Presentations

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.

Beacon v2 - Feature-rich Implementation of the Genomic Data Discovery Protocol

GA4GH 2022 Plenary Barcelona

Michael Baudis

The “Beacon” protocol - developed with support from ELIXIR, the European bioinformatics infrastructure organization, as a standard of the Global Alliance for Genomics and Health (GA4GH) - represents an emerging standard for an “Internet for Genomics”. While the initial version of the protocol served as a widely adopted test bed for the sharing of genomic variants over federated query systems connecting hundreds of internationally distributed resources, the version 2 of the protocol provides a framework for extended, metadata-rich query and response options in both public and restricted federated access scenarios. Continue reading

Beacon - Ethical & Legal Aspects of a Genomic Data Discovery Protocol

DSI Ethics Project Pitch

Michael Baudis

Here Michael provides a very brief presentation about the GA4GH Beacon protocol, especially as a target for projects discussing the ethical implications of genome data discovery & sharing as well as the relevant legal frameworks, with emphasis on the Swiss context. Continue reading

A cancer genomics resource built on GA4GH standards

Rahel Paloots, Michael Baudis

CGC St Louis 2022

Progenetix is a cancer genomics resource that includes genomic profiling data as well as biomedical annotations and provenance data for cancer studies. The main goal of the Progenetix database is to provide easy, open access for research studies and clinical diagnostics. To facilitate sharing of genomic data, Progenetix complies with and contributes to GA4GH and Beacon data standards. Beacon, developed with the support from ELXIR (the European bioinformatics infrastructure organization), started out as protocol to share genomic variants over federated queries.

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Progenetix, BeaconPlus & GA4GH

A cancer genomics reference resource powered by GA4GH standards

Michael Baudis

Roche Data Science Seminar

The presentation reports about the Progenetix cancer genomics resource and its role in the GA4GH ecosystem & the Beacon genomics API development process.

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Implementation of the GA4GH Beacon protocol for discovery and sharing of genomic copy number variation data

Michael Baudis

ESHG Vienna 2022

Background & Objectives Genomic copy number variations (CNV) are a major contributor to inter-individual genomic variation, can be causative events in rare diseases, but especially represent the majority of the mutational landscape in the most malignancies. While specific CNV events and some recurring patterns have contributed to the identification of individual cancer drivers and the recognition of cancer subtypes, the complexity of genomic CNV patterns requires large amounts of well-defined genomic profiles for statistically meaningful analyses. At the other end of the spectrum, in the area of rare disease genomics the potential pathogenicity of individual CNV events requires validation against a vast set of disease-related and reference genomic profiles and annotations.

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Progenetix & BeaconPlus

An open cancer genomics resource on a stack of Beacon code...

Michael Baudis

ELIXIR All Hands Amsterdam 2022

Here Michael provides some overview of the multi-year trajectory of the Beacon API development, and how BeaconPlus & Progenetix have been utilized for "implementation driven design".

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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.

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Technical, legal and ethics aspects of genomic data sharing

Genomes | Privacy | Laws | Society - DSI Ethics Seminar

Michael Baudis

The presentation introduces the need for sharing and federated discovery of genome data in the contexts of personalized health and genomic researchand some of teh current developments in international standards and practices in the area. Continue reading

Progenetix & GA4GH Beacon

GRIC sponsored workshop with the Swiss Institute of Bioinformatics

A cancer genomics resource built around and driving GA4GH standards

Michael Baudis

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.

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A Standardized Format for Federated Genomic Data Exchange

The GA4GH Beacon Protocol Presented at BC2

Michael Baudis

BC2 Basel 2021

Session "Federating computational analyses with GA4GH standards"

BC2 logoDuring 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.

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Cancer genomics reference resource and toolkit around GA4GH standards

Q. Huang, B. Gao, R. Paloots, P. Carrio-Cordo, Z. Yang, M. Baudis

ESHG 2021

ESHG LogoThis poster presentation at the European Society of Human Genetics meeting 2021 discusses the integration and development of GA4GH standards by the Progenetix oncogenomics resource.

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Progenetix - An open reference resource for copy number vatiation data in cancer

Qingyao Huang

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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.

