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
- SNP2pop at Github baudisgroup
- ICDOntologies at Github in Progenetix - mapping disease concepts
Latest News
The GA4GH Beacon Protocol
A Standardized Format for Federated Genomic Data Exchange
Michael Baudis
BC2 Basel 2021
Session “Federating computational analyses with GA4GH standards”
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
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.
2021-08-31: more ...
Progenetix - An open reference resource for copy number vatiation data in cancer
Qingyao Huang
Cancer Genomics Consortium Annual Meeting 2021 Aug 1-4
2021-08-03: more ...
The Progenetix oncogenomic resource in 2021
Qingyao Huang, Paula Carrio Cordo, Bo Gao, Rahel Paloots, Michael Baudis
Database (Oxford). 2021 Jul 17;2021:baab043.
- doi: 10.1093/database/baab043.
- PMID: 34272855
- PMCID: PMC8285936.
- bioRxiv. doi: https://doi.org/10.1101/2021.02.15.428237
This article provides an overview of recent changes and additions to the Progenetix database and the services provided through the resource.
2021-06-30: more ...
hCNV Community and Implementation Studies
Michael Baudis
ELIXIR All Hands 2021 Human Data Day
At the Human Data Day Michael presents a very brief overview of the ending and upcoming ELIXIR hCNV implementation studies.
2021-06-11: more ...
Support or Contact
For requests & support, please use standard Github procedures such as pull requests or issues on our project repositories, or contact us.
Address
| Winterthurerstrasse 190 | Y-13F-01 | CH-8057 Zurich | Switzerland |
