Es gibt drei Dinge, die sich nicht vereinen lassen: Intelligenz, Anständigkeit und Nationalsozialismus.
Man kann intelligent und Nazi sein. Dann ist man nicht anständig.
Man kann anständig und Nazi sein. Dann ist man nicht intelligent.
Und man kann anständig und intelligent sein. Dann ist man kein Nazi.
~ Gerhard Bronner ~

E-Mail: franziska.hufsky@uni-jena.de
Room: 08S03
Phone: +49-3641-9-46482

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
Memberships & Awards
  • since 2021 Member of FIFI e.V. (Förderverein des Instituts für Informatik) of the Friedrich Schiller University Jena
  • since 2017 Founding member of the European Virus Bioinformatics Center
  • 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)
  • 2012 ISMB 2012 Travel fellowship of the International Society for Computational Biology (ISCB)
Research interests
  • Virus Bioinformatics
  • 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
  • organizing committee MINT Festival Jena 2020/21
  • interviews and articles in science magazines for laypersons (e.g. VAA Magazin, Laborjournal, BIOSpektrum)
  • Judge at EC2U Science Battle 2021
  • 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
  • 2022 International Virus Bioinformatics Meeting (Valencia, Spain), Main organizer
  • 2020 International Virus Bioinformatics Meeting (Bern, Switzerland | online), Main organizer
  • 2019 Third Meeting of the European Virus Bioinformatics Centre (Glasgow, UK), Main organizer
  • 2017 First Meeting of the European Virus Bioinformatics Centre (Jena, Germany), Main 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
  • 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.
University self­administration

Equal opportunities representative of the Faculty of Mathematics and Computer Science (since 2016)

Publications

2022

Žarković, Milena; Hufsky, Franziska; Markert, Udo R; Marz, Manja

The Role of Non-Coding RNAs in the Human Placenta Journal Article

In: Cells, vol. 11, iss. 9, pp. 1588, 2022.

Abstract | Links | BibTeX

Hufsky, Franziska; Beslic, Denis; Boeckaerts, Dimitri; Duchene, Sebastian; González-Tortuero, Enrique; Gruber, Andreas J; Guo, Jiarong; Jansen, Daan; Juma, John; Kongkitimanon, Kunaphas; Luque, Antoni; Ritsch, Muriel; Lovate, Gabriel Lencioni; Nishimura, Luca; Pas, Célia; Domingo, Esteban; Hodcroft, Emma; Lemey, Philippe; Sullivan, Matthew B; Weber, Friedemann; González-Candelas, Fernando; Krautwurst, Sarah; Pérez-Cataluña, Alba; Randazzo, Walter; Sánchez, Gloria; Marz, Manja

The International Virus Bioinformatics Meeting 2022 Journal Article

In: Viruses, vol. 14, iss. 5, pp. 973, 2022.

Abstract | Links | BibTeX

2020

Hufsky, Franziska; Beerenwinkel, Niko; Meyer, Irmtraud M.; Roux, Simon; Cook, Georgia May; Kinsella, Cormac M.; Lamkiewicz, Kevin; Marquet, Mike; Nieuwenhuijse, David F.; Olendraite, Ingrida; Paraskevopoulou, Sofia; Young, Francesca; Dijkman, Ronald; Ibrahim, Bashar; Kelly, Jenna; Mercier, Philippe Le; Marz, Manja; Ramette, Alban; Thiel, Volker

The International Virus Bioinformatics Meeting 2020 Journal Article

In: Viruses, vol. 12, no. 12, pp. 1398, 2020.

Abstract | Links | BibTeX

Hufsky, Franziska; Lamkiewicz, Kevin; Almeida, Alexandre; Aouacheria, Abdel; Arighi, Cecilia; Bateman, Alex; Baumbach, Jan; Beerenwinkel, Niko; Brandt, Christian; Cacciabue, Marco; Chuguransky, Sara; Drechsel, Oliver; Finn, Robert D; Fritz, Adrian; Fuchs, Stephan; Hattab, Georges; Hauschild, Anne-Christin; Heider, Dominik; Hoffmann, Marie; Hölzer, Martin; Hoops, Stefan; Kaderali, Lars; Kalvari, Ioanna; Kleist, Max; Kmiecinski, Renó; Kühnert, Denise; Lasso, Gorka; Libin, Pieter; List, Markus; Löchel, Hannah F; Martin, Maria J; Martin, Roman; Matschinske, Julian; McHardy, Alice C; Mendes, Pedro; Mistry, Jaina; Navratil, Vincent; Nawrocki, Eric P; O'Toole, Áine Niamh; Ontiveros-Palacios, Nancy; Petrov, Anton I; Rangel-Pineros, Guillermo; Redaschi, Nicole; Reimering, Susanne; Reinert, Knut; Reyes, Alejandro; Richardson, Lorna; Robertson, David L; Sadegh, Sepideh; Singer, Joshua B; Theys, Kristof; Upton, Chris; Welzel, Marius; Williams, Lowri; Marz, Manja

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research Journal Article

In: Brief Bioinform, vol. 22, no. 2, pp. 642–663, 2020.