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hCNV data and the Progenetix Beacon

Presentation at ELIXIR All Hands 2021

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.

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Progenetix, Beacon and GA4GH at RDA

Research Data Alliance - RDA Virtual Plenary 17

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).

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Implementing GA4GH Standards to Drive an Open Oncogenomics Resource

Research Seminar Kinderspital Zürich - Neuroonkologie

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).

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Discovering copy number variation across multiple cancer types

Qingyao Huang

Abstract

Genomic variations are direct cause of tumor formation and accomplice in its continuous evolution. While point mutations can be pinpointed to a targeted genetic element, copy number variations (CNVs) involve copy number gain or loss of a large DNA segment which often covers hundreds of genetic elements in one event. Continue reading

EACR conference - The Progenetix Oncogenomic Resource

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GA4GH Connect - Beacon v2 and SchemaBlocks

GA4GH Connect 2020

Michael Baudis

Beacon v2 Structural Variants [slides]
SchemaBlocks {S}[B] [slides]
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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.

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Beacon v2 – Towards flexible use and clinical applications for a reference genomic data protocol

SPHN Webinar

Michael Baudis

Genomic “Beacons” provide discovery services for genomic data using the Beacon API developed as a key driver project of the Global Alliance for Genomics and Health (GA4GH). The Beacon protocol itself defines an open standard for genomics data discovery and provides a framework for web services responding to queries against genomic data collections, for instance from population based or disease specific genome repositories. Continue reading

Update of Progenetix Oncogenomics Resource

Research Progress Report, DMLS, University of Zurich

Qingyao Huang

Copy number aberration (CNA) is frequently observed in cancer genomes. Meta-analysis of genomic variations helps to disentangle the multiplex molecular mechanism underlying tumorigenesis as well as identify and characterize molecular subtypes. Over the years, cancer genomic research have resulted in a considerable amount of data segregated by studies. The Progenetix project (www.progenetix.org), initiated in 2001, aims to systematize the published cancer genomic profiles and provide accurate annotation to facilitate integrative analysis. Continue reading

GA4GH Beacon v2 at GA4GH Plenary

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

The Beacon driver project was one of the earliest initiatives of the Global Alliance for Genomics and Health with the Beacon v1.0 API as first approved GA4GH standard. Version 2 of the protocol is slated to provide fundamental changes, towards a Internet of Genomics foundational standard: * requests beyond genomic variants ("filters") * payload responses, secured through open AAI * aligning w/ GA4GH standards (Phenopackets, VRS, DUO...) through SchemaBlocks {S}[B] * Working with international partners on deployment of advanced implementations

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Progenetix - A cancer genomics reference resource around GA4GH standards

GA4GH 8th Plenary

Michael Baudis

The Progenetix oncogenomics resource provides sample-specific cancer genome profiling data and biomedical annotations as well as provenance data from cancer studies. Especially through currently 113322 curated genomic copy number number (CNV) profiles from 1600 individual studies representing over 500 cancer types (NCIt), Progenetix empowers aggregate and comparative analyses which vastly exceed individual studies or single diagnostic concepts. Continue reading

Cancer Data - ELIXIR::GA4GH: Advancing genomics resources through standards and ontologies

ECCB2020

Michael Baudis

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Beacon v2 - Towards Flexible Use and Clinical Applications for a Reference Genomic Data Sharing Protocol

Personalized Health Technologies 2020

Michael Baudis

Beacons provide discovery services for genomic data using the Beacon API developed under the leadership of ELIXIR, as a key driver project of the Global Alliance for Genomics and Health (GA4GH). The Beacon protocol itself defines an open standard for genomics data discovery. It provides a framework for public web services responding to queries against genomic data collections, for instance from population based or disease specific genome repositories. Sites offering beacons can scale through aggregation in "Beacon Networks", which distribute single genome queries among a potentially large number of international beacons and assemble their responses. Continue reading

ELIXIR All Hands - Beacon Evolution

ELIXIR All Hands 2020 - Beacon Workshop

Michael Baudis

This presentation covers some of Beacon's origins, features and directions.

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SchemaBlocks and GA4GH TASC

A brief presentation about SchemaBlocks concepts and its possible integration into the new GA4GH TASC effort.

