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: https://github.com/eggzilla
ORCID: orcid.org/0000-0001-9564-7525

Publications

● 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
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy
Nucleic Acid Research, 2017
● 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
Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells
Scientific Reports, 2016
Eggenhofer, Florian and Hofacker, Ivo L. and Höner zu Siederdissen, Christian
RNAlien - Unsupervised RNA family model construction
Nucleic Acid Research, 2016
● Wolfinger, MT and Fallmann, J and Eggenhofer, F and Amman, F
ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines [v2; ref status: indexed]
F1000Research, 2015
Eggenhofer, Florian and Hofacker, Ivo L. and Höner zu Siederdissen, Christian
CMCompare webserver: comparing RNA families via covariance models
Nucleic Acids Research,41: W499-W503, 2013
Florian Eggenhofer, Hakim Tafer, Peter F. Stadler and Ivo L. Hofacker
RNApredator: Fast accessibility-based prediction of sRNA targets
Nucleic Acids Research, 39: W149-W154, 2011
● Hakim Tafer, Fabian Amman, Florian Eggenhofer, Peter F. Stadler, and Ivo L. Hofacker
Fast accessibility-based prediction of RNA-RNA interactions
Bioinformatics, 27: 1934-1940, 2011

Teaching

● 2017 Sommersemester - University of Freiburg
Lecture Bioinformatics II (english)
Lecturer
● 2016 Wintersemester - University of Freiburg
Lecture Algorithms and Datastructures (english)
Lecturer
● 2016 Sommersemester - University of Freiburg
Exercises Bioinformatics II (english)
Tutor
● 2015 Wintersemester - University of Vienna
Exercises for Foundations of Bioinformatics (german)
Lecturer
2.0 ECTS credits
● 2014 Wintersemester - University of Vienna
Exercises for Foundations of Bioinformatics (german)
Lecturer
2.0 ECTS credits
● 2013 Wintersemester - University of Vienna
Exercises for Foundations of Bioinformatics (german)
Tutor/teaching assistant
2.0 ECTS credits
● 2010 Summersemester - University of Vienna
Laboratory Course I B - Microbiology and Genetics (german)
Tutor/teaching assistant
4.0 ECTS credits
● 2009 Wintersemester - University of Vienna
Laboratory Course: Molecular Biology Techniques (german)
Tutor/teaching assistant
6.0 ECTS credits
● 2009 Summersemester - University of Vienna
Laboratory Course I B - Microbiology and Genetics
Tutor/teaching assistant
4.0 ECTS credits

Software

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
MemeXML - Parsing MEME motif finder xml output
GitHub Hackage Travis CI
ViennaNGS - Utilities for Next-Generation Sequencing (NGS) data analysis.
GitHub cpan

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