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 ...
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.
2022-03-15: more ...
2021-11-30: more ...
2021-11-10: more ...
This article was published as part of a special GA4GH edition of Cell Genomics.
2021-11-10: more ...
This article was published as part of a special GA4GH edition of Cell Genomics.
2021-11-10: more ...
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 ...
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 ...
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 ...
2021-08-03: more ...
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 ...
At the Human Data Day Michael presents a very brief overview of the ending and upcoming ELIXIR hCNV implementation studies.
2021-06-11: more ...
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 ...
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 ...
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 ...
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 ...
2021-03-25: more ...
2021-03-24: more ...
2021-03-02: more ...
This article explores the correlation between subsets of cancer entities, grouped by their somatic CNV patterns, and levels of diagnostic classification systems.
2021-03-01: more ...
The group is an active contributor to several public ontologies, both through mapping efforts (ICDOntologies, icdot2uberon) and by requesting terms relevant for genomic and metadata e.g. for EFO.
@mbaudis 2021-01-14: more ...
The understanding of the impact of individual inherited and somatic genome variants on phenotypes and diseases requires a thorough understanding of the occurrence of such variants amongst populations in general and carriers of the phenotypes and diseases in particular. This information can only be provided through the inclusion of data from a multitude of genome resources in variant evaluation efforts, including such from outside (international) jurisdictions. However, opening such resources carries the inherent risk of breaching privacy, particularly through re-identification of individuals or their relatives and potentially through the exposure of individual genome-related personal information including phenotypic and “performance” prediction and relative disease risk.
2020-12-07: more ...
2020-12-02: more ...
2020-11-04: more ...
2020-10-30: more ...
Today Ziying Yang arrived as a new member of the baudisgroup.
Welcome Ziying!
mbaudis 2020-10-26: more ...
2020-10-13: more ...
2020-09-30: more ...
2020-09-30: more ...
2020-09-02: more ...
2020-08-10: more ...
2020-06-10: more ...
2020-05-14: more ...
2020-05-06: more ...
Originally planned for their stays at UCB and LBNL, Laura & Michael were interviewed by Tabea Stoeckel from swissnex San Francisco about their stay in the Bay Area and their research & family life as internationally active scientists.
mbaudis 2020-05-06: more ...
@mbaudis 2020-04-02: more ...
2020-03-16: more ...
Between 2020-02-08 and 2020-04-10, Michael has switched his office for a desk at the Berkeley Bioinformatics Open-source Projects (BBOP) where he will work with members of Chris Mungall’s team on projects related to biomedical ontologies, data standards and the analysis of cancer genome data.
mbaudis 2020-02-08: more ...
2020-02-06: more ...
@mbaudis 2020-01-11: more ...
@mbaudis 2019-08-27: more ...
@mbaudis 2019-07-31: more ...
@mbaudis 2019-01-23: more ...
qingyao 2019-01-19: more ...
mbaudis 2019-01-14: more ...
qingyao 2018-09-20: more ...
Michael 2018-08-02: more ...
Michael 2018-07-31: more ...
mbaudis 2018-07-14: more ...
To unify the general website handling processes, I’ve implemented some changes:
mbaudis 2018-06-26: more ...
The info.baudisgroup.org site noe resides on Dropbox and is locally created/updated.
mbaudis 2018-06-09: more ...
2018-04-01: more ...
2012-04-16: more ...