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’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.
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
Beacon v2 and Beacon networks: A “lingua franca” for federated data discovery in biomedical genomics, and beyond
Rambla J, Baudis M, Ariosa R, Beck T, Fromont LA, Navarro A, Paloots R, Rueda M, Saunders G, Singh B, Spalding JD.
Human Mutation. 2022 Mar 17. PMID:35297548
Abstract Beacon is a basic data discovery protocol issued by the Global Alliance for Genomics and Health (GA4GH). The main goal addressed by version 1 of the Beacon protocol was to test the feasibility of broadly sharing human genomic data, through providing simple “yes” or “no” responses to queries about the presence of a given variant in datasets hosted by Beacon providers.
@rahelp 2022-03-17: more ...
hCNV Implementation Studies Old and New
Michael Baudis
ELIXIR Human Data Communities
This presentation provided an overview about the hCNV community, implementation studies and ongoing work, e.g. interaction with the GA4GH VRS standard group and Beacon development.
Additional Links
2022-03-15: more ...
The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine
Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Callahan TJ, Chute CG, Courtot M, Danis D, Elemento O, Freimuth RR, Gargano MA, Groza T, Hamosh A, Harris NL, Kaliyaperumal R, Khalifa A, Krawitz PM, Koehler S, Laraway BJ, Lehvaeslaiho H, Lloyd KC, Matalonga L, McMurry JA, Metke-Jimenez A, Mungall CJ, Munoz-Torres MC, Ogishima S, Papakonstantinou A, Piscia D, Pontikos N, Queralt-Rosinach N, Roos M, Schofield PN, Siapos A, Smedley D, Smith LD, Steinhaus R, Sundaramurthi JC, Swietlik EM, Thun S, Vasilevsky NA, Wagner AH, Warner JL, Weiland C, Haendel MA, Robinson PN.
medRxiv, 2021.11.27.21266944. doi:10.1101/2021.11.27.21266944
2021-11-30: more ...
GA4GH: International policies and standards for data sharing across genomic research and healthcare
Heidi L. Rehm, Angela J.H. Page, Lindsay Smith, Jeremy B. Adams, Gil Alterovitz, Lawrence J. Babb, Maxmillian P. Barkley, Michael Baudis, Michael J.S. Beauvais, Tim Beck, Jacques S. Beckmann, Sergi Beltran, David Bernick, Alexander Bernier, James K. Bonfield, Tiffany F. Boughtwood, Guillaume Bourque, Sarion R. Bowers, Anthony J. Brookes, Michael Brudno, Matthew H. Brush, David Bujold, Tony Burdett, Orion J. Buske, Moran N. Cabili,
2021-11-10: more ...
International federation of genomic medicine databases using GA4GH standards
Adrian Thorogood, Heidi L. Rehm, Peter Goodhand, Angela J.H. Page, Yann Joly, Michael Baudis, Jordi Rambla, Arcadi Navarro, Tommi H. Nyronen, Mikael Linden, Edward S. Dove, Marc Fiume, Michael Brudno, Melissa S. Cline, Ewan Birney
Thorogood, Adrian et al. Cell Genomics, Volume 1, Issue 2, 100032 doi:10.1016/j.xgen.2021.100032
Note
This article was published as part of a special GA4GH edition of Cell Genomics.
2021-11-10: 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 |
