What do we do?
Our focus at the Computational Oncogenomics Group is the analysis of structural variations in cancer genomes using computational genomics, including bioinformatics and systems biology methods. Our work centres around our collections of molecular tumour data, assembled from genomic screening experiments in cancer e.g. through molecular-cytogenetic and genome sequencing studies. Specific projects deal with the development of computational methods for structural data analysis, genomic analyses in selected tumour entities as well as with the large-scale exploration of genomic patterns across malignancies.
Other aspects of the groups work are the development of computational methods for genome profiling datasets as well as the design and implementation of standards for genome and metadata annotation and sharing. Recently, we have become increasingly interested in questions of genome data epistemology, e.g. the identification of analysis biases related to geographic provenance and disease type in cancer.
In 2016, much of the group’s activity was focused on advancing projects for the Global Alliance for Genomics and Health (GA4GH). In particular, we contributed to GA4GH schema elements for the exchange of data describing biological and clinical features. Additionally, our team designed a GA4GH data implementation project which has been accepted as one of the ELIXIR human data pilot studies. Also, together with the SIB technology group, we developed an implementation of a GA4GH Beacon, based on our arraymap data resource, to facilitate a forward looking development of the Beacon protocol for the incorporation of structural genomic variants (beacon.arraymap.org).
Main publications 2016
- Ai N, Cai H, Solovan C, Baudis M. CNARA: reliability assessment for genomic copy number profiles. BMC Genomics. 2016 Oct 12;17(1):799. PMID 27733115.
- Andersson A, Bluwstein A, Kumar N, Teloni F, Traenkle J, Baudis M, Altmeyer M, Hottiger MO. PKCÎ± and HMGB1 antagonistically control hydrogen peroxide-induced poly-ADP-ribose formation. Nucleic Acids Res. 2016 Sep 19;44(16):7630-45. doi: 10.1093/nar/gkw442. PubMed PMID 27198223.