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
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 ...
hCNV data and the Progenetix Beacon
Michael Baudis
ELIXIR All Hands 2021
This presentation gives a brief overview of the use of the Progenetix resource to test and implement a genomics reference resource using the emerging Beacon v2 protocol.
2021-06-08: more ...
Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes
Bo Gao and Michael Baudis (2021)
Published at Frontiers in Genetics, 2021-05-13
Abstract
Copy number aberrations (CNA) are one of the most important classes of genomic mutations relatedto oncogenetic effects. In the past three decades, a vast amount of CNA data has been generated bymolecular-cytogenetic and genome sequencing based methods. While this data has been instrumentalin the identification of cancer-related genes and promoted research into the relation between CNA andhisto-pathologically defined cancer types, the heterogeneity of source data and derived CNV profilespose great challenges for data integration and comparative analysis. Furthermore, a majority of exist-ing studies have been focused on the association of CNA to pre-selected ”driver” genes with limitedapplication to rare drivers and other genomic elements.
2021-05-13: more ...
ELIXIR Beacon Project
Concepts | Status | History | Outlook
Michael Baudis
Research Data Alliance - RDA Virtual Plenary 17
This seminar gives an overview of current state of the Progenetix Beacon project and the overall connection to the Global Alliance for Genomics and Health (GA4GH).
2021-04-20: more ...
A Reference Resource for Copy Number Variations in Cancer
Implementing GA4GH Standards to Drive an Open Oncogenomics Resource
Michael Baudis
Seminar Neurooncology Childrens Hospital Zürich
This seminar gives an overview of the history & current state of the Progenetix resource, it’s role in Beacon API development and the overall connection to the Global Alliance for Genomics and Health (GA4GH).
2021-03-29: 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 |
