Bioinformatics

Background

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 and 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.

Selected Articles

Shahin, T., Kuehn, H. S., Shoeb, M. R., Gawriyski, L., Giuliani, S., Repiscak, P., Hoeger, B., Yuce Petronczki, O., Bal, S. K., Zoghi, S., Dmytrus, J., Seruggia, D., Castanon, I., Rezaei, N., Varjosalo, M., Halbritter, F., Rosenzweig, S. D., & Boztug, K. (2021). Germline biallelic mutation affecting the transcription factor Helios causes pleiotropic defects of immunity. Sci Immunol, 6(65), eabe3981. https://doi.org/10.1126/sciimmunol.abe3981

Lazic, D., Kromp, F., Rifatbegovic, F., Repiscak, P., Kirr, M., Mivalt, F., Halbritter, F., Bernkopf, M., Bileck, A., Ussowicz, M., Ambros, I. M., Ambros, P. F., Gerner, C., Ladenstein, R., Ostalecki, C., & Taschner-Mandl, S. (2021). Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging. Cancers (Basel), 13(17). https://doi.org/10.3390/cancers13174311

Popitsch, N., Preuner, S., & Lion, T. (2021). Nanopanel2 calls phased low-frequency variants in Nanopore panel sequencing data. Bioinformatics. https://doi.org/10.1093/bioinformatics/btab526 

Fortschegger, K., Husa, A. M., 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, 22(14). https://doi.org/10.3390/ijms22147576

Staff Members

Peter Zöscher
peter.zoescher@ccri.at

Celine Prakash
celine.prakash@ccri.at

Aleksandr Bykov
aleksandr.bykov@ccri.at

Chloe Casey
chloe.casey@ccri.at

Jan Oppelt
jan.oppelt@ccri.at