Second AUB Biomedical Engineering Winter School
February 4-6, 2016

The Joint FEA/FM Biomedical Engineering Program and the Center for Advanced Mathematical Sciences (CAMS) at AUB cordially invite you to the Second AUB Biomedical Engineering Winter School. The event will take place over three days and will feature five 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. This event is supported partially under the auspices of the Atiyah Distinguished Visitors Program. A generous gift from the Simons Foundation created the Michael Atiyah Chair in Mathematical Sciences and the Atiyah Distinguished Visitors Program to provide outstanding intellectual scholarship in the Middle East and to stimulate the flow of visiting scholars in the mathematical sciences to AUB.

Dr. Fredrik Höök

Professor/Head of Division, Biological Physics, Chalmers University

Surface-Sensitive Imaging of Cell-Membrane Mimics, Individual Extracellular Vesicles and Virus Particles

Based on the development of the quartz crystal microbalance with dissipation (QCM-D) technique on the mid-90th, my group entered into the field of surface-based studies of cell-membrane mimics. More recently, this line of research was combined with microfluidics and optical microscopy, enabling investigations of direct medical diagnostics and pharmaceutical relevance. Measurements of ligand-binding events to membrane-protein receptors in a near-natural environment display an opportunity in mechanistic studies of cell membranes. With membrane proteins embedded in nanoscale lipid vesicles derived from native cell membranes and detection methods with single molecule sensitivity, information about ligand binding events can be gained in a broad dynamic range, as requested in both drug-screening and diagnostic applications. A diverse set of tools with single-nanoparticle sensitivity is now available, to which we recently contributed a concept that enables simultaneous fluorescent and scattering-based label-free imaging of thousands of surface-bound nanoscale entities. The principle is based on the use of lipid vesicles as enhancer elements in optical waveguide based fluorescence and label-free evanescent-wave scattering microscopy, making the concept compatible with analysis of both water-soluble and cell-membrane bound receptors. The concept is currently evaluated as a diagnostic assay for biomarker detection and in drug-screening applications, previously explored by us using conventional total internal reflection fluorescence (TIRF) microscopy. The use of scattering microscopy in the context of single-enzyme detection in complex biological fluids will be presented, with focus on single-molecule biomarker detection in cerebrospinal fluid from individuals suffering from Alzheimer’s disease. A new means to utilize the two-dimensional fluidity of supported cell-membrane derived lipid bilayers in microfluidic designs for nanoparticle size determination and sorting applications will also be discussed.

Fredrik Höök obtained his Doctors degree of Physics in 1997 from an inter‐disciplinary PhD program between the Department of Applied Physics and the Department of Biochemistry and Biophysics at Chalmers and Gothenburg University, Gothenburg, Sweden. After that he had a one and a half year assistant professor position in surface biotechnology at Cell and Molecular Biology, Gothenburg University, which was in 2000 transferred into an assistant professor position in Biological Physics at the Department of Applied Physics at Chalmers. In 2004 he was appointed a professor position in Nanoscience for Biophysics at the Department of Physics at Lund University and in 2007 he was appointed full professor in Physics at Chalmers.

His research has focused on the development of surface‐based bioanalytical tools, such as QCM‐D, localized SPR and more recently TIRF microscopy and imaging ellipsometry and their combination with microfluidics for fundamental studies of cell‐membrane mimics but also for use in diagnostic, drugscreening applications and the development of drug delivery concepts. Efforts are presently focused on (i) new methods with single molecule sensitivity for studies of single liposomes and individual membrane proteins, (ii) microfluidic platforms for detergent‐free separation of cell‐membrane components and (iii) sophisticated surface modifications and nanofabrication schemes to facilitate improved analysis of supported cell‐membrane mimics, membrane proteins and virus binding.

Fredrik Höök is presently heading the Biological Physics division at Chalmers, which is composed of around 20 scientists on various levels. He has published around 130 scientific papers, has an H‐index of 42, with 20 papers cited more than 100 times and more than 7000 citations in total. He is also cofounder of the companies Q‐Sense AB, LayerLab AB and Gothenburg Sensor Devices AB. He has been awarded the Akzo Nobels Nordic research award in 2002, an individual grant for the Advancement of Research Leaders and in 2005 by the Swedish Foundation for Strategic Research and the prestigious Göran Gustafsson prize in Physics in 2012 by the Royal Swedish Academy of Sciences (KVA). In 2015 he was elected member of The Royal Swedish Academy of Engineering Sciences (IVA).

