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RNA, Bioinformatics, Molecular Biology, High Throughput Sequencing
Germany

Activities

Employment (2)

Albert-Ludwigs-Universität Freiburg: Freiburg im Breisgau, Baden-Württemberg, DE

2016-03-15 to present | Postdoctoral Researcher (Department of computer science)
Employment
Source: Self-asserted source
Florian Eggenhofer

University of Vienna: Vienna, AT

2012-02 to 2015-12-31 | PhD student (Institute for theoretical chemistry)
Employment
Source: Self-asserted source
Florian Eggenhofer

Education and qualifications (1)

Universität Wien: Wien, Wien, AT

2012-02-01 to 2016-11-17 | Doctor of philosophy
Education
Source: Self-asserted source
Florian Eggenhofer

Works (21)

CheRRI—Accurate classification of the biological relevance of putative RNA–RNA interaction sites

GigaScience
2024-01-02 | Journal article
Contributors: Teresa Müller; Stefan Mautner; Pavankumar Videm; Florian Eggenhofer; Martin Raden; Rolf Backofen
Source: check_circle
Crossref

Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimized mass spectrometry

microLife
2023-01-04 | Journal article
Contributors: Lydia Hadjeras; Jürgen Bartel; Lisa-Katharina Maier; Sandra Maaß; Verena Vogel; Sarah L Svensson; Florian Eggenhofer; Rick Gelhausen; Teresa Müller; Omer S Alkhnbashi et al.
Source: check_circle
Crossref

Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogenCampylobacter jejuni

2022-11-09 | Preprint
Contributors: Kathrin Froschauer; Sarah L. Svensson; Rick Gelhausen; Elisabetta Fiore; Philipp Kible; Alicia Klaude; Martin Kucklick; Stephan Fuchs; Florian Eggenhofer; Susanne Engelmann et al.
Source: check_circle
Crossref

The long noncoding RNA mimi scaffolds neuronal granules to maintain nervous system maturity

Science Advances
2022-09-30 | Journal article
Contributors: Dominika Grzejda; Jana Mach; Johanna Aurelia Schweizer; Barbara Hummel; Andrew Mischa Rezansoff; Florian Eggenhofer; Amol Panhale; Maria-Eleni Lalioti; Nina Cabezas Wallscheid; Rolf Backofen et al.
Source: check_circle
Crossref

Peakhood: individual site context extraction for CLIP-seq peak regions

Bioinformatics
2022-01-27 | Journal article
Contributors: Michael Uhl; Dominik Rabsch; Florian Eggenhofer; Rolf Backofen; Can Alkan
Source: check_circle
Crossref

HRIBO: high-throughput analysis of bacterial ribosome profiling data

Bioinformatics
2021-08-04 | Journal article
Contributors: Rick Gelhausen; Sarah L Svensson; Kathrin Froschauer; Florian Heyl; Lydia Hadjeras; Cynthia M Sharma; Florian Eggenhofer; Rolf Backofen; Valencia Alfonso
Source: check_circle
Crossref
grade
Preferred source (of 3)‎

CRISPRloci: comprehensive and accurate annotation of CRISPR–Cas systems

Nucleic Acids Research
2021-07-02 | Journal article
Contributors: Omer S Alkhnbashi; Alexander Mitrofanov; Robson Bonidia; Martin Raden; Van Dinh Tran; Florian Eggenhofer; Shiraz A Shah; Ekrem Öztürk; Victor A Padilha; Danilo S Sanches et al.
Source: check_circle
Crossref

RiboReport - Benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria

2021-06-09 | Other
Contributors: Rick Gelhausen; Teresa Müller; Sarah L. Svensson; Omer Alkhnbashi; Cynthia M. Sharma; Florian Eggenhofer; Rolf Backofen
Source: check_circle
Crossref

A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence

microLife
2020-11-26 | Journal article
Contributors: Elisa Venturini; Sarah L Svensson; Sandra Maaß; Rick Gelhausen; Florian Eggenhofer; Lei Li; Amy K Cain; Julian Parkhill; Dörte Becher; Rolf Backofen et al.
Source: check_circle
Crossref
grade
Preferred source (of 3)‎

uORF-Tools-Workflow for the determination of translation-regulatory upstream open reading frames.

