Chair of Experimental Bioinformatics
Technical University of Munich
Systems Medicine - The next generation of computer-assisted precision medicine
Recent advances in modern OMICS technology allow measuring the expression of all kinds of biological entities (genes, proteins, metabolites, miRNAs, etc.) at low cost and in high-throughput. Computational challenges for analyzing such big data emerge, ranging from the low signal to noise ratio to high model complexity, which render simple statistical questions arbitrarily complicated. We will discuss several bioinformatics tools for de-isolating biological networks and multiple OMICS data types: de novo pathway enrichment, in vitro high-throughput screening (HTS) data integration, time-course network enrichment, cancer subtyping, and breath analysis. Using Huntington’s disease patients’ expression data we will employ a guilt-by-association approach to illuminate the power of molecular networks to identify novel disease mechanisms. We will then extend this principle to study HTS data gained from large-scale drug screens, siRNA knock-down and CRISPR/CAS9 knock-out screens, as well as microRNA screens. In addition, we will show how to unravel temporal systems-level response patterns using whole-genome time-series gene expression profiles of lung cells after Influenza infection. We discuss how this kind of computational network biology has strong potential to enable precision medicine by classifying breast cancer subtypes utilizing complex combo-features gained from combining networks with multiple OMICS data. Finally, we will show how modern image analysis technology can be used for non-invasive precision medicine by profiling metabolic patterns in human breath from COPD and lung cancer patients.
Jan Baumbach studied Applied Computer Science in the Natural Sciences at Bielefeld University in Germany. His research career started at Rothamsted Research in Harpenden (UK) where he worked on computational methods for the integration of molecular biology data. He returned to the Center for Biotechnology in Bielefeld for his PhD studies on the reconstruction of bacterial transcriptional regulatory networks. He developed CoryneRegNet, the reference database and analysis platform for corynebacterial gene regulations. Afterwards, at the University of California at Berkeley, he worked in the Algorithms group of Richard Karp on protein homology detection. In Berkeley, he also developed Transitivity Clustering, a novel clustering framework for large-scale biomedical data sets. Since March 2010, Jan was head of the Computational Systems Biology group at the Max Planck Institute for Informatics in Saarbrücken, Germany. In October 2012, he moved to the University of Southern Denmark as head of the Computational BioMedicine group. His current research concentrates on the combined analysis of biological networks together with multiple OMICS data as well as the development of computational methods for precision medicine. In January 2018 he moved to the Technical University of Munich as chair of Experimental Bioinformatics.
Prof. Dr. Philippe C. Cattin
Department of Biomedical Engineering, University of Basel, Switzerland
Philippe Cattin was born in Switzerland in 1967. He received his B.Sc.
degree from the University of Applied Science in Brugg/Wind
isch in 1991. In 1995 he received the M.Sc. degree in computer science
and in 2003 the Ph.D. degree in robotics from ETH Zurich, S
witzerland. From 2003 to 2007 he was a Postdoctoral Fellow with the
Computer Vision Laboratory at ETH Zurich. In 2007 he became an
Assistant Professor at the University of Basel and was promoted to
Associate Professor in 2015. He is the founder of the Center f
or medical Image Analysis and Navigation (CIAN) group at the Medical
Faculty of the University of Basel. He is currently heading t
he recently founded Department of Biomedical Engineering at the
University of Basel. Philippe just was this year a Research Fellow
at Brigham and Women's Hospital in Boston/MA.
His research interests include medical image analysis, image-guided
therapy, robotics-guided laser osteotomy and virtual reality.
As a Principal Investigator he has finished many projects in these areas
and published over 100 papers, patents and book chapters.
He is also the founder of two spin-off companies and licensed his
patents and software to medtech companies.
PhD, IEEE Fellow,
Professor of Biomedical Image Computing,
CISTIB Centre for Computational Imaging & Simulation Technologies in Biomedicine,
The University of Sheffield, UK
Precision imaging: from population imaging analytics to in silico clinical trials
will be sent later as we get closer to the dates.
Alejandro (Alex) obtained his undergraduate degree in Telecommunications Engineering from the Technical University of Catalonia (Barcelona) in 1996. In 2001, he obtained his PhD in Radiology at the Image Sciences Institute of the University Medical Centre Utrecht on model-based cardiovascular image analysis. During this period he was visiting researcher at the Imperial College in London, UK, and in Philips Medical Systems BV, The Netherlands.
Prof Frangi has main research interests lay at the crossroad of medical image analysis and modelling with emphasis on machine learning (phenomenological models) and computational physiology (mechanistic models). He has particular interest in statistical methods applied to population imaging and in silico clinical trials. His highly interdisciplinary work has been translated to the areas of cardiovascular, musculoskeletal and neuro sciences. He been principal investigator or scientific coordinator of over 25 national and European projects, both funded by public and private bodies totalling over £ 45M over the last 15 years.
Prof Frangi has edited several books, published 7 editorial articles and over 190 journal papers in key international journals of his research field and more than over 200 book chapters and international conference papers. He was General Chair for ISBI 2012 held in Barcelona and is the General Chair of MICCAI 2018 to be held in Granada, Spain. Prof Frangi is Chair of the Editorial Board of the MICCAI-Elsevier Book Series (2017-2020), and serves as Associate Editor of IEEE Trans on Medical Imaging, Medical Image Analysis, SIAM Journal Imaging Sciences, Computer Vision and Image Understanding journals. Prof Frangi is a recipient of the IEEE Engineering in Medicine and Biology Early Career Award in 2006. He also was awarded the UPF Medal (2011) for his service as Dean of the Escuela Politècnica Superior, and the ICREA-Academia Prize by the Institució Catalana de Recerca i Estudis Avançats (ICREA) in 2008
Under his leadership, CISTIB develop GIMIAS and MULTIX, two open-source platforms for rapidly developing pre-commercial software prototypes in the areas of image computing and image-based computational physiology modelling, and for the extraction of quantitative image analysis and modelling of large-scale imaging databases, respectively.
Dr. Zeike Taylor
CISTIB Centre for Computational Imaging and Simulation Technologies in Biomedicine, The University of Sheffield.
Dr Zeike Taylor is a Senior Lecturer in Mechanical Engineering at the University of Sheffield, and a member of the CISTIB Centre for Computational Imaging and Simulation Technologies in Biomedicine, with expertise in computational methods for real-time surgical modelling. He has co-authored over 80 peer-reviewed journal and conference papers in areas of biomedical simulation and image computing, particularly focused on applications in surgical simulation, planning, and guidance. He is the original architect of the NiftySim simulation package, leads the Intervention Planning and Real-Time Computational Update theme within the EPSRC UK Image-Guided Therapies Network+, and is a Steering Committee member of the EPSRC-NIHR HTC Medical Image Analysis Network. He is also PI/co-I on various national and European projects.