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Dr. Ghaleb Husseini

Professor of Chemical Engineering, Head of Drug Delivery Lab, American University of Sharjah (AUS)

Drug Delivery and Ultrasound

Chemotherapy is the most extensively used treatment in the fight against malignant neoplasms. Unfortunately, chemotherapy use is plagued with numerous side effects. These side effects are caused primarily because of the non-specific nature of the treatment as the drug is capable of killing normal and cancerous cells alike. Several drug delivery systems have been investigated to reduce these side effects by encapsulating the chemotherapeutic agent in a nano-sized carrier until it reaches the tumor site. These carriers include: solid nanoparticles, micelles, liposomes and e-liposomes. Once the nanoparticle reaches the desired location, ultrasound is applied to release the chemotherapy drug directly to the cancer site, thus avoiding any interaction with the healthy cells in the body. This way the adverse side effects of chemotherapy are minimized. This presentation will discuss two novel chemotherapy carriers (micelles and emulsion-Liposomes) used in conjunction with acoustic radiation to treat malignancies. The tutorial will examine the structure of echogenic micelles and liposomes, the equations governing the use of acoustic power in drug delivery, and will summarize the in vitro and in vivo results when using ultrasound in chemotherapeutic drug delivery.

Dr. Ghaleb Husseini graduated with a PhD in Chemical Engineering (Biomedical Engineering emphasis) from Brigham Young University in 2001 and joined the American University of Sharjah (AUS in the United Arab Emirates) as an Assistant Professor in the Chemical Engineering Department January 2004. He was promoted to Associate Professor and Professor in 2008 and 2013, respectively. Two years ago, Dr. Husseini took a sabbatical leave which enabled me to travel to Ecole Polytechnique Fédérale de Lausanne (EPFL, and work in Dr. Jeffrey Hubbell’s laboratory).

He works is in the area of ultrasound activated drug delivery. His research involves sequestering chemotherapeutic agents in liposomes, micelles and other nanoparticles. The contents of this drug delivery system can then be released using ultrasound (US). This way the drug has minimal interactions with the healthy cells in the host body, and it can carry out its therapeutic effect at the sonicated cancerous region only and reduce the undesirable side effects associated with chemotherapy. He has recently established a Drug Delivery laboratory at AUS using an internal grant.

Dr. Husseini has published 79 journal articles (in addition to 1 book chapter and 1 patent) and 42 conference papers/abstracts. In addition, he was a Theme Editor for a special issue in Advanced Drug Delivery Reviews and is currently serving on the Editorial Board of the International Review of Applied Sciences and Engineering (IRASE). He has been elected into the Distinguished Lecturer Program- IEEE-EMBS (Jan 2014- Dec 2015).

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Dr. Yehia Mechref

Professor of Biochemistry, Texas Tech University

Integrative “Omics” Analyses for the Effective Diagnosis and Prognosis of Human Diseases

Genomics, transcriptomics, proteomics, glycomics, and metabolomics are active and dynamic areas of research that are generating a vast body of biochemical information. The integration of such complex data from diverse bioanalytical techniques to understand the interactions in biological systems is a daunting task commonly referred to as Systems Biology. Many research laboratories are focusing their efforts on the overwhelming task of characterizing proteins and their extensive posttranslational modifications in a similar manner undertaken by the Human Genome Project. Significant advances in biomolecular mass spectrometry, microscale separation science, and bioinformatics have resulted in novel inquiries into the proteomes, glycomes, and metabolomes of physiological fluids and tissues. Bioinformatics has greatly facilitated data interpretation and visualization and has yielded a powerful and informative tool for the Systems Biology field. This presentation will describe and discuss the principles of the different “omics” approaches, including transcriptomics, proteomics, glycoproteomics, and glycomics. The utility and advantage of incorporating a multiple “omics” approach to understand human disease development and progression will be highlighted with our work in breast cancer brain metastasis.

Dr. Yehia Mechref is an internationally renowned researcher in the areas of glycomics and glycoproteomics, which are essential to our understanding of many aspects of human and animal health. His research is focused on the development of exceptionally sensitive instrumental techniques, mainly mass spectrometry, that enable this important area of scientific research world-wide. This research is critical in the understanding of the development and progression of many diseases, including cancer, HIV, and immune system diseases.