PloS one
2019-09 | Journal article
Contributors: Scholz A; Eggenhofer F; Gelhausen R; Grüning B; Zarnack K; Brüne B; Backofen R; Schmid T
Source: Self-asserted source
Florian Eggenhofer via Europe PubMed Central

The RNA workbench 2.0: next generation RNA data analysis

Nucleic Acids Research
2019-07-02 | Journal article
Contributors: Jörg Fallmann; Pavankumar Videm; Andrea Bagnacani; Bérénice Batut; Maria A Doyle; Tomas Klingstrom; Florian Eggenhofer; Peter F Stadler; Rolf Backofen; Björn Grüning
Source: check_circle
Crossref

CMV: visualization for RNA and protein family models and their comparisons

Bioinformatics
2018-08-01 | Journal article
Contributors: Florian Eggenhofer; Ivo L Hofacker; Rolf Backofen; Christian Höner zu Siederdissen; Alfonso Valencia
Source: check_circle
Crossref

Bioconda: sustainable and comprehensive software distribution for the life sciences

Nature Methods
2018-07 | Journal article
Part of ISSN: 1548-7091
Contributors: Björn Grüning; The Bioconda Team; Ryan Dale; Andreas Sjödin; Brad A. Chapman; Jillian Rowe; Christopher H. Tomkins-Tinch; Renan Valieris; Johannes Köster
Source: Self-asserted source
Florian Eggenhofer via Crossref Metadata Search

Freiburg RNA tools: a central online resource for RNA-focused research and teaching

Nucleic Acids Research
2018-07-02 | Journal article
Contributors: Martin Raden; Syed M Ali; Omer S Alkhnbashi; Anke Busch; Fabrizio Costa; Jason A Davis; Florian Eggenhofer; Rick Gelhausen; Jens Georg; Steffen Heyne et al.
Source: check_circle
Crossref

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

Nucleic Acids Research
2017-07-03 | Journal article
Contributors: Björn A. Grüning; Jörg Fallmann; Dilmurat Yusuf; Sebastian Will; Anika Erxleben; Florian Eggenhofer; Torsten Houwaart; Bérénice Batut; Pavankumar Videm; Andrea Bagnacani et al.
Source: check_circle
Crossref

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

Scientific Reports
2016 | Journal article
Source: Self-asserted source
Florian Eggenhofer

RNAlien – Unsupervised RNA family model construction

Nucleic Acids Research
2016-09-30 | Journal article
Contributors: Florian Eggenhofer; Ivo L. Hofacker; Christian Höner zu Siederdissen
Source: check_circle
Crossref

ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines [v1; ref status: approved with reservations 3]

F1000Research
2015 | Journal article
Source: Self-asserted source
Florian Eggenhofer

CMCompare webserver: comparing RNA families via covariance models.

2013-07 | Journal article
DOI:

10.1093/nar/gkt329

PMID:

23640335

PMC:

PMC3692125

Contributors: Eggenhofer F; Hofacker IL; Höner Zu Siederdissen C
Source: Self-asserted source
Florian Eggenhofer via Europe PubMed Central

Fast accessibility-based prediction of RNA-RNA interactions.

2011-07 | Journal article
DOI:

10.1093/bioinformatics/btr281

PMID:

21593134

Contributors: Tafer H; Amman F; Eggenhofer F; Stadler PF; Hofacker IL
Source: Self-asserted source
Florian Eggenhofer via Europe PubMed Central

RNApredator: fast accessibility-based prediction of sRNA targets.

2011-07 | Journal article
DOI:

10.1093/nar/gkr467

PMID:

21672960

PMC:

PMC3125805

Contributors: Eggenhofer F; Tafer H; Stadler PF; Hofacker IL
Source: Self-asserted source
Florian Eggenhofer via Europe PubMed Central

Peer review (16 reviews for 6 publications/grants)

Review activity for Bioinformatics (10)
Review activity for BMC bioinformatics (2)
Review activity for Nucleic acids research. (1)
Review activity for RNA biology. (1)
Review activity for Theory in biosciences. (1)
Review activity for Theory in biosciences. (1)