Niko Popitsch

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:

Education:

• 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.

Degrees/Awards:

• 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

Publications

Addresses

Postal Address:

Niko Popitsch - Last Change: . foaf