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8. CMV - Visualization for RNA and protein family models and their comparisons Florian Eggenhofer, Ivo L Hofacker, Rolf Backofen, Christian Höner zu Siederdissen Bioinformatics, 2018 [ www | bib ] |
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7. 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 C. Lott, Youri Hoogstrate, Wolfgang R. Hess, Olaf Wolkenhauer, Steve Hoffmann, Altuna Akalin, Uwe Ohler, Peter F. Stadler, Rolf Backofen Nucleic Acid Research, 2017 [ www ] |
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6. Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells Martin Hölzer, Verena Krähling, Fabian Amman, Emanuel Barth, Stephan H. Bernhart, Victor A. O. Carmelo, Maximilian Collatz, Gero Doose, Florian Eggenhofer, Jan Ewald, Jörg Fallmann, Lasse M. Feldhahn, Markus Fricke, Juliane Gebauer, Andreas J. Gruber, Franziska Hufsky, Henrike Indrischek, Sabina Kanton, Jörg Linde, Nelly Mostajo, Roman Ochsenreiter, Konstantin Riege, Lorena Rivarola-Duarte, Abdullah H. Sahyoun, Sita J. Saunders, Stefan E. Seemann, Andrea Tanzer, Bertram Vogel, Stefanie Wehner, Michael T. Wolfinger, Rolf Backofen, Jan Gorodkin, Ivo Grosse, Ivo Hofacker, Steve Hoffmann, Christoph Kaleta, Peter F. Stadler, Stephan Becker, Manja Marz Scientific Reports, 2016 [ www ] |
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5. RNAlien - Unsupervised RNA family model construction Florian Eggenhofer, Ivo L. Hofacker, Christian Höner zu Siederdissen Nucleic Acid Research, 2016 [ www ] |
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4. ViennaNGS: A toolbox for building efficient next generation sequencing analysis pipelines Michael Wolfinger, Jörg Fallmann, Florian Eggenhofer Fabian Amman F1000Research, 2015 [ www ] |
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3. CMCompare webserver: comparing RNA families via covariance models Florian Eggenhofer, Ivo L. Hofacker, Christian Höner zu Siederdissen Nucleic Acids Research, 2013 [ www ] |
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2. RNApredator: Fast accessibility-based prediction of sRNA targets Florian Eggenhofer, Hakim Tafer, Peter F. Stadler and Ivo L. Hofacker Nucleic Acids Research, 39: W149-W154, 2011 [ www ] |
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1. Fast accessibility-based prediction of RNA-RNA interactions Hakim Tafer, Fabian Amman, Florian Eggenhofer, Peter F. Stadler, and Ivo L. Hofacker Bioinformatics, 2011 [ www ] |
| ● 2019 Wintersemester - University Freiburg - Lecture Bioinformatics I (english) - Lecturer |
| ● 2018 Winter term - University Freiburg - Lecture Algorithms and Datastructures (english) - Lecturer |
| ● 2018 Sommer term - University Freiburg - Lecture Bioinformatics II (english) - Lecturer |
| ● 2017 Winter term - University Freiburg - Lecture Algorithms and Datastructures (english) - Lecturer |
| ● 2017 Sommer term - University Freiburg - Lecture Bioinformatics II (english) - Lecturer |
| ● 2016 Winter term - University Freiburg - Lecture Algorithms and Datastructures (english) - Lecturer |
| ● 2016 Sommer term - University Freiburg - Exercises Bioinformatics II (english) - Tutor |
| ● 2015 Winter term - University Vienna - Exercises for Foundations of Bioinformatics (german) - Lecturer - 2.0 ECTS |
| ● 2014 Winter term - University Vienna - Exercises for Foundations of Bioinformatics (german) - Lecturer - 2.0 ECTS |
| ● 2013 Winter term - University Vienna - Exercises for Foundations of Bioinformatics (german) - Tutor - 2.0 ECTS |
| ● 2010 Summer term - University Vienna - Laboratory Course I B - Microbiology and Genetics (german) - Tutor - 4.0 ECTS |
| ● 2009 Winter term - University Vienna - Laboratory Course: Molecular Biology Techniques (german) - Tutor - 6.0 ECTS |
| ● 2009 Summer term - University Vienna - Laboratory Course I B - Microbiology and Genetics - Tutor - 4.0 ECTS |
SelectSequencesFromMSA - Sample representative sequences form multiple sequence alignments  
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StockholmAlignment - Datastructures and parsers for StockholmAlignments  
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BiobaseHTTPTools - Tools to query NCBI and Ensembl bioinformatic webservices  
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BiobaseEnsembl - Datastructures for Ensembl services and files  
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CMV - Visualization for RNA and protein family models and their comparisons  
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AlienServer - Yesod based web interface for RNAlien 
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RNAlien - Unsupervised RNA family model construction   
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BlastHTTP - Query the NCBI blast REST interface   
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Genbank - Tools, parser and datastructures for the NCBI Genbank format.  
