Group members
News
Publications
Talks & Posters
The GA4GH Beacon Protocol
Cancer genomics reference resource and toolkit around GA4GH standards
Progenetix - An open reference resource for copy number vatiation data in cancer ↗
hCNV Community and Implementation Studies
all ...
Teaching
Notes & Guides
Open Positions
The shows a probably incomplete following list of presentations (posters, talks, abstracts) from group members. Usually, PDF versions of the slides or posters are linked from the details pages.
2021
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 ...
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 ...
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 ...
ZH Sem Bioinfo - Qingyao Huang
Discovering copy number variation across multiple cancer types
- Thursday, 2021-03-25
- 12:15 om ZOOM Call
2021-03-25: more ...
EACR conference - The Progenetix Oncogenomic Resource
The Progenetix Oncogenomic Resource
2021-03-24: more ...
GA4GH Connect - Beacon v2 and SchemaBlocks
GA4GH Connect 2020
Michael Baudis
Beacon v2 Structural Variants [slides]
SchemaBlocks {S}[B] [slides]
2021-03-02: more ...
2020
Genomic data and Privacy
Michael Baudis
ETHZ Lecture
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 ...
Beacon v2 – Towards flexible use and clinical applications for a reference genomic data protocol
SPHN Webinar
Michael Baudis
2020-11-04: more ...
Update of Progenetix Oncogenomics Resource
Research Progress Report, DMLS, University of Zurich
Qingyao Huang
2020-10-30: more ...
Progenetix - A cancer genomics reference resource around GA4GH standards
GA4GH 8th Plenary
Michael Baudis
2020-09-30: more ...
GA4GH Beacon v2 - Evolving Reference Standard for Genomic Data Exchange
GA4GH 8th Plenary
Gary Saunders, Jordi Rambla de Argila, Anthony Brookes, Juha Törnroos and Michael Baudis
For the ELIXIR Beacon project, GA4GH Discovery work stream and the international network of Beacon API developers
2020-09-30: more ...
Cancer Data - ELIXIR::GA4GH: Advancing genomics resources through standards and ontologies
ECCB2020
Michael Baudis
2020-09-02: more ...
Beacon v2 - Towards Flexible Use and Clinical Applications for a Reference Genomic Data Sharing Protocol
Personalized Health Technologies 2020
Michael Baudis
2020-06-30: more ...
SchemaBlocks and GA4GH TASC
2020-04-20: more ...
SWISSNEX SF Lunch Seminar - Data Mining in Genomics
Genomic Research and Personalised Health Strategies
Resources | Standards | Protocols | Tools | Discourse
2020-03-19: more ...
ELIXIR Open Day - Wellcome Trust Genome Campus Hinxton
ELIXIR Beacon Project - Networking Resources Across and Beyond ELIXIR Human Data Communities
Michael Baudis
2020-02-06: more ...
GA4GH SchemaBlocks for Human Cell Atlas
2020-01-28: more ...
2019
3rd St. Gallen Radiation Oncology Informatics Meeting
Bioinformatics and data exchange for genomics in an international context
Michael Baudis
2019-11-08: more ...
Mini-Symposium about CNV and Data Standards at AMED Japan, Tokyo
Cancer Genomics and Implementation of Data Driven Standards for Genomic Data Exchange
Michael Baudis
2019-10-08: more ...
BC2 2019, Basel
Minimum Error Calibration and Normalization for Genomic Copy Number Analysis
Bo Gao
2019-09-10: more ...
BC2 2019, Basel
Minimum Error Calibration and Normalization for Genomic Copy Number Analysis
Bo Gao
2019-09-10: more ...
Seminar Universita degli Studi Firenze - Dipartimento di Biologia
Structural Genome Variants in Cancer: Research, resources standards
Michael Baudis
2019-09-03: more ...
Human Genome Variation Society - Gothenburg 2019
Implementation Driven Development of Standards for Genomic Data Exchange from Cancer Genome Data Collections
Michael Baudis
2019-06-14: more ...
R&D Data Intelligence Leaders Forum Basel
Connecting the silos - Genomic Data Standards, Resources and the Global Alliance for Genomics and Health
Michael Baudis
2019-01-25: more ...
2018
UZH BIO390 “Introduction to Bioinformatics”
Bioinformatics - Introduction
Michael Baudis
2018-09-17: more ...
Abstract: ECCB 2018
ELIXIR Beacon - A Driver Project for the Global Alliance for Genomics and Health
Michael Baudis for the ELIXIR Beacon Project
2018-09-08: more ...
IMLS Progress Report
Towards understanding population effect on cancer
Qingyao Huang
Qingyao 2018-06-29: more ...
ELIXIR All Hands, Berlin
The ELIXIR Beacon in 2018: A driver project of GA4GH
Michael Baudis
2018-06-06: more ...
