Center for Integrative Bioinformatics Vienna
Max F. Perutz Laboratories
Dr. Bohr Gasse 9
A-1030 Vienna, Austria
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   Max F. Perutz Laboratories
   University of Vienna
   Medical University, Vienna

   Deep Metazoan Phylogeny
   MaBS group
   Max Perutz Library
Niko Popitsch

Niko Popitsch

I am currently working at IMBA, see my current website for an up-to-date list of my publications.
I am currently working at the Children's Cancer Research Institute
I am currently working in Jenny Taylor's group at the Wellcome Trust Centre for Human Genetics, see my current website for a more up-to-date research profile.

Research Interests:

  • Analysis and management of next generation sequencing (NGS) data
    • Repetitive Sequences
    • Compression of NGS data
    • Methods and algorithms for NGS data management, analysis and manipulation
  • Semantic data organization
    • Linked Biological Data
    • Semantic information systems

Short Vita:


  • 2007 - 2011: University of Vienna, computer science, Dr. techn. (PhD)
  • 2005 - 2012: University of Vienna, molecular biology, Mag. rer. nat. (M.Sc.)
  • 1994 - 2000: Technical University of Vienna, computer science, Dipl.-Ing. (M.Sc.)

Professional Experience:

  • since 2017 : Bioinformatician at the Children's Cancer Research Institute (CCRI)
  • 2014 - 2016: High-throughput sequencing bioinformatician at the Wellcome Trust Centre for Human Genetics (WTCHG)
  • 2011 - 2014: Post-doctoral researcher at the Center for Integrative Bioinformatics Vienna (CIBIV)
  • 2007 - 2011: Research assistant, multimedia information systems (MIS) group at the University of Vienna
  • 2003 - 2007: Senior Researcher/Chief Software Engineer, Austrian Research Centers GmbH, Research Studio Digital Memory Engineering
  • 2001 - 2003: Senior developer, uma information technology ag
  • 2000 - 2001: Junior developer, BLUE C Internet GmbH

Past and ongoing projects:

  • RG (since 2016) is a method for partitioning genomes into regions that can be genotyped with high/low confidence.
  • BBDB (since 2016) is a database of B. burgdorferi small RNAs
  • ARGOS (since 2014) is pipeline for extracting signals from a genomic sequence that characterize its repetitiveness.
  • CODOC (since 2014) is a format and API for the efficient representation and processing of depth-of-coverage data (complementing formats such as TDF or BigWig). It supports highly-efficient lossless and lossy data compression.
  • NGC (since 2011) is a compressor for high-throughput sequencing data (BAM files). It supports lossless and lossy compression.
  • NGV (since 2010) is a data set preprocessor and a desktop application for the visual inspection of next generation sequencing data.
  • Y2 (2007-2011) is an infrastructure for the efficient management of external metadata records on the desktop and in the Web of Data. Y2 was developed in the course of my doctoral thesis.
  • DSNotify (2009-2011) is a flexible event-detection framework that informs actors about various types of changes and allows them to maintain links to resources in distributed linked data sets.
  • Urobe (2009-2011) is a prototype for wiki preservation that implements a migration strategy for wiki contents based on Semantic Web and Linked Data principles. Urobe is the contribution of the University of Vienna to the digital long-term preservation project Research Studio Digital Memory Engineering.
  • Ylvi (2006-2008) is a semantic, multi-media enabled semantic wiki that was used for the realization of several individual projects. Examples include PoWiki, a specialized encyclopedia for political science terms, and EuWiki, a wiki and e-learning tool concerned with European Union-related terms.
  • METIS (2004-2007) is a flexible multimedia database foundation for the unified management of media of arbitrary types. It was used, among other projects, as a middleware component for the semantic wiki implementation Ylvi.


  • Dr. techn. (2011), University of Vienna
    Thesis: Building Blocks for Semantic Data Organization on the Desktop
  • Mag. rer. nat. (2012), University of Vienna
    Thesis: A Novel Compression Approach for Mapped High-Throughput Sequencing Data Sets
    passed with distinction/mit ausgezeichnetem Erfolg bestanden.
  • Dipl.-Ing. (2000), Technical University of Vienna
    Thesis: BIS-WCM: A WWW-based editorial and information system in support of the Medical Faculty of Vienna
  • "doc.award 2011", awarded by the University of Vienna/City of Vienna, 2011
  • "Certificate of Appreciation", awarded by the faculty of computer science, 2011


Find a complete list of my publications online at https://www.researchgate.net/profile/Niko_Popitsch


Niko Popitsch

Center for Integrative Bioinformatics Vienna (CIBIV)
(CIBIV is a joint institute of Vienna University, and Medical University Vienna, Vienna, Austria)
Max F. Perutz Laboratories (MFPL)
Campus Vienna Biocenter 5 (VBC5), Ebene 1, Room 1812.3
A-1030 Wien, Austria
Phone: ++43 +1 / 4277-24024
Fax: ++43 +1 / 4277-24098
Email: niko.popitsch(AT)univie.ac.at

Postal Address:

Center for Integrative Bioinformatics Vienna (CIBIV)
Max F. Perutz Laboratories (MFPL)
Dr. Bohr Gasse 9
A-1030 Wien, Austria

Niko Popitsch - Last Change: 06.May.2019 . foaf