Email: florian.pflug(AT)
Phone: ++43 +1 / 4277 - 74323

Postal address:
Center for Integrative Bioinformatics Vienna (CIBIV)
Max Perutz Labs
Campus Vienna Biocenter 5 (VBC5)
A-1030 Wien, Austria

Research interests

  • Stochastic models of biological and experimental systems (stem cell homeostatis, organoid development, PCR amplification)
  • Statistical Modelling of NGS-based quantitative methods (e.g. RNA-Seq)
  • Single-cell Sequencing
  • Absolute quantification methods (e.g. RNA-seq with UMIs)


  • Jul 2015 - Dec 2019: Max F. Perutz Laboratories, Center for Integrative Bioinformatics VIenna, Phd.
  • Oct 2000 - Dec 2015: Technical University of Vienna, Computer Science, B.Sc.
  • Oct 2000 - Dec 2014: Technical University of Vienna, Mathematics, Dipl.Ing.
  • Sep 1994 - Jun 2000: HTL TGM Wien Wexstraße, Department for Electronics

Professional Experience

  • Jan 2020 - present: Postdoc at the Center for Integrative Bioinformatics Vienna (CIBIV)
  • 2015 - Dec 2019: PhD Student at the Center for Integrative Bioinformatics Vienna (CIBIV)
  • 2008 - 2015: Self-employed software developer
  • Summer 2007: Various contributions to the open-source database system PostgreSQL (, payed through the “Google Summer of Code” program
  • 1995 - 2007” Sofwaredeveloper at “solution-X software GmbH”

Talks and Posters


  • CMStatistics 2016 (9th International Conference of the ERCIM WG on Computational and Methodological Statistics), Sevilla, Spain, December 9-11 2016.
    Talk: Stochastic modelling of PCR to estimate and correct for unobserved molecules in quantitative NGS experiments


  • MASAMB 2017 (27th Annual Workshop on Mathematical and Statistical Aspects of Molecular Biology), Vienna, Austria, April 3-4 2017.
    Poster: Correcting for unobserved Molecules in quantitative NGS Experiments

  • Interscience - 1st Symposium of the Vienna Doctoral Schools, Vienna, Austria, Semptember 14-15.
    Talk: Unbiased Counting Absolute Numbers of Molecules Using Unique Molecular Identifiers (Best Talk Award)


  • Stochastic models of evolving populations: from bacteria to cancer (at the ICMS – International Centra of Mathematical Sciences), Edinburgh, UK, July 16-20.
    Talk: Correctly counting molecules with a little help from a well-known population model

  • GCB 2018 (German Conference on Bioinformatics), Vienna, Austria, September 25-28.
    Talk: Correctly counting molecules using unique molecular identifiers

Software Constributions

  • TRUmiCount (
  • gwpcR – An R package to simulate NGS library amplification and sequencing (
  • iPoolSeq-pipeline (



  • C. Esk, D. Lindenhofer, S. Haendeler, R.A. Wester, F.G. Pflug, B. Schroeder, J.A. Bagley, U. Elling, J. Zuber, A. von Haeseler, and J.A. Knoblich (2020) A human tissue screen identifies a regulator of ER secretion as a brain size determinant. Science, 370, 935-941. (DOI: 10.1126/science.abb5390, PMID: 33122427)
  • 2019

  • S. Uhse, F.G. Pflug, A. von Haeseler, and A. Djamei (2019) Insertion pool sequencing for insertional mutant analysis in complex host-microbe interactions. Current Protocols in Plant Biology, 4, e20086. (DOI: 10.1002/cppb.20097, PMID: 31479207)
  • 2018

  • F.G. Pflug and A. von Haeseler (2018) TRUmiCount: Correctly counting absolute numbers of molecules using unique molecular identifiers. Bioinformatics, 34, 3137-3144. (DOI: 10.1093/bioinformatics/bty283, PMID: 29672674, software)
  • S. Uhse, F.G. Pflug, A. Stirnberg, K. Ehrlinger, A. von Haeseler, and A. Djamei (2018) In vivo Insertion Pool Sequencing identifies Virulence Factors in a complex Fungal-Host Interaction. PLoS Biol., 16, e2005129. (DOI: 10.1371/journal.pbio.2005129, PMID: 29684023)