Bioinformatics
Institute of Computer Science
University Freiburg
de

Florian Eggenhofer

About me:

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

Publications

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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
5. RNAlien - Unsupervised RNA family model construction
Florian Eggenhofer, Ivo L. Hofacker, Christian Höner zu Siederdissen
Nucleic Acid Research, 2016
[ www ]
4. ViennaNGS: A toolbox for building efficient next generation sequencing analysis pipelines
Michael Wolfinger, Jörg Fallmann, Florian Eggenhofer Fabian Amman
F1000Research, 2015
[ www ]
3. CMCompare webserver: comparing RNA families via covariance models
Florian Eggenhofer, Ivo L. Hofacker, Christian Höner zu Siederdissen
Nucleic Acids Research, 2013
[ www ]
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 ]
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 ]

Teaching

● 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

Software

SelectSequencesFromMSA - Sample representative sequences form multiple sequence alignments
GitHub Hackage Travis CI
StockholmAlignment - Datastructures and parsers for StockholmAlignments
GitHub Hackage Travis CI
BiobaseHTTPTools - Tools to query NCBI and Ensembl bioinformatic webservices
GitHub Hackage Travis CI
BiobaseEnsembl - Datastructures for Ensembl services and files
GitHub Hackage Travis CI
CMV - Visualization for RNA and protein family models and their comparisons
GitHub Hackage Travis CI
AlienServer - Yesod based web interface for RNAlien
GitHub
RNAlien - Unsupervised RNA family model construction
GitHub Hackage Travis CI
BlastHTTP - Query the NCBI blast REST interface
GitHub Hackage Travis CI
Genbank - Tools, parser and datastructures for the NCBI Genbank format.
GitHub Hackage Travis CI
ClustalParser - Parser and datastructures for Clustalw2 and ClustalOmega format.
GitHub Hackage Travis CI
ViennaRNAParser - Parser and datastructures for the ViennaRNA package
GitHub Hackage Travis CI
Taxonomy Parsers, datastructures and visualisation for NCBI Taxonomy
GitHub Hackage Travis CI
EntrezHTTP - Query the NCBI Entrez REST interface.
GitHub Hackage Travis CI
TaxonomyTools - Programs for NCBI Taxonomy
GitHub Hackage Travis CI
CMCcompare Webserver - webserver for comparison of RNA family models
GitHub
MemeXML - Parsing MEME motif finder xml output
GitHub Hackage Travis CI
ViennaNGS - Utilities for Next-Generation Sequencing (NGS) data analysis.
GitHub cpan
RNApredator - webserver for small RNA target prediction
GitHub

Talks

● October 2017
15. Herbstseminar der Bioinformatik
"Visualisation of probabilistic models and their comparisons"
● June 2017
Galaxy Community Conference 2017 in Montpellier, France
"The RNA Workbench - reproducible, transparent, and accessible RNA research"
● Februar 2015
30th TBI Winterseminar in Bled, Slovenia
"RNAlien - revisited"
● April 2014
Young Investigator Day in Vienna, Austria
"RNAlien - unsupervized RNA family model construction"
● February 2014
29th TBI Winterseminar in Bled, Slovenia
"RNAlien - unsupervised RNA family model construction"
● Monday, October 14th, 2013
Vienna RNA Meeting 2013 in Vienna, Austria
"Comparison and visualization of RNA family models"
● October 2013
11th Bioinf Herbstseminar in Doubice, Czech republic
"Lost in the Woods - Detailed visualization of covariance model comparison"
● February 2013
28th TBI Winterseminar in Bled, Slovenia
"Conservation and interaction of RNA in regulatory networks"
● October 2012
10th Bioinf Herbstseminar in Doubice, Czech republic
"CMCompare webserver revisited"
● February 2012
27th TBI Winterseminar in Bled, Slovenia
"CMCompare webserver"
● February 2011
26th TBI Winterseminar in Bled, Slovenia
"A sRNA target prediction webserver"
● October 2010
Herbstseminar Bioinformatik 2010 in Vysoka Lipa, Czech republic
"A sRNA target prediction webserver"

Poster Presentations

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
GENAU Evaluation Conference, 02-04.05.2011, Vienna, Austria, RNApredator - sRNA target prediction for everybody

Meetings & Workshops

HacFreiburg2017
Date: 04.08.2017 - 06.08.2017
Location: Freiburg, Germany
32th TBI Winterseminar
Date: 12.02.2017 - 19.02.2017
Location: Bled, Slovenia
3rd Swiss German Galaxy Days
Date: 20.10.2016 - 21.10.2016
Location: University of Freiburg, Freiburg, Germany
14. Herbstseminar der Bioinformatik
Date: 03.10.2016 - 08.10.2016
Location: Hotel Jef, Doubice, Czech Republic
Galaxy DevOps Workshop
Date: 06.04.2016 - 07.04.2016
Location: Heidelberg Center for Human Bioinformatics (HD-HuB), Heidelberg, Germany
13. Herbstseminar der Bioinformatik
Date: 28.09.2015 - 03.10.2015
Location: Hotel Jef, Doubice, Czech Republic
Elixir Tools Registry Hackaton
Date: 23.09.2015
Location: RTH, University of Copenhagen, Denmark
● Sinergia - cis Natural Antisense Transcripts project meeting
Date: 04.09.2015
Location: University of Lausanne, Switzerland
● Research stay - "Benchmarking of unsupervised RNA family model construction"
Date: 01.03.-10.04.2015
Location: Bioinformatics,University of Leipzig, Germany
● Fight against Ebola Hackerton - tvspot(german)
Date: 17.11 - 23.11.2014
Location: University of Jena, Germany
HaL8 - Haskell-Meeting
Date: 21.07.2013
Location: University of Leipzig
Utrecht Summer School in Computer Science, Applied Functional Programming
Date: 20.08 - 31.08.2012
Location: Utrecht University, Netherlands