Abstract | Links | BibTeX

Hufsky, Franziska; Lamkiewicz, Kevin; Almeida, Alexandre; Aouacheria, Abdel; Arighi, Cecilia; Bateman, Alex; Baumbach, Jan; Beerenwinkel, Niko; Brandt, Christian; Cacciabue, Marco; Chuguransky, Sara; Drechsel, Oliver; Finn, Robert D.; Fritz, Adrian; Fuchs, Stephan; Hattab, Georges; Hauschild, Anne-Christin; Heider, Dominik; Hoffmann, Marie; Hölzer, Martin; Hoops, Stefan; Kaderali, Lars; Kalvari, Ioanna; Kleist, Max; Kmiecinski, Rene; Kühnert, Denise; Lasso, Gorka; Libin, Pieter; List, Markus; Löchel, Hannah F.; Martin, Maria J.; Martin, Roman; Matschinske, Julian; McHardy, Alice C.; Mendes, Pedro; Mistry, Jaina; Navratil, Vincent; Nawrocki, Eric; O'Toole, Áine Niamh; Palacios-Ontiveros, Nancy; Petrov, Anton I.; Rangel-Piñeros, Guillermo; Redaschi, Nicole; Reimering, Susanne; Reinert, Knut; Reyes, Alejandro; Richardson, Lorna; Robertson, David L.; Sadegh, Sepideh; Singer, Joshua B.; Theys, Kristof; Upton, Chris; Welzel, Marius; Williams, Lowri; Marz, Manja

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research Journal Article

In: Preprints, 2020, (Now published in Brief Bioinform: https://dx.doi.org/10.1093/bib/bbaa232).

Abstract | Links | BibTeX

Marz, Manja; Ibrahim, Bashar; Hufsky, Franziska; Robertson, David L. (Ed.)

Virus Bioinformatics Book

MDPI - Multidisciplinary Digital Publishing Institute, 2020, ISBN: 3039218824.

Links | BibTeX

2019

Hufsky, Franziska; Ibrahim, Bashar; Modha, Sejal; Clokie, Martha R. J.; Deinhardt-Emmer, Stefanie; Dutilh, Bas E.; Lycett, Samantha; Simmonds, Peter; Thiel, Volker; Abroi, Aare; Adriaenssens, Evelien M.; Escalera-Zamudio, Marina; Kelly, Jenna Nicole; Lamkiewicz, Kevin; Lu, Lu; Susat, Julian; Sicheritz, Thomas; Robertson, David L.; Marz, Manja

The Third Annual Meeting of the European Virus Bioinformatics Center Journal Article

In: Viruses, vol. 11, no. 5, pp. 420, 2019.

Abstract | Links | BibTeX

2018

Ibrahim, Bashar; McMahon, Dino P; Hufsky, Franziska; Beer, Martin; Deng, Li; Mercier, Philippe Le; Palmarini, Massimo; Thiel, Volker; Marz, Manja

A new era of virus bioinformatics Journal Article

In: Virus Res, vol. 251, pp. 86–90, 2018.

Abstract | Links | BibTeX

Hufsky, Franziska; Ibrahim, Bashar; Beer, Martin; Deng, Li; Mercier, Philippe Le; McMahon, Dino P; Palmarini, Massimo; Thiel, Volker; Marz, Manja

Virologists-Heroes need weapons Journal Article

In: PLoS Pathog, vol. 14, no. 2, pp. e1006771, 2018.

Abstract | Links | BibTeX

2017

Riege, Konstantin; Hölzer, Martin; Klassert, Tilman E; Barth, Emanuel; Bräuer, Julia; Collatz, Maximilian; Hufsky, Franziska; Mostajo, Nelly F.; Stock, Magdalena; Vogel, Bertram; Slevogt, Hortense; Marz, Manja

Massive Effect on LncRNAs in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins A and D Journal Article

In: Sci Rep, vol. 7, pp. 40598, 2017.

Abstract | Links | BibTeX

2016

Hölzer, Martin; Krähling, Verena; Amman, Fabian; Barth, Emanuel; Bernhart, Stephan H; Carmelo, Victor A O; Collatz, Maximilian; Doose, Gero; Eggenhofer, Florian; Ewald, Jan; Fallmann, Jörg; Feldhahn, Lasse M; Fricke, Markus; Gebauer, Juliane; Gruber, Andreas J; Hufsky, Franziska; Indrischek, Henrike; Kanton, Sabina; Linde, Jörg; Mostajo, Nelly F.; Ochsenreiter, Roman; Riege, Konstantin; Rivarola-Duarte, Lorena; Sahyoun, Abdullah H; Saunders, Sita J; Seemann, Stefan E; Tanzer, Andrea; Vogel, Bertram; Wehner, Stefanie; Wolfinger, Michael T; Backofen, Rolf; Gorodkin, Jan; Grosse, Ivo; Hofacker, Ivo; Hoffmann, Steve; Kaleta, Christoph; Stadler, Peter F; Becker, Stephan; Marz, Manja

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

In: Sci Rep, vol. 6, pp. 34589, 2016.

Abstract | Links | BibTeX

For publications in previous groups, please refer to Google Scholar