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Data Mining in the Life Sciences The Path to Personalized Medicine Karsten Borgwardt Machine Learning and Computational Biology Research Group Max Planck Institute for Intelligent Systems & Max Planck Institute for Developmental Biology, Tu¨bingen Eberhard Karls Universit¨at Tu¨bingen Machine Learning for Personalized Medicine ITN Summer School September 23-27, 2013 Karsten Borgwardt Data Mining in the Life Sciences September 2013 1 Our FP7 Marie Curie Initial Training Network: MLPM Karsten Borgwardt Data Mining in the Life Sciences September 2013 2 Our Initial Training Network: In Numbers ◮ 6 countries: Belgium, France, Germany, Spain, United Kingdom, United States ◮ 13 ESRs + 1 ER ◮ 12 labs at 10 nodes, 8 academic partners and 2 industrial nodes (Siemens, Pharmatics) ◮ Duration: 4 years, January 2013 — December 2016 ◮ Funding: Up to 3.75 million EUR ◮ 3 years of funding per student ◮ 2 three-month secondments per student ◮ 4 annual summer schools (Tu¨bingen, UK, France, Spain) Karsten Borgwardt Data Mining in the Life Sciences September 2013 3 Our Initial Training Network: As a Map ◮ Pharmatics, Edinburgh ◮ University of Sheffield ◮ University of Li`ege ◮ INSERM and ARMINES, Paris ◮ MPI for Intelligent Systems, Tu¨bingen ◮ MPI for Psychiatry, & Siemens Munich ◮ Universidad Carlos III de Madrid ◮ Prince Felipe Research Centre (CIPF) in Valencia ◮ MSKCC New York Karsten Borgwardt Data Mining in the Life Sciences September 2013 4 Our Initial Training Network: Who is Who? The PIs ◮ Belgium: University of Li`ege (Prof. Kristel Van Steen) ◮ France: ARMINES (Prof. Jean-Philippe Vert), INSERM (Prof. Florence Demenais) ◮ Spain: UC3 Madrid (Prof. Fernando Perez-Cruz), CIPF Valencia (Prof. Joaquin Dopazo) ◮ United Kingdom: University of Sheffield (Prof. Neil Lawrence, Prof. Magnus Rattray - now Manchester), Pharmatics (Dr. Felix Agakov) ◮ United States: MSKCC (Prof. Gunnar R¨atsch) ◮ Germany: Siemens (Prof. Volker Tresp), Max-Planck-Society (Prof. Bertram Mu¨ller-Myhsok, Prof. Bernhard Scho¨lkopf and Prof. Karsten Borgwardt) Karsten Borgwardt Data Mining in the Life Sciences September 2013 5 Our Initial Training Network: Who is Who? The ESRs MPG (Borgwardt) Mr Felipe Llinares-Lo´pez MPG (Borgwardt) Mr Carl-Johann Simon-Gabriel MPG (Scho¨lkopf) Mr James McMurray MPG (Mu¨ller-Myhsok) Ms Meiwen Jia Siemens Mr Cristo´bal Esteban U Sheffield Mr Max Zwießele U Li`ege Ms Ramouna Fouladi ARMINES Paris Mr Yunlong Jiao INSERM Paris Mr Yuanlong Liu UC3 Madrid Ms M´elanie Fern´andez Pradier CIPF Valencia Mr Cancut Cubuk MSKCC Mr Yi Zhong Karsten Borgwardt Data Mining in the Life Sciences September 2013 6 Our Initial Training Network: Our Topics ◮ Research Goal A.1: Biomarker discovery ◮ Research Goal A.2: Data Integration ◮ Research Goal B.1: Causal Mechanisms of Disease ◮ Research Goal B.2: Gene- Environment Interactions Karsten Borgwardt Data Mining in the Life Sciences September 2013 7 The Need for Machine Learning in Computational Biology High-throughput technologies: ◮ Genome and RNA sequencing ◮ Compound screening ◮ Genotyping chips ◮ Bioimaging BGI Hong Kong, Tai Po Industrial Estate, Hong Kong Molecular databases are growing much faster than our knowledge of biological processes. Karsten Borgwardt Data Mining in the Life Sciences September 2013 8 The Evolution of Bioinformatics ◮ Classic Bioinformatics: Focus on Molecules Karsten Borgwardt Data Mining in the Life Sciences September 2013 9 Classic Bioinformatics: Focus on Molecules ◮ Large collections of molecular data ◮ Gene and protein sequences ◮ Genome sequence ◮ Protein structures ◮ Chemical compounds ◮ Focus: Inferring properties of molecules ◮ Predict the function of a gene given its sequence ◮ Predict the structure of a protein given its sequence ◮ Predict the boundaries of a gene given a genome segment ◮ Predict the function of a chemical compound given its molecular structure Karsten Borgwardt Data Mining in the Life Sciences September 2013 10

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