Franziska Hufsky


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

*@uni-jena.de

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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
  • 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
  • 2010Workshop on Algorithms in Bioinformatics (Liverpool, GB), Talk, Swiftly computing center strings
Publications

Google Scholar

  • K. Riege, M. Hölzer, T.E. Klassert, E. Barth, J. Bräuer, M. Collatz, F. Hufsky, N. Mostajo, M. Stock, B. Vogel, H. Slevogt, and M. Marz. Massive effect on lncRNAs in human monocytes during fungal and bacterial infections and in response to vitamins A and D. Sci Rep 7: 40598, 2017.
  • M. Hölzer, V. Krähling, F. Amman, E. Barth, S. H. Bernhart, V.A.O. Carmelo, M. Collatz, G. Doose, F. Eggenhofer, J. Ewald, J. Fallmann, L.M. Feldhahn, M. Fricke, J. Gebauer, A.J. Gruber, F. Hufsky, H. Indrischek, S. Kanton, J. Linde, N.M. Berrospi, R. Ochsenreiter, K. Riege, L. Rivarola-Duarte, A. H. Sahyoun, S.J. Saunders, S.E. Seemann, A. Tanzer, B. Vogel, S. Wehner, M.T. Wolfinger, R. Backofen, J. Gorodkin, I. Grosse, I. Hofacker, S. Hoffmann, C. Kaleta, P.F. Stadler, S. Becker, and M. Marz. Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells. Sci Rep 6:34589, 2016.
  • M. Meusel, F. Hufsky, F. Panter, D. Krug, R. Müller, and S. Böcker. Predicting the presence of uncommon elements in unknown biomolecules from isotope patterns. Anal Chem, 88(15):7556-7566, 2016.
  • F. Hufsky, and S. Böcker. Mining Molecular Structure Databases: Identification of Small Molecules Based on Fragmentation Mass Spectrometry Data. Mass Spectrom Rev (Epub ahead of print), 2016.
  • F. Hufsky, K. Scheubert, and S. Böcker. New kids on the block: Novel informatics methods for natural product discovery. Nat Prod Rep, 31(6):807-817, 2014.
  • F. Hufsky, K. Scheubert, and S. Böcker. Computational mass spectrometry for small molecule fragmentation. Trends Anal Chem, 53:41-48, 2014.
  • K. Scheubert, F. Hufsky, and S. Böcker. Multiple mass spectrometry fragmentation trees revisited: Boosting performance and quality. In Proc. of Workshop on Algorithms in Bioinformatics (WABI 2014), volume 8701 of Lect Notes Comput Sci, pages 217–231. Springer, Berlin, 2014
  • K. Dührkop, F. Hufsky, and S. Böcker. Molecular formula identification using isotope pattern analysis and calculation of fragmentation trees. Mass Spectrom, 3:S0037, 2014
  • K. Scheubert, F. Hufsky, and S. Böcker. Computational mass spectrometry for small molecules. J Cheminform, 5:12, 2013 Research monographs
  • L. Ullmann-Zeunert, A. Muck, N. Wielsch, F. Hufsky, M. A. Stanton, S. Bartram, S. Böcker, I. T. Baldwin, K. Groten, and A. Svatoš. Determination of 15N-incorporation into plant proteins and their absolute quantitation: a new tool to study nitrogen flux dynamics and protein pool sizes elicited by plant-herbivore interactions. J Proteome Res, 11(10):4947–4960, 2012
  • F. Rasche, K. Scheubert, F. Hufsky, T. Zichner, M. Kai, A. Svatoš, and S. Böcker. Identifying the unknowns by aligning fragmentation trees. Anal Chem, 84(7):3417–3426, 2012
  • F. Hufsky, M. Rempt, F. Rasche, G. Pohnert, and S. Böcker. De novo analysis of electron impact mass spectra using fragmentation trees. Anal Chim Acta, 739:67–76, 2012
  • M. Ludwig, F. Hufsky, S. Elshamy, and S. Böcker. Finding characteristic substructures for metabolite classes. In Proc. of German Conference on Bioinformatics (GCB 2012), volume 26 of OpenAccess Series in Informatics (OASIcs), pages 23–38. Schloss Dagstuhl–Leibniz-Zentrum für Informatik, 2012
  • F. Hufsky and S. Böcker. Comparing fragmentation trees from electron impact mass spectra with annotated fragmentation pathways. In Proc. of German Conference on Bioinformatics (GCB 2012), volume 26 of OpenAccess Series in Informatics (OASIcs), pages 12–22. Schloss Dagstuhl–Leibniz- Zentrum für Informatik, 2012
  • F. Hufsky, K. Dührkop, F. Rasche, M. Chimani, and S. Böcker. Fast alignment of fragmentation trees. Bioinformatics, 28:i265–i273, 2012. Proc. of Intelligent Systems for Molecular Biology (ISMB 2012)
  • K. Scheubert, F. Hufsky, F. Rasche, and S. Böcker. Computing fragmentation trees from metabolite multiple mass spectrometry data. J Comput Biol, 18(11):1383–1397, 2011
  • K. Scheubert, F. Hufsky, F. Rasche, and S. Böcker. Computing fragmentation trees from metabo- lite multiple mass spectrometry data. In Proc. of Research in Computational Molecular Biology (RECOMB 2011), volume 6577 of Lect Notes Comput Sci, pages 377–391. Springer, Berlin, 2011
  • F. Hufsky, L. Kuchenbecker, K. Jahn, J. Stoye, and S. Böcker. Swiftly computing center strings. BMC Bioinformatics, 12:106, 2011
  • F. Hufsky, L. Kuchenbecker, K. Jahn, J. Stoye, and S. Böcker. Swiftly computing center strings. In Proc. of Workshop on Algorithms in Bioinformatics (WABI 2010), volume 6293 of Lect Notes Comput Sci, pages 325–336. Springer, Berlin, 2010

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