Bioinformatics

Bioinformatics

CCRI Bioinformatics Team

The bioinformatics team provides advice and support for CCRI researchers with regard to analysis, integration and interpretation of large-scale genomics datasets. We maintain and run computational pipelines for processing raw next-generation sequencing (NGS) data and data quality checks for all genomics data held within the CCRI/St.Anna Children´s Hospital. We are also performing high quality data analyses in close collaboration with CCRI/St.Anna Children´s Hospital researchers in the following thematic areas:

  • Variant analyses (small variants, SVs, CNVs, fusions) in genomics data (WGS, WES, low-coverage WGS, targeted sequencing, array technologies)
  • Transcriptomics (RNA-Seq, scRNA-Seq)
  • Epigenomics (WGBS, ChIP-Seq, ATAC-Seq)
  • Functional genomics (integrated analyses of the above)
  • Database and scientific software development and maintenance

We are furthermore conducting translational bioinformatics research in cooperation with CCRI researchers and external professionals.

Staff

Ohne Namen

 

Peter Repiscak
peter.repiscak@ccri.at
+43 1 40470-4075

 

 

 

Dagmar Schinnerl
dagmar.schinnerl@ccri.at
+43 1 40470-4023

 

 

Former members

  • Niko Popitsch
  • Maximilian Kauer
  • Murat Tugrul
  • Christian Frech (Seven Bridges Genomics)

Selected Articles

  • Shahin T, …, Repiscak P,…, Boztug K. (2021) Germline biallelic mutation affecting the transcription factor Helios causes pleiotropic defects of immunity. Sci. Immunol. 6, doi: 10.1126/sciimmunol.abe3981
  • Lazic D, Kromp F, Rifatbegovic F, Repiscak P, …, Taschner-Mandl S. (2021)  Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging. Cancers, 13(17), 4311, doi: 10.3390/cancers13174311
  • Popitsch N, Preuner S and Lion T. (2021) Nanopanel2 calls phased low-frequency variants in Nanopore panel sequencing data. Bioinformatics, 1–6, doi: 10.1093/bioinformatics/btab526
  • Robbe P, Popitsch N, …, (2018) Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project. Genet Med, doi:10.1038/gim.2017.241
  • Fortschegger K, Husa AM, Schinnerl D, Nebral K, Strehl S. (2021) Expression of RUNX1-JAK2 in Human Induced Pluripotent Stem Cell-Derived Hematopoietic Cells Activates the JAK-STAT and MYC Pathways. Int J Mol Sci. 15;22(14):7576, PMID: 34299194; PMCID: PMC8304339; doi: 10.3390/ijms22147576.
  • Schinnerl D, …, Kauer MO, Popitsch N, …, Strehl S. (2019) CD371 cell surface expression: a unique feature of DUX4-rearranged acute lymphoblastic leukemia. Haematologica, 104(8):e352-e355. Epub 2019 Jan 31. PMID: 30705095; PMCID: PMC6669149; doi: 10.3324/haematol.2018.214353.

Software

  • Nanopanel2 is a variant caller for Nanopore panel sequencing data.