The research efforts of Dr. Mechref have culminated in the publication of over 182 scientific papers and book chapters, including 19 review articles, 12 book chapters and 151 peer-reviewed research articles. Dr. Mechref current ISI H-index is 43 with 5254 citations. His research at Texas Tech University is funded by the National Institutes of Health (NIH) and Cancer Prevention and Research institute of Texas (CPRIT), totaling over $2.5M.

Dr. Mechref’s research efforts have brought national and international recognition to Texas Tech University and the State of Texas. Dr. Mechref is an authority in Glycomics and Glycoproteomics. He was recently quoted in a cover story article entitled “Complex Carbohydrates” recently published in Chemical and Engineering News- an ACS magazine. In October 2014, Dr. Mechref was the organizer of the ASMS Asilomar Conference (the 2nd most prestigious conference of the American Society for Mass Spectrometry)

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Dr. Christos Ouzounis

Director of Research, Biological Computation and Process Laboratory, CERTH, Greece

From Reading to Writing (and Rewriting) the Code of Life: Genome, Systems and Synthetic Biology

The deciphering of the genetic code for multiple species across the tree of life has revolutionized research and applications in the life sciences. Ever since the first genomic sequence was published more than twenty years ago, thousands of genomes have been decoded and analyzed at multiple levels regarding their structure, function and evolution. The emerging challenges for the processing and distribution of genomic information have established modern biology as one of the main producers and consumers of big data in a global context. Genome biology has revealed intricate patterns of regulation and deep phylogenetic connections that explain the fundamental architecture of living organisms and their interactions with the environment. Systems biology, in parallel, has exploited these patterns and connections for genome-wide experimentation in model organisms to further our understanding of molecular and cellular processes and their manipulation. In all, the implications of genome and systems biology for biomedical and biotechnological innovation have been immense and are thus paving the way for the direct control of genetic material for the synthesis of engineered biological components. This convergence of the two fields has resulted in the new field of synthetic biology. We will attempt to highlight key contributions from our work and other laboratories on genomic information processing, the coupling of genomics with systems biology and biomedicine, and certain inroads towards a computational approach to synthetic biology with ancestral state reconstructions and metabolic pathway inference.

Prof. Christos Ouzounis is the Director of the BCPL at CPERI-CERTH. He led the Computational Genomics Group at EMBL's European Bioinformatics Institute (Cambridge, United Kingdom) (-2005), the Computational Genomics Unit at CERTH (-2007), and the Centre for Bioinformatics at King's College London (-2010). He is serving as Associate Editor for PLoS Computational Biology, PLoS ONE and BioSystems, as senior editor for Microbial Genomics, has been an Associate Editor for Bioinformatics and currently an Honorary Editor, and an editorial board member of a number of journals and the Faculty of 1000. He is a founding officer of the International Society for Computational Biology (ISCB), the Mikrobiokosmos initiative (Greece), and the Hellenic Society for Computational Biology and Bioinformatics (HSCBB). His scientific interests revolve around genome structure, function and evolution, biological sequence comparison, knowledge representation for genomics, synthetic biology, exobiology, personalized biomedicine, and science communication. He has published over 190 scientific reports, with 13,000 citations and an H-index of 60. Some of his best known contributions in the field of computational genomics include automated sequence annotation, discovery of genome-aware methods, inference of metabolic pathways from genome sequences, development of methods for large-scale clustering of sequence similarities, definition of the Last Universal Common Ancestor (LUCA), quantification of horizontal gene transfer patterns across the ‘net of life’, and applications of computational genomics in biomedicine and biotechnology. He also maintains a strong interest in the development of computational biology as an exemplary paradigm in the history of contemporary science.

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Dr. Walid Soussou

President of Wearable Sensing, CEO of Quantum Applied Science & Research Inc. (QUASAR), CA

Wearable Brain Activity Monitoring: Methods, Applications, and Demonstrations

Over the past decades, concerted neuroscience research and developments in brain activity monitoring technology have revealed new insight into the workings of the brain in dynamic environments, which is propelling new applications for wearable brain activity monitoring in the real-world.

