Wednesday, 24 July 2019

Thursday, 25 July 2019

Christine Moissl-Eichinger, PhD

Head of Center for Microbiome Research at Medical University of Graz, Austria
International Space Station and hospital environments: Composition and function of microbiomes in confined built environments – Keynote

Indoor environments, where people spend most of their time, are characterized by a specific microbial community, the indoor microbiome. Most indoor environments are connected to the natural environment, but some habitats are more confined: intensive care units, operating rooms, cleanrooms and the international space station (ISS) are extraordinary living and working areas for humans, with a limited exchange with the environment. All of these man-made confined habitats are microbiologically monitored and controlled. However, these measures might apply constant selective pressures, which support microbes with resistance capacities against chemical and physical stresses and thus might facilitate the rise of survival specialists and multi-resistant strains. In this talk, special characteristics of confined indoor microbiomes will be highlighted, and their specific functions and the consequences thereof will be discussed.

Gunnar Rätsch, PhD

Head of Biomedical Informatics at ETH Zurich, Switzerland
Transcriptome Alterations in Cancer:Challenges and Opportunities – Keynote

I will cover two recent works related to transcriptive aberrations in cancer. In the first part I will describe a comprehensive analysis of alternative splicing across 32 TCGA cancer types from 8,705 patients. We detect alternative splicing events and tumor variants by reanalyzing RNA and whole-exome sequencing data. Tumors have up to 30% more alternative splicing events than normal samples. Association analysis of somatic variants with alternative splicing events confirmed known trans-associations with variants in SF3B1 and U2AF1 and identified additional trans-acting variants. Many tumors have thousands of alternative splicing events not detectable in normal samples; on average, we identified ≈930 exon-exon junctions (“neojunctions”) in tumors not typically found in GTEx normals. I will discuss possible implications for immunotherapies. In the second part, I will discuss an analysis within the contact of the ICGC/PCAWG project. Here we analyzed different transcriptome alterations, including expression, allelic imbalance, RNA-editing, alternative splicing and perform a novel recurrence analysis across RNA alterations that give rise to new insights into oncogenic processes.

About the speaker: Gunnar Rätsch leads the Biomedical Informatics group at the Institute of Machine Learning at ETH Zurich since May 2016. Before, he was an Associate Professor at Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College in New York City, where he will continue to hold adjunct positions for the coming years.
Gunnar Rätsch studied computer science and physics and obtained his Ph.D. degree in Machine Learning in 2001 at the National Institute for Data Analysis in Berlin. As a postdoctoral fellow he was at the Research School of Information Sciences and Engineering of the Australian National University in Canberra (Australia) and at the Max Planck Institute for Biological Cybernetics in Tübingen (Germany). Between 2005 and 2011 he also led a research group at the Friedrich Miescher Laboratory of the Max Planck Society in Tübingen (Germany).
His group’s research at ETH lies at the interface between methods research in machine learning & sequence analysis and relevant application areas in biology & medicine. In interdisciplinary collaborations, his group has significantly contributed to the understanding of several RNA- dependent processes including RNA splicing and translation.
Current research focuses include large-scale Machine Learning, accurate transcriptome reconstruction, identification of RNA-processing regulators, developing clinical decision support systems (analysis of electronic health records (EHR)) and developing methods and resources for international data sharing of genomic and clinical data. He is leading multiple international working groups, including the RNA analysis group of the International Cancer Genome Consortium. He is an active contributor to the Global Alliance of Genomics and Health (GA4GH), an international organization that promotes and technically supports data sharing across institutional and country boundaries. He leads the data group of the BRCA Challenge project, a driver project of GA4GH.