First AUB Biomedical Engineering Winter School
FEBRUARY 19-20, 2015

The Joint FEA/FM Biomedical Engineering Program and the Center for Advanced Mathematical Sciences (CAMS) at AUB cordially invite you to the First AUB Biomedical Engineering Winter School. The event will take place over two days and will feature four international distinguished lecturers giving tutorials on emerging topics in Biomedical Engineering. The tutorials will highlight the importance of mathematical and computational modeling in biomedical research at the molecular and physiological levels with cardiovascular, cancer, and neural clinical applications. Each tutorial will be divided into two parts: the first part will cover basics and fundamentals, whereas the second part will cover state-of-the-art research findings and open research directions.

Dr. Bart Bijnens

Universitat Pompeu Fabra, Barcelona, Spain

Cardiovascular Computational Modeling: From Imaging to Clinical Applications

The modelling of organs in health and disease has rapidly evolved over the past years. In this tutorial, we will discuss the state of the art in modelling of the cardiovascular system. Since all physiological modelling starts from realistic data, we will first give an overview of current medical imaging modalities and how they can provide information over the cardiac and vascular anatomy, function and remodelling induced by disease. This includes the standard clinical applications and tools as well as contemporary approaches to produce highly detailed data, on the macro- as well as the micro-structure, for research purposes. Using statistical atlas based approaches, information obtainable from imaging can be complemented with information about e.g. the microstructure of the electrical activation system or the fibre-like distribution of the contractile cells in the heart muscle. Next an overview of different approaches for computational modelling of the cardiovascular system will be provided. This will go from ‘simple’ lumped models to high-resolution complex finite element approaches. For studying the vascular systems, 0D and 1D models, describing pressure-flow relations, as well as Computational Fluid Dynamics applications will be shown and how these can be used to e.g. study dissections of the aorta, cerebral aneurisms or remodelling of the vasculature induced by insults during fetal development. For assessing the heart, different approaches allow to address different applications. With lumped models, cardiac function and especially its adaptation to different conditions (e.g. exercise, coronary artery disease,…) can be assessed. Using finite element approaches, both the detailed electrical activation as well as muscle deformation and overall performance can be simulated, for example in case of abnormalities of the conduction system. These approaches can also be used in modelling the anisotropic behaviour of individual cells. During the tutorial, a major focus will be on how advanced imaging and computational modelling can help in understanding physiology and how disease induces remodelling as well as how this can be used to select and improve therapy in individual patients.

Bart Bijnens graduated as Master of Electro-Mechanical Engineering Sciences at the KULeuven, Belgium, and obtained a PhD in Medical Sciences on advanced echocardiographic data acquisition and analysis. He became Associate Professor at the Medical Faculty of the KU Leuven, where he established a Cardiac Imaging Research Group. He extended his experience in a mixed research/hospital management position in St. George’s Hospital in London (UK) and established a new interdisciplinary Cardiology-Engineering research group in Zagreb (Croatia). Currently he is ICREA Research Professor at the Universitat Pompeu Fabra, Barcelona, Spain where he is performing multidisciplinary research in cardiovascular patho-physiology and image analysis/modelling. His research interests are Translational Cardiovascular Pathophysiology, focussing on assessing cardiac function and understanding and recognising the changes induced by disease and how treatment strategies can be used to modulate this remodelling. He is author of >150 peer reviewed papers in International Journals (both in Medicine and Engineering) having an h-index >36 (ISI) and 46 (Google Scholar), >70 full proceedings papers in International Conferences and over >350 abstracts at International Conferences and >130 invited lectures. Most of the research was performed in the field of Cardiac Imaging, Mechanics and Physiology and in close collaboration with clinical researchers. He is involved in several research project, among which the EU FP7 project VP2HF investigating computer model derived indices for optimal patient-specific treatment selection and planning in Heart Failure.