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SWISSNEX SF Lunch Seminar - Data Mining in Genomics

Genomic Research and Personalised Health Strategies

Resources | Standards | Protocols | Tools | Discourse

These are the slides of a short presentation, given (virtually, since COVID-19) for a SWISSNEX San Francisco lunch meeting.

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BBOP Presentation - Baudisgroup Projects & Interests

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ELIXIR Beacon Project - Networking Resources Across and Beyond ELIXIR Human Data Communities

ELIXIR Open Day - Wellcome Trust Genome Campus Hinxton

Michael Baudis

In this presentation I introduce the Beacon project and provide my opinions about its future trajectory, and especially its role in driving the alignment of ELIXIR and GA4GH projects in related to (human) genome data sharing.

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GA4GH SchemaBlocks for Human Cell Atlas

This is a presentation of the SchemaBlocks initiative and the overall GA4GH context, for the Human Cell Atlas project, given by Michael at one of their teleconferences.

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Talk at St. Gallen Radiation Oncology - Bioinformatics and Data Exchange

3rd St. Gallen Radiation Oncology Informatics Meeting

Bioinformatics and data exchange for genomics in an international context

Michael Baudis

The presentation at the St. Gallen meeting introduced the audience to the group's research and resources, and how this is connected to the different national & international data standards and sharing initiatives.

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Talk at AMED Tokyo - Cancer Genomics and Standards

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

At this meeting, several Japanese participants presented their research and results, with a focus on Copy Number Variants and other structural genome variations. Continue reading

Minimum Error Calibration and Normalization for Genomic Copy Number Analysis

BC2 2019, Basel

Bo Gao

Abstract

Background:
Copy number variations (CNV) are regional deviations from thenormal autosomal bi-allelic DNA content. While germline CNVs are a majorcontributor to genomic syndromes and inherited diseases, the majority of cancersaccumulate extensive ”somatic” CNV (sCNV or CNA) during the process ofoncogenetic transformation and progression. While specific sCNV have closelybeen associated with tumorigenesis, intriguingly many neoplasias exhibitrecurrent sCNV patterns beyond the involvement of a few cancer driver genes.Currently, CNV profiles of tumor samples are generated using genomicmicro-arrays or high-throughput DNA sequencing. Regardless of the underlyingtechnology, genomic copy number data is derived from the relative assessmentand integration of multiple signals, with the data generation process being proneto contamination from several sources. Estimated copy number values have noabsolute and linear correlation to their corresponding DNA levels, and the extentof deviation differs between sample profiles which poses a great challenge fordata integration and comparison in large scale genome analysis. Continue reading

Cancer cell lines in focus: somatic copy number & germline variation

BC2 2019, Basel

Qingyao Huang

Abstract

Background:
Human cell lines are convenient model systems in cancer research, for validation of proposed molecular mechanisms as well as to evaluate potential therapeutic approaches, e.g. through high- throughput screening of potential anti-tumour compounds against cancer cell line panels. However, conclusions about biological pathways or pharmacological potential depend on a close molecular relation between the cancer type represented and the cell line model used for analyses. Continue reading

Structural Genome Variants in Cancer: Research, resources standards

Seminar at the University of Florence

Seminar Universita degli Studi Firenze - Dipartimento di Biologia

Structural Genome Variants in Cancer: Research, resources standards

Michael Baudis

Abstract

Genomic copy number variations are major contributors to malignant transformation and progression and constitute - at least in their quantitative extension - the largest contributors to genomic mutation landscapes, in the majority of cancer types. Such mutations occur in the vast majority of tumors as somatic genome alterations (sCNV) during clonal development and expansion and are promoted by a variety of mechanisms leading to extended or focal changes in the number of genomic segments. Continue reading

ELIXIR All Hands - Beacon Introduction

Michael Baudis

This presentation was the opener for the ELIXIR Beacon session, and introduces to current developments and especially the interactions between GA4GH :: Discovery and ELIXIR Beacon.

