Members » Franziska Hufsky

E-Mail: franziska.hufsky*
Room: 08S01
Phone: +49-3641-9-46482

*@uni-jena.de

CV

• since 2017 Scientific coordinator, European Virus Bioinformatics Center
• since 2014 Research assistant, RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University Jena
• 2014 Doctorate degree Dr. rer. nat, Friedrich Schiller University Jena, Faculty of Mathematics and Computer Science
• 2010 — 2016 Research assistant, Chair of Bioinformatics, Friedrich Schiller University Jena
• 2010 — 2013 PhD student fellowship, International Max Planck Research School, Max Planck Institute for Chemical Ecology, Jena
• 2010 Diploma in Bioinformatics, Friedrich Schiller University Jena
• 2008 — 2009 Student assistant, Chair of Bioinformatics, Friedrich Schiller University Jena
• 2007 — 2008 Student assistant, Medical Physics Group, University Hospital Jena

Theses

• Doctoral Thesis: Novel Methods for the Analysis of Small Molecule Fragmentation Mass Spectra (Supervisor S. Böcker)
• Diploma Thesis: Algorithm Engineering for the Center String Problem (Supervisor S. Böcker)

Awards

• 2015 Doctoral Thesis Award of the Dean of the Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena
• 2014 Excellent computer science dissertation, German Informatics Society (GI)

Research interests

• Metabolomics and mass spectrometry
  • Significance estimation of spectral database search results
  • Prediction of uncommon elements in unkown biomolecules
  • Local tree alignment for automated comparison of fragmentation trees
  • Fragmentation trees for electron impact mass spectra and multiple MS data
  • Estimation of enrichment of heavy isotopes in labeled proteins using isotope pattern analysis
• Transcriptomics
  • Viral RNA bioinformatics
  • Effect of long non-coding RNAs during fungal infection
• Integrated analysis
  • Combined metabolome and transcriptome analysis of the circadian cycle of cyanobacteria
• Algorithms/Theoretical informatics/NP-hard problems
  • Computing center strings
  • Local tree alignment for automated comparison of fragmentation trees

Grants

• 2014 — 2016 Combined metabolome and transcriptome analysis of the circadian cycle of cyanobacteria, Postdoctoral fellowship of the Carl-Zeiss-Stiftung, own position and one PhD student

Public relations work

• regular workshops as part of the Campus Thüringen Tour (since 2013)
• regular workshops for the Girls’Day (since 2016)
• creating a station for the Tech Parcour of the Thüringer Universities
• posters and presentations during the Long Night of Sciences
• own bioinformatics blog BioinfoWelten
• own podcast Die 3 Formeltiere

Conference contributions

as organizer

• 2020 International Virus Bioinformatics Meeting (Bern, Switzerland | online), Organizer
• 2019 Third Meeting of the European Virus Bioinformatics Centre (Glasgow, UK), Organizer
• 2017 First Meeting of the European Virus Bioinformatics Centre (Jena, Germany), Organizer
• 2016 International Study Group for Systems Biology meeting (Jena, Germany), YSGSB Organizer
• 2012 German Conference on Bioinformatics (Jena, Germany), Organizing committee, Editorial board member

as participant

• 2016 Metabolomics (Dublin, Ireland), Talk, Significance of metabolite identifications from searching mass spectral libraries
• 2015 Dagstuhl Seminar on Computational Metabolomics (Dagstuhl, Germany), Invited participant
• 2014 Herbstseminar der Bioinformatik (Doubice, CZ), Talk, Novel Methods for the Analysis of Small Molecule Fragmentation Mass Spectra
• 2014 Workshop on Algorithms in Bioinformatics (Wrocław, Poland), Poster, Multiple mass spectrometry fragmentation trees revisited: Boosting performance and quality
• 2013 Intelligent Systems in Molecular Biology (Berlin, Germany), Poster, De novo analysis of electron ionization mass spectra using fragmentation trees
• 2012 German Conference on Bioinformatics (Jena, Germany), Talk, Comparing fragmentation trees from electron impact mass spectra with annotated fragmentation pathways
• 2012 Intelligent Systems in Molecular Biology (Long Beach, CA, USA), Talk, Fast alignment of fragmentation trees
• 2012 IMPRS Symposium (Jena, Germany), Talk, Automated interpretation of electron impact mass spectra
• 2011 Conference on Mass Spectrometry and Allied Topics (Denver, Colorado, USA), Poster, Computation of fragmentation trees from metabolite GC/MS data
• 2011 Conference on Research in Computational Molecular Biology (Vancouver, Canada), Poster, Fragmentation trees from MSn data
• 2010 Workshop on Algorithms in Bioinformatics (Liverpool, GB), Talk, Swiftly computing center strings

Commissions of trust

• I am an editor of the special issues
  • Coronavirus Evolution, Cross-Species Transmission and Recombination (2021) in Frontiers in Microbiology
  • Virus Bioinformatics (2019, 2020) in Viruses
• I am an editor of conference proceedings of German Conference on Bioinformatics 2012.
• I have been ad hoc reviewer for several journals and conferences: Journal of Proteome Research, Journal of Mass Spectrometry, Analytical Chemistry, Metabolites, Rapid Communications in Mass Spectrometry, Annual International Conference on Research in Computational Molecular Biology (RECOMB), Annual International Conference on Intelligent Systems for Molecular Biology/ European Conference on Computational Biology (ISMB/ECCB), Workshop on Algorithms in Bioinformatics (WABI), IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB), German Conference on Bioinformatics (GCB), International Workshop on Combinatorial Algorithms (IWOCA).
• I am a founding member of the European Virus Bioinformatics Center.

Publications

Google Scholar

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Publications in Previous Groups

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