The baudisgroup website represents projects and information by the Computational Oncogenomics Group of the University of Zurich (UZH) and the Swiss Institute of Bioinformatics (SIB). For visitors more interested in Particle Astrophysics, we strongly recommend the website of another, although related, Professor Baudis.
The Computational Oncogenomics Group’s research focus lies in the exploration of structural genome variations in cancer. Our work centres around our Progenetix resource of curated molecular-cytogenetic and sequencing data. Specific projects explore computational methods, genomics of selected tumour entities and genomic variant patterns across malignancies. As members of the Global Alliance for Genomics and Health, the group is developing standards in biocuration and data sharing for genomic variants and phenotypic data, for instance in driving development of the ELIXIR Beacon project. Other research is related to genome data epistemology, e.g. geographic and diagnostic sampling biases in cancer studies.
Ongoing software and service projects can be visited at our Github organizations ([progenetix] and [baudisgroup]) and when looking at individual contributions to e.g. GA4GH and ELIXIR.
Progenetix is a cancer genomics resource that includes genomic profiling data as well as biomedical annotations and provenance data for cancer studies. The main goal of the Progenetix database is to provide easy, open access for research studies and clinical diagnostics. To facilitate sharing of genomic data, Progenetix complies with and contributes to GA4GH and Beacon data standards. Beacon, developed with the support from ELXIR (the European bioinformatics infrastructure organization), started out as protocol to share genomic variants over federated queries.
2022-07-31: more ...
2022-07-01: more ...
The presentation reports about the Progenetix cancer genomics resource and its role in the GA4GH ecosystem & the Beacon genomics API development process.
2022-06-27: more ...
@mbaudis 2022-06-15: more ...
One of the known features of cancer is the instability of its genome. Vast changes in the genome lead to duplications and deletions in the chromosome, that can be detected in most types of cancer. These chromosomal aberrations are also called copy number variants. Cancer cell lines are necessary tools for understanding the disease mechanisms as well as the development of new cancer treatments. However, they may not always be the best representation of their neoplasm of origin, due to cell line contamination and misidentification, as well as higher numbers of accumulated mutations in the cancer cell line genome.
2022-06-13: more ...
For requests & support, please use standard Github procedures such as pull requests or issues on our project repositories, or contact us.
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