Dr. Janos Vörös

ETH Zurich, Switzerland

Bioelectronic Devices that Interact with Biology at the Micro-Nano Scale

Micro- Nanotechnology has enabled the informatics and communication revolution by contributing to the quantitative understanding, miniaturization and manufacturing of semiconductor devices. Can a similar approach help us addressing biological and medical problems? Many new concepts and nanodevices emerge that can address serious problems in biomedicine. Several examples for such concepts will be presented in this talk with special focus on tools that can be used to interact with biological molecules, cells and the human body: The first part of this tutorial will introduce the fundamental limitations of biosensors with typical thought experiment examples. This will be followed by experimental results that illustrate the possibilities of nanotechnology in overcoming the conventional limits. A possible explanation will be derived using standard Langmuir equilibrium assumptions. Besides sensing, nanotechnology also provides the possibility to interface cells in their natural environment at the nanometer scale. The FluidFM is a nanosyringe that can be used to inject, patch, or manipulate single cells without compromising their integrity. Such a tool proves also highly useful for fundamental neurosciences: Neurons can be precisely positioned and the outgrowth of neurites and axons can be controlled in situ by locally replacing cell-repellent polymers to cell-adhesive molecules. Finally, a new class of electronic devices based on stretchable materials can interact with the soft human body in an unprecedented manner. Stretchable and biocompatible microelectrode arrays can be used to stimulate intact spinal cord circuits below an injury to control the movement of the limbs aiding rehabilitation and increasing recovery of spinal-cord injured patients.

János Vörös is a Professor in the Institute for Biomedical Engineering of the University and ETH Zurich (Department for Information Technology and Electrical Engineering) heading the Laboratory for Biosensors and Bioelectronics since 2006. János Vörös has studied Physics at the Eötvös Loránd University in Budapest. After receiving a diploma in Physics in 1995, he was a doctoral student at the Department of Biological Physics of the Eötvös University (in collaboration with Microvacuum Ltd.) where he received his PhD in Biophysics in 2000. Since 1998 he was a member of the BioInterface group in the Laboratory for Surface Science and Technology at the Department of Materials of ETH Zurich as visiting scientist, postdoc, and from 2004 as group leader of the Dynamic BioInterfaces group until 2006. Prof. Vörös also has an adjunct appointment at the Department of Engineering Science and Mechanics of the Pennsylvania State University. Prof. Vörös is interested in research and teaching in the areas of Biosensors, Bioelectronics, Nano-Biotechnology, Biophysics, Biomaterials and Neurosciences with special focus on the understanding, monitoring and controlling of molecular and cellular processes at biological interfaces. His research group focuses on the development of novel biosensor techniques for diagnostics and drug discovery; on using nanobiotechnology for interfacing neural networks; as well as on implanted stretchable electronic devices.

Dr. Byung-Jun Yoon

Texas A&M University, College Station, TX, USA & HBKU, Doha, Qatar

Mathematical Models and Computational Methods in Biomedical Research

Recent advances in high-throughput experimental techniques for sequencing genomes, measuring gene expression, and identifying molecular interactions have enabled the systematic study of the genome, transcriptome, and interactome of living organisms on a global scale. This tutorial aims to provide a broad overview of various mathematical models and computational techniques that have been recently applied to biomedical research and to show how such computational methods can be used for effectively analyzing biological data and gaining novel insights into biological organisms; especially, the function and structure of biomolecules, the functional organization and dynamics of biological networks, and the complex regulatory mechanisms that underlie various biological processes. In the first part of the tutorial, we will briefly review several probabilistic models and computational methods that have been widely used in bioinformatics and computational biology. Following the review, in the second part of the tutorial, we will present some of the important research activities, applications, and recent trends in computational biomedical research.

Dr. Byung-Jun Yoon received the B.S.E. (summa cum laude) degree from the Seoul National University, Seoul, Korea, in 1998, and the M.S. and Ph.D. degrees from the California Institute of Technology, Pasadena, in 2002 and 2007, respectively, all in Electrical Engineering. In 2008, he joined the Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, where he was an Assistant Professor during 2008-2014 and an Associate Professor since 2014. Recently, Dr. Yoon joined the College of Science, Engineering, and Technology at the Hamad bin Khalifa University (HBKU), Doha, Qatar, as a founding faculty member, where he is currently an Associate Professor. His recent honors include the National Science Foundation (NSF) CAREER Award and the Best Paper Award at the 9th Asia Pacific Bioinformatics Conference (APBC). His main research interests include genomic signal processing (GSP), bioinformatics, and computational network biology.