Abstract: ELIXIR All Hands 2018
Genomic profiles of cancer cell lines - A systematic review
Rahel Paloots, Qingyao Huang, Paula Carrio Cordo and Michael Baudis
2018-06-04: more ...
Abstract: ELIXIR All Hands 2018
Update on arrayMap Cancer Genome Resource
Qingyao Huang and Michael Baudis
2018-06-04: more ...
Abstract: ELIXIR All Hands 2018
Biocuration for cancer genome databases: arrayMap and Progenetix
Paula Carrio Cordo and Michael Baudis
2018-06-04: more ...
Abstract: ELIXIR All Hands 2018
ELIXIR Beacon - A Driver Project for the Global Alliance for Genomics and Health
Michael Baudis for the ELIXIR Beacon Project
2018-06-04: more ...
Abstract: ELIXIR All Hands 2018
segment_liftover : a Python tool to convert segments between genome assemblies
Bo Gao, Qingyao Huang and Michael Baudis
2018-06-04: more ...
DPPH - Data Protection in Personalized Health 2018, Lausanne
Genome Beacons for Data Discovery - Technical advances in a challenging environment
Michael Baudis
2018-02-15: more ...
2017
Special seminar at University of Timisoara Dermatology
Cancer Genome (Data) Analysis in Personalised Medicine
Michael Baudis
2017-12-07: more ...
UZH Cancer Biology course “Research with clinical samples
Personalised Medicine - Genome Variation / Data Formats / Resources / Sharing / Privacy
Michael Baudis
2017-12-01: more ...
GA4GH 2017 Plenary / Workstream Day
Developing Beacons for Data Discovery
Michael Baudis
2017-10-15: more ...
UZH BIO390 “Introduction to Bioinformatics”
Bioinformatics - Introduction
Michael Baudis
2017-09-19: more ...
[BC]2 2017 - Basel Computational Biology Conference
Advancing the Global Alliance for Genomics and Health data schemas through data-driven implementations
Michael Baudis
2017-09-13: more ...
Seminar at SDU Odense
Somatic CNV databases as resources for cancer research && GA4GH schema development
Michael Baudis
2017-08-29: more ...
Seminar at SDU Odense
Somatic CNV databases as resources for cancer research && GA4GH schema development
Michael Baudis
2017-08-29: more ...
Seminar - Stanford Center for Genomics & Personalized Medicine
Personalized medicine in cancer
Michael Baudis
2017-02-21: more ...
Brupbacher Meeting
Implementing Data Models for the Global Alliance for Genomics and Health
Bo Gao
2017-02-01: more ...
R&D Data Intelligence Leaders Forum Basel
Genome data access - Application to personalized health and cancer research
Michael Baudis
2017-01-26: more ...
2016
Antrittsvorlesung Universität Zürich - Inaugural Lecture at University of Zurich
Cancer Genome (Data) Analysis
Michael Baudis
2016-12-19: more ...
LSZGS Cancer Biology course 2016
Personalized medicine in cancer
Michael Baudis
2016-12-02: more ...
VIB Conference “Applied Bioinformatics in Life Sciences”
Gene-based analysis of focal copy number aberration patterns in cancer genomes
Saumya Gupta
2016-03-17: more ...
2001
First BCATS Meeting - Biocomputing @ Stanford 2001
progenetix.net: storage and visualization of genomic aberration data in human malignancies
Michael Baudis
2001-10-20: more ...
Archive …
- 2017-11-05: Qingyao Huang. EMBL Cancer Genomics poster: integrative analysis of cancer genome profiling data to study the interplay of genetic background and molecular mechanisms in cancer [pdf]
- 2017-09-11: Michael Baudis, SIB-Novartis Workshop: Group projects “Biocuration to Cancer Genomics: Resources, Standards, Data Science” pdf
- 2017-03-21: Bo Gao, ELIXIR All Hands, Rome: Implementing Data Models for the Global Alliance for Genomics and Health (poster)
- 2017-03-02: Michael Baudis, SPHN Basel-Zürich cluster workshop: Project proposal slides “Knowledge infrastructure for cancer related personalized health applications”
- 2017-02-01: Paula Carrio Cordo, Brupbacher Meeting: arrayMap & Progenetix 2017: Oncogenomic Databases Towards Personalized Medicine pdf
- Poster about the ongoing development of our arrayMap and Progenetix resources, with emphasis on the identification of geographic and cancer type related biases in global oncogenomic data production
- 2002-10-25: Michael Baudis, “BCATS - BioComputing AT Stanford 2002”: Collection and Transformation of Chromosomal Imbalances in Human Neoplasias for Data Mining Procedures
- From the second BCATS meeting, an update on the Progenetix data repository and analysis tools