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HGVS 2019 - Development of Standards for Genomic Data Exchange

Human Genome Variation Society - Gothenburg 2019

Implementation Driven Development of Standards for Genomic Data Exchange from Cancer Genome Data Collections

Michael Baudis

Abstract

Cancers are genomic diseases, arising from the clonal propagation of somatic mutation events, with a limited contribution from inherited genomic variants. Genomic copy number variations are major contributors to malignant transformation and progression and constitute - at least in their quantitative extension - the largest contributors to genomic mutation landscapes, in the majority of cancer types. Continue reading

Connecting the silos - Genomic Data Standards, Resources and the Global Alliance for Genomics and Health

R&D Data Intelligence Leaders Forum Basel

Michael Baudis

Abstract

This presentation discusses the need for data sharing in genomics, provides information about the Global Alliance for Genomics and Health (GA4GH), and shows some of our group's contributions, especially regarding Beacon development.

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2018 09 18 BIO390 Michael Baudis Introduction to Bioinformatics

UZH BIO390 "Introduction to Bioinformatics"

Bioinformatics - Introduction

Michael Baudis

Abstract

First lecture in the UZH BIO390 "Introduction to Bioinformatics" series, introducing concepts and scope of bioinformatics as a field - 2018 version.

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ECCB 2018 - Beacon

Abstract: ECCB 2018

ELIXIR Beacon - A Driver Project for the Global Alliance for Genomics and Health

Michael Baudis for the ELIXIR Beacon Project

The Global Alliance for Genomics and Health (GA4GH) develops standards and guidelines to facilitate the international sharing of genomic and health related metadata. The creation of GA4GH work stream products is moved forward through driver projects, which address particular scientific, technical, regulatory or security related aspects of data access and sharing. Continue reading

Qingyao - Institute Progress Report

IMLS Progress Report

Towards understanding population effect on cancer

Qingyao Huang

Abstract

With a combination of ~50,000 curated oncogenomic array data from the arrayMap database and ~20,000 profiles from TCGA project depository, we perform a meta- analysis to investigate influence of genetic background on the CNV patterns in cancer. From sequencing data of 26 world-wide populations from 1000 Genomes project, we extract the SNP markers and use them for subsequent sample analysis. Continue reading

The ELIXIR Beacon in 2018: A driver project of GA4GH

ELIXIR All Hands, Berlin

Michael Baudis

Abstract

The core mission of the Global Alliance for Genomics and Health is to "...enable genomic data sharing for the benefit of human health". One of the instruments to enact this mission is the selection and support of driver projects, which address particular scientific, technical, regulatory or security related aspects of federated access to human genomes and related metadata. Continue reading

segment_liftover : a Python tool to convert segments between genome assemblies

Abstract: ELIXIR All Hands 2018

Bo Gao, Qingyao Huang and Michael Baudis

The process of assembling a species’ reference genome may be performed in a number of iterations, with subsequent genome assemblies differing in the coordinates of mapped elements. The conversion of genome coordinates between different assemblies is required for many integrative and comparative studies. While currently a number of bioinformatics tools are available to accomplish this task, most of them are tailored towards the conversion of single genome coordinates. When converting the boundary positions of segments spanning larger genome regions, segments may be mapped into smaller sub-segments if the original segment’s continuity is disrupted in the target assembly. Continue reading

ELIXIR Beacon - A Driver Project for the Global Alliance for Genomics and Health

Abstract: ELIXIR All Hands 2018

Michael Baudis for the ELIXIR Beacon Project

The core mission of the Global Alliance for Genomics and Health is to "...enable genomic data sharing for the benefit of human health". One of the instruments to enact this mission is the selection and support of driver projects, which address particular scientific, technical, regulatory or security related aspects of federated access to human genomes and related metadata.

The "Beacon" project had been initiated at the first GA4GH plenary in 2014, to test the willingness of genome resource providers to allow web-based queries in the most simple format, against aggregated genome variant data. While this particular model had limited practical utility, it established the foundation for automated queries against world-wide data resources, using a unified protocol. A secondary aspect of the Beacon project was the, intentional, challenge of existing notions of data security and privacy protection, including possible re-identification attacks and risk mitigation scenarios.