Dr. Muhammad H. Zaman

Boston University, USA

Understanding Tumor Invasion: Tools Rooted in Multi-Scale Modeling and Mechanobiology

Cell migration and cell-matrix interactions regulate some of the most critical stages of tumor invasion and metastasis, which is responsible for nearly all cancer related deaths. However, our understanding of the systems level behavior of these processes is often plagued by culturing cells in artificial environments, focusing on a single protein or ignoring the interplay between cell-signaling and cellular mechanics. To quantitatively understand complex cellular and extracellular processes regulating various stages of tumor invasion, we need to utilize multi-disciplinary toolbox rooted in mathematics, physics, mechanics and cellular and molecular biology. This tutorial will aim at understanding and applying these tools. This tutorial will first cast the problem of tumor invasion in a quantitative light and identify fundamental questions that need to be answered. We will then focus on a key question, namely, how do cells move in native 3D environments ? To answer this question, we will utilize tools of multi-scale modeling, that will connect processes from a single protein level, all the way to extra-cellular matrices. This will use a combination of statistical and continuum mechanics, agent based modeling and probability theory. Parallel to these tools, our discussion will focus on new techniques in microrheology to understand cellular interior and mechanics as well as new imaging methods to uncover cellular form and function. Our work will focus on specific examples, both in single and collective cellular environments, in 2D and in 3D, how both passive thermal and active motor-driven processes within the cell control cellular motion. We will also study, during this tutorial results from our lab and other groups that demonstrate the synergistic roles of tension and signaling, dimensionality and disease progression. The final aspect of the tutorial will focus on specific examples as to how this integrated approach of multi-scale modeling and experiments has resulted in discovery of novel mechanisms of collective cellular motion, new regulators of cellular persistence in 3D environments and the role of ECM in modulating chemoresistance in breast and prostate cancer.

Muhammad H. Zaman is Howard Hughes Medical Institute Professor of Biomedical Engineering and International Health at Boston University. He received his PhD from the University of Chicago, where he was Burroughs-Wellcome Interdisciplinary Research Fellow. He then moved to MIT where he worked in the Department of Bioengineering as Herman and Margaret Sokol Foundation Post-Doctoral Fellow in Cancer Research. Prof. Zaman’s current research is focused on two main areas:1)developing novel tools, rooted in engineering, multi-scale modeling and cellular and molecular biology to understand in vivo tumor progression and 2)developing robust technologies for high-value healthcare problems in the developing world. His work has appeared in Science, Nature, Proceedings of the National Academy of Sciences, Physical Review Letters and other high profile journals. He has won numerous awards for his research and teaching from IEEE, FEBS, American Society for Engineering Education, USAID, The US National Academy of Sciences, The University of Texas System, Boston University and other national and international organizations. Most recently, he was named Howard Hughes Professor by the Howard Hughes Medical Institute. His current research is supported by NIH, NSF, USAID, UNECA, CIMIT, Saving Lives at Birth Consortium, and a number of other private foundations. In 2015, he was elected fellow of American Institute of Medical and Biological Engineering (AIMBE), which is among the most prestigious honors for a biomedical engineer. In addition to his research, Prof. Zaman is actively engaged in bringing quality engineering education in several developing nations. He is currently involved in setting up biomedical engineering departments at universities in Kenya, Zambia, Uganda and Ethiopia. He is co-Director of the UN Africa Biomedical Initiative. He is a regular contributor on issues of STEM education and global health for the Project Syndicate, Huffington Post and writes a weekly column on higher education for leading Pakistan daily, Express Tribune (part of International New York Times).


Day 1 – Thursday February 19, 2015

Tutorial 1 [8:30-12:30]: Dr. Muhammad Zaman, “Understanding Tumor Invasion: Tools Rooted in Multi-Scale Modeling and Mechanobiology“

8:00-8:30: Morning coffee

8:30-10:30: Session I

10:30-10:45: Coffee break

10:45-12:30: Session II

12:30-14:00: Lunch break

Tutorial 2 [14:00-18:00]: Dr. Byung-Jun Yoon, “Mathematical Models and Computational Methods in Biomedical Research“

14:00-16:00: Session I

16:00-16:15: Coffee break

16:15-18:00: Session II




Day 2 – Friday February 20, 2015

Tutorial 3 [8:30-12:30]: Dr. Janos Vörös, “Bioelectronic Devices that Interact with Biology at the Micro-Nano Scale“

8:00-8:30: Morning coffee

8:30-10:30: Session I

10:30-10:45: Coffee break

10:45-12:30: Session II

12:30-14:00: Lunch break

Tutorial 4 [14:00-18:00]: Dr. Bart Bijnens, “Cardiovascular Computational Modeling: From Imaging to Clinical Applications“

14:00-16:00: Session I

16:00-16:15: Coffee break

16:15-18:00: Session II

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Seats are limited, priority will be given to faculty members and graduate students