Medically, demand is for early diagnosis on sport or battle fields and long-term home for various neurological disorders, including: Traumatic Brain Injury (TBI), Post-Traumatic Stress Disorder (PTSD), Mild Cognitive Impairment (MCI), Alzheimer’s Disease (AD), … Furthermore, pharmaceutical companies and individual patients are seeking methods for rapid quantification of neuro-active drugs effects outside the lab, whether for treatment of depression, Attention Deficit Hyperactivity Disorder (ADHD), or other neuropsychological ailments. On the consumer side, potential applications of wearable brain activity monitoring are burgeoning into entire fields: Brain Computer Interfaces (BCI), NeuroGaming, NeuroErgonomics, NeuroMarketing, NeuroEducation, Peak-Performance Neurofeedback, Augmented Cognition…

This presentation will highlight some of the engineering and design challenges for wearable brain activity monitoring and discuss innovative commercial solutions to date, and potential future applications of this latest frontier of wearable sensors. The lecture will highlight several types of brain activity measurement modalities, and focus on Electroencephalography (EEG). Basic principles of neuroscience, electrophysiology, signal processing and feature extraction will be discussed in the context of medical and consumer applications. The practical portion of the tutorial will offer hands-on demonstrations of EEG signal acquisition and explore some challenges in Brain Computer Interface (BCI), NeuroFeedback, NeuroMarketing, NeuroEducation, NeuroGaming...

Dr. Walid Soussou, CEO of Quantum Applied Science and Research Inc. (QUASAR), leads and manages QUASAR’s efforts at developing applications of QUASAR’s dry-electrode EEG technology for cognitive state assessment. Dr. Soussou leverages his PhD in Neuroscience from the University of Southern California (USC), expertise in Brain-Computer-Interfaces, and experience in sleep research, for developing commercial applications of QUASAR’s wearable EEG/EOG/EMG/ECG sensors. With funding from NIH, NSF, and DoD, QUASAR has developed a suite of uniquely non-invasive and high-fidelity physiological sensors with interpretive gauges for assessment of cognitive engagement, workload, fatigue, and stress. These sensors and gauges are valuable tools with medical and consumer applications, as they enable monitoring brain activity in real-world environments. As President of Wearable Sensing, which has licensed QUASAR’s Dry Sensor Interface technology, Dr. Soussou is engaged in exploring and developing commercial applications of wearable brain monitoring.

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Day 1 – Thursday February 4, 2016

Tutorial 1 [13:30-17:00]: Dr. Walid Soussou

Wearable Brain Activity Monitoring: Methods, Applications, and Demonstrations

13:00-13:30: Welcome coffee

13:30-15:00: Session I

15:00-15:30: Coffee break

15:30-17:00: Session II



Day 2 – Friday February 5, 2016

Tutorial 2 [9:00-12:30]: Dr. Christos Ouzounis

From Reading to Writing (and Rewriting) the Code of Life: Genome, Systems and Synthetic Biology

8:30 - 9:00: Welcome coffee

9:00 - 10:30: Session I

10:30 - 11:00: Coffee break

11:00 - 12:30: Session II

12:30 – 13:30: Lunch break

Tutorial 3 [13:30-17:00]: Dr. Yehia Mechref

Integrative “Omics” Analyses for the Effective Diagnosis and Prognosis of Human Diseases

13:30-15:00: Session I

15:00-15:30: Coffee break

15:30-17:00: Session II



Day 3 – Saturday February 6, 2016

Tutorial 4 [9:00-12:30]: Dr. Fredrik Höök

Surface-Sensitive Imaging of Cell-Membrane Mimics, Individual Extracellular Vesicles and Virus Particles

8:30 - 9:00: Welcome coffee

9:00 - 10:30: Session I

10:30 - 11:00: Coffee break

11:00 - 12:30: Session II

12:30 – 13:30: Lunch break

Tutorial 5 [13:30-17:00]: Dr. Ghaleb Husseini

Drug Delivery and Ultrasound

13:30-15:00: Session I

15:00-15:30: Coffee break

15:30-17:00: Session II

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Organizing Committee:


  • Zaher Dawy (Faculty of Engineering and Architecture, AUB)
  • Ayad Jaffa (Faculty of Medicine, AUB)
  • Wafic Sabra (Department of Physics & CAMS, AUB)