Now continued through the ELIXIR-Beacon GA4GH driver project, extensions to the Beacon protocol will provide real-world utility for genome resource access under a number of different usage scenarios. With its support for developing the Beacon protocol and distributing it throughout its members, ELIXIR is providing one of the first, widespread implementations of a GA4GH related products. Additionally, the upcoming version of the Beacon protocol is expected to be one of the first official standards which underwent the GA4GH product approval process, facilitating widespread international adoption.

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Biocuration for cancer genome databases: arrayMap and Progenetix

Abstract: ELIXIR All Hands 2018

Paula Carrio Cordo and Michael Baudis

Screening for somatic mutations in cancer has become integral to diagnostic and target evaluation for personalized therapeutic approaches. arrayMap is a curated oncogenomic resource, focusing on copy number aberration (CNA) profiles derived from genomic arrays. The information has been processed from data accessed through NCBI’s Gene Expression Omnibus (GEO), EBI’s ArrayExpress, and, importantly, through targeted mining of publication data. Whereas this database is based on raw probe data sets, the parental project, Progenetix, allows for genome variant analysis from additional sources and serves as metadata reference. Continue reading

ELIXIR All Hands 2018 - arrayMap

Abstract: ELIXIR All Hands 2018

Update on arrayMap Cancer Genome Resource

Qingyao Huang and Michael Baudis

arrayMap is a cancer-related genome profile database, curated from public data repositories. The resources’s data processing pipelines handle the homogeneous conversion of available raw data from various genomic array platforms (e.g. cCGH, SNP) and represents pre-computed copy number variation (CNV) profiles, allowing the evaluation of target gene involvement as well as the comparative analysis of whole-genome CNV patterns, e.g. for assessing between-sample CNV heterogeneity and associate sets of similar patterns with metadata qualifiers such as diagnostic classifications. In addition to the representation of cancer-related samples, we also plan to generate copy number profiles from non-cancer samples, in an effort to represent population-related CNV patterns. Continue reading

Genomic profiles of cancer cell lines - A systematic review

Abstract: ELIXIR All Hands 2018

Rahel Paloots, Qingyao Huang, Paula Carrio Cordo and Michael Baudis

Human cell lines are convenient model systems in cancer research, for validation of proposed molecular mechanisms as well as to evaluate potential therapeutic approaches, e.g. through high-throughput screening of potential antitumor compounds against cancer cell line panels. Thousands of established cell lines are available from commercial or academic providers, covering a wide selection of cancer types. However, conclusions about biological pathways or pharmacological potential depend on a close molecular relation between the cancer type represented and the cell line model used for analyses. Continue reading

2018 02 15 talk DPPH michael

DPPH - Data Protection in Personalized Health 2018, Lausanne

Genome Beacons for Data Discovery - Technical advances in a challenging environment

Michael Baudis

Abstract

The core mission of the Global Alliance for Genomics and Health is to "...enable genomic data sharing for the benefit of human health". One of the instruments to enact this mission is the selection and support of driver projects, which address particular scientific, technical, regulatory or security related aspects of federated access to human genomes and related metadata. The "Beacon" project had been initiated at the first GA4GH plenary in 2014, to test the willingness of genome resource providers to allow web-based queries in the most simple format, against aggregated genome variant data. While this particular model had limited practical utility, it established the foundation for automated queries against world-wide data resources, using a unified protocol. A secondary aspect of the Beacon project was the, intentional, challenge of existing notions of data security and privacy protection, including possible re-identification attacks and risk mitigation scenarios. Now continued through the ELIXIR-Beacon GA4GH driver project, extensions to the Beacon protocol will provide real-world utility for genome resource access under a number of different usage scenarios, some of which will be addressed in this presentation.

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2017 12 07 talk timisoara michael

Special seminar at University of Timisoara Dermatology

Cancer Genome (Data) Analysis in Personalised Medicine

Michael Baudis

Abstract

General presentation about challenges and possibilities of cancer genome screening for medical applications.

