baudisgroup @ UZH

Welcome to the baudisgroup Pages

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 focus lies in the exploration of structural genome variations in cancer. Our work centres around our [arrayMap] Progenetix resource of curated molecular-cytogenetic and sequencing data. Specific projects explore computational methods, genomics of selected tumour entities as well as 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 through the Beacon+ implementation. Other projects are related to genome data epistemology, e.g. geographic and diagnostic sampling biases.

Some Projects

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.

bycon at Github in Progenetix - Python based implementation of a GA4GH Beacon
segment-liftover at Github baudisgroup
- publication
SNP2pop at Github baudisgroup
- publication at ScientificReports
ICDOntologies at Github in Progenetix - mapping disease concepts

Latest News

Progenetix & GA4GH Beacon

A cancer genomics resource built around and driving GA4GH standards

Michael Baudis

GRIC sponsored workshop with the Swiss Institute of Bioinformatics

The Progenetix oncogenomics resource provides sample-specific cancer genome profiling data and biomedical annotations as well as provenance data for cancer studies. With more than 100k genomic copy number number (CNV) profiles from over 700 cancer types, Progenetix empowers comparative analyses beyond individual studies and diagnostic concepts.

2021-09-22: more ...

The GA4GH Beacon Protocol

A Standardized Format for Federated Genomic Data Exchange

Michael Baudis

BC² Basel 2021

Session “Federating computational analyses with GA4GH standards”

BC2 logo During the “Federating computational analyses with GA4GH standards” workshop at BC² 2021 Michael presented history and the current status of the Beacon project, as well as its integration with specific data resources and analysis initiatives.

2021-09-13: more ...

A cancer genomics reference resource and implementation toolkit around GA4GH standards

Q. Huang, B. Gao, R. Paloots, P. Carrio-Cordo, Z. Yang, M. Baudis

ESHG 2021

ESHG Logo This poster presentation at the European Society of Human Genetics meeting 2021 discusses the integration and development of GA4GH standards by the Progenetix oncogenomics resource.