Drs. Tuuli Lappalainen and Julio Saez-Rodriguez
This seminar is a joint event between the Sven Furberg seminars in Bioinformatics and Statistical genomics and the Hans Prydz Guest Lectures.
The two lectures will be presented by Dr. Tuuli Lappalainen, Junior Investigator and Core Member at the New York Genome Center, and Assistant Professor in the Department of Systems Biology at Columbia University, New York, USA, and Dr. Julio Saez-Rodriguez, Professor of Computational Biomedicine at the RWTH-Aachen University Hospital, Aachen, German, and visiting group leader at the EMBL-EBI.
Dr. Tuuli Lappalainen's lecture
Dr. Tuuli Lappalainen will present the lecture entitled "Functional variation in the human genome: lessons from the transcriptome."
Detailed characterization of cellular effects of genetic variants is essential for understanding biological processes that underlie genetic associations to disease, as well as basic genome function. One approach to address this challenge is map genetic effects on the transcriptome across multiple human tissues and conditions. In this talk, I will discuss our recent work in integrated analysis of genome and transcriptome variation as a powerful approach to understanding genetic variants, their variable penetrance, and their contribution to human disease.
Dr. Tuuli Lappalainen did her PhD at the University of Helsinki, Finland, under the supervision of Drs. Kere, Lahermo, and Huoponen. In 2009, she started her postdoc at the University of Geneva, Switzerland, with Dr. Dermitzakis. Then she joined Stanford University in 2013 for a postdoc with Dr. Bustamante. Since 2014, she launched her own group as a Junior Investigator and Core Member at the New York Genome Center, and Assistant Professor in the Department of Systems Biology at Columbia University, New York, USA. During the years she has taken part in leading research as an important contributor of international consortia in human genomics, including the 1000 Genomes Project, the Genotype Tissue Expression (GTEx) Project, and the Geuvadis Consortium.
Dr. Julio Saez-Rodriguez' lecture
Dr. Julio Saez-Rodriguez will present the lecture entitled "Understanding and predicting drug efficacy in cancer: from machine learning to biochemical models."
Large-scale genomic studies provide unprecedented insights into the molecular basis of cancer, but it remains challenging to leverage this information for the development and application of therapies. We analysed the molecular profiles of over 11,000 primary tumours and 1,000 cancer cell lines, along with the response of the cell lines to 265 anti-cancer compounds. We identified alterations in tumours that confer drug sensitivity or resistance, shedding light on which data types are most informative to prioritize treatment. Integration of this data with prior knowledge on signaling pathways and transcription factors points at molecular processes involved in resistance mechanisms, and offer hypotheses for novel combination therapies. Our own analysis as well as the results of a crowdsourcing effort (as part of a DREAM challenge) reveals that prediction of drug efficacy is far from accurate, implying important limitations for personalised medicine. I will argue than an important aspect that needs to be further studied is the dynamics of signaling networks and how they response to drug treatment. I will show how applying logic models, trained with phosphoproteomic measurements upon perturbations, can further improve our understanding of the molecular basis of drug resistance, thereby providing new treatment opportunities not noticeable by static molecular characterisation.
Dr. Julio Saez-Rodriguez did his PhD at the Max Planck Institute and University of Magdeburg, Germany, under the supervision of Dr. Gilles. In 2007, he started his postdoc at Harvard Medical School and MIT, with Peter Sorger and Doug Lauffenburger. He became a group leader at EMBL-EBI in 2010, with a joint appointment in the EMBL Genome Biology Unit in Heidelberg as well as a senior fellow at Wolfson College, Cambridge, UK. Since 2015, he is currently professor at RWTH Aachen Univeristy, Aachen, Germany.
The guest lectures will be preceded by a talk given by Dr. Jonas Paulsen, postdoctoral fellow in Dr. Collas' group at the Institute of Basic Medical Sciences, University of Oslo. He will be presenting the talk entitled "TAD cliques shape the 4D genome during dual-lineage terminal differentiation."