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2017 12 01 talk lszgs michael

UZH Cancer Biology course "Research with clinical samples

Personalised Medicine - Genome Variation / Data Formats / Resources / Sharing / Privacy

Michael Baudis

Abstract

Personalised Medicine - Genome Variation / Data Formats / Resources / Sharing / Privacy, presented for PhD program in Cancer Biology

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Developing Beacons for Data Discovery

GA4GH 2017 Plenary - Workstream Day

Michael Baudis

  • presenting concepts on how to advance the Beacon protcol for practical use cases
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UZH BIO390 - Introduction to Bioinformatics

Michael Baudis

Abstract

First lecture in the UZH BIO390 "Introduction to Bioinformatics" series, introducing concepts and scope of bioinformatics as a field.

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Advancing the Global Alliance for Genomics and Health data schemas through data-driven implementations

[BC]2 2017 - Basel Computational Biology Conference

###$ Michael Baudis

Abstract

The core mission of the Global Alliance for Genomics and Health (GA4GH) is to advance the utility of biomedical data through facilitating of federated analyses, across geographic, regulatory and technical boundaries. A central component is the development of standardised data schemas and application programming interfaces (APIs), for molecular screening data as well as biological and technical metadata. Continue reading

Somatic CNV databases as resources for cancer research && GA4GH schema development

Seminar at SDU Odense

Michael Baudis

  • Presentation about pProgenetix and the group's research projects
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GA4GH Metadata & Beyond

ELIXIR All Hands, Rome

Michael Baudis

Presentation about GA4GH metadata standards work

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Personalized medicine in cancer

Seminar - Stanford Center for Genomics & Personalized Medicine

Michael Baudis

Abstract

Some reasoning for the need of genome profiling data in cancer and reference samples, and our own work on structural aberration data in cancer as well as contributions to the projects and standard definitions of the Global Alliance for Genomics and Health

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Implementing Data Models for the Global Alliance for Genomics and Health

Brupbacher Meeting 2017

Bo Gao

Abstract

Poster about our implementation studies for testing and developing data schemas and resources for the Global Alliance for Genomics and Health, based on data from our arrayMap resource

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Genome data access - Application to personalized health and cancer research

R&D Data Intelligence Leaders Forum Basel

Michael Baudis

Abstract
  • Discussing genome data access, with focus ion cancer, GA4GH and own contributions
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Cancer Genome (Data) Analysis

Antrittsvorlesung Universität Zürich - Inaugural Lecture at University of Zurich

Michael Baudis

Abstract
  • General lecture introducing the "Why"s of cancer genome analysis and some specific problems, as well as some of our own contributions
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Personalized medicine in cancer

LSZGS Cancer Biology course 2016

Michael Baudis

Abstract

Lecture as part of the LSZGS Cancer Biology PhD program, touching some aspects of cancer genome data analysis (why, amount and cost of genome sequencing, genome variation, privacy & data sharing ...

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Harvesting Cancer Genome Data

Biocuration 2016, Geneva

Michael Baudis

Abstract

While the analysis of cancer genomes using high-throughput technologies has generated tens of thousands of oncogenomic profiles, meta-analyses of datasets is greatly inhibited through limited data access, technical fragmentation and a multitude of raw data and annotation formats.

For the arrayMap cancer genome resource, our group collects, re-processes and annotates cancer and associated reference data from genomic array experiments, retrieved from public repositories (e.g. NCBI GEO, EBI ArrayExpress) as well as from publication supplements and through direct requests to the primary producers. Continue reading

Gene-based analysis of focal copy number aberration patterns in cancer genomes

VIB Conference "Applied Bioinformatics in Life Sciences"

Saumya Gupta

Poster about the project to evaluate focal copy number variants in cancer, based on data from arraymap.org

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BCATS 2001 - progenetix.net: storage and visualization of genomic aberration data in human malignancies

First BCATS Meeting - Biocomputing @ Stanford 2001

Michael Baudis

Note Down memory lane, for historical reference: The first public presentation of the Progenetix database.

Abstract

Over the last decade, techniques for the genome wide scanning for genomic imbalances in malignant neoplasia have been developed, e.g. Comparative Genomic Hybridization (CGH).

Currently, no comprehensive online source for CGH data with a standardized format suitable for data mining procedures has been made available for public access. Such a data repository could be valuable in identifying genetic aberration patterns with linkage to specific disease entities, and provide additional information for validating data from large scale expression array experiments. Continue reading