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ClustalParser - Parser and datastructures for Clustalw2 and ClustalOmega format.  
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ViennaRNAParser - Parser and datastructures for the ViennaRNA package  
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Taxonomy Parsers, datastructures and visualisation for NCBI Taxonomy  
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EntrezHTTP - Query the NCBI Entrez REST interface.  
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TaxonomyTools - Programs for NCBI Taxonomy  
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CMCcompare Webserver - webserver for comparison of RNA family models |
MemeXML - Parsing MEME motif finder xml output   
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ViennaNGS - Utilities for Next-Generation Sequencing (NGS) data analysis. 
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RNApredator - webserver for small RNA target prediction |
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● October 2017 15. Herbstseminar der Bioinformatik "Visualisation of probabilistic models and their comparisons" |
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● June 2017 Galaxy Community Conference 2017 in Montpellier, France "The RNA Workbench - reproducible, transparent, and accessible RNA research" |
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● Februar 2015 30th TBI Winterseminar in Bled, Slovenia "RNAlien - revisited" |
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● April 2014 Young Investigator Day in Vienna, Austria "RNAlien - unsupervized RNA family model construction" |
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● February 2014 29th TBI Winterseminar in Bled, Slovenia "RNAlien - unsupervised RNA family model construction" |
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● Monday, October 14th, 2013 Vienna RNA Meeting 2013 in Vienna, Austria "Comparison and visualization of RNA family models" |
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● October 2013 11th Bioinf Herbstseminar in Doubice, Czech republic "Lost in the Woods - Detailed visualization of covariance model comparison" |
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● February 2013 28th TBI Winterseminar in Bled, Slovenia "Conservation and interaction of RNA in regulatory networks" |
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● October 2012 10th Bioinf Herbstseminar in Doubice, Czech republic "CMCompare webserver revisited" |
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● February 2012 27th TBI Winterseminar in Bled, Slovenia "CMCompare webserver" |
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● February 2011 26th TBI Winterseminar in Bled, Slovenia "A sRNA target prediction webserver" |
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● October 2010 Herbstseminar Bioinformatik 2010 in Vysoka Lipa, Czech republic "A sRNA target prediction webserver" |
| RNA Meeting 2015, 22-24.10.2015, Vienna, Austria |
| ISMB 2013, 21-23.07.2013, Berlin, Germany CMCompare webserver - Comparing RNA families via Covariance Models |
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GENAU Evaluation Conference, 02-04.05.2011, Vienna, Austria,
RNApredator - sRNA target prediction for everybody |
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● HacFreiburg2017 Date: 04.08.2017 - 06.08.2017 Location: Freiburg, Germany |
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● 32th TBI Winterseminar Date: 12.02.2017 - 19.02.2017 Location: Bled, Slovenia |
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● 3rd Swiss German Galaxy Days Date: 20.10.2016 - 21.10.2016 Location: University of Freiburg, Freiburg, Germany |
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● 14. Herbstseminar der Bioinformatik Date: 03.10.2016 - 08.10.2016 Location: Hotel Jef, Doubice, Czech Republic |
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● Galaxy DevOps Workshop Date: 06.04.2016 - 07.04.2016 Location: Heidelberg Center for Human Bioinformatics (HD-HuB), Heidelberg, Germany |
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● 13. Herbstseminar der Bioinformatik Date: 28.09.2015 - 03.10.2015 Location: Hotel Jef, Doubice, Czech Republic |
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● Elixir Tools Registry Hackaton Date: 23.09.2015 Location: RTH, University of Copenhagen, Denmark |
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● Sinergia - cis Natural Antisense Transcripts project meeting Date: 04.09.2015 Location: University of Lausanne, Switzerland |
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● Research stay - "Benchmarking of unsupervised RNA family model construction" Date: 01.03.-10.04.2015 Location: Bioinformatics,University of Leipzig, Germany |
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● Fight against Ebola Hackerton - tvspot(german) Date: 17.11 - 23.11.2014 Location: University of Jena, Germany |
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● HaL8 - Haskell-Meeting Date: 21.07.2013 Location: University of Leipzig |
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● Utrecht Summer School in Computer Science, Applied Functional Programming Date: 20.08 - 31.08.2012 Location: Utrecht University, Netherlands |