May 2012
Poster Session
Institute for Computational Medicine & Department of Biomedical Engineering
Foundations of Computational Biology and Bioinformatics II
"Spring 2012 Final Projects"
Date: Wednesday, May 2, 2012
Time: 6:00 PM
Location: Hackerman Hall, 3rd floor - near 316
Abstract:
To view the event poster for more information, Click Here.
Note: Wine and snacks will be served.
ICM Distinguished Seminar Series
Donald Geman
Professor, Department of Applied Mathematics and Statistics, JHU
"Computational Challenges in Molecular Medicine"
Date: Tuesday, May 1, 2012
Time: 1:30 PM
Location: Hackerman Hall Auditorium (B17)
Abstract:
The goal of translational medicine is to carry fundamental research into clinical practice. This is very ambitious and rarely realized. I will talk about computational barriers in attempting to carry out this program in the context of statistical learning applied to cancer genomics with high-throughput "omics" data. In particular, I will focus on learning predictors of disease phenotypes, tumor sites-of-origin and pathway deregulation with limited sample sizes and massive study-to-study (non-biological) variability. Finally, I will argue that low-dimensional order statistics are easy to interpret, can account for combinatorial interactions among genes and gene products and might even support a mechanistic interpretation for the underlying decision rules. Most of this is joint work with Nathan Price, Luigi Marchionni, David Simcha or Bahman Afsari.
Note: Light lunch will be served starting at 1:00pm. The presentation will begin at 1:30pm.
Bio:
Donald Geman received a B.A. degree in Literature from the University of Illinois and a Ph.D. in Mathematics from Northwestern University. He was Distinguished Professor at the University of Massachusetts until 2001, when he joined the Department of Applied Mathematics and Statistics at Johns Hopkins University, where he is a member of the Center for Imaging Science and the Institute for Computational Medicine. He is an IMS and SIAM fellow.
April 2012
ICM Distinguished Seminar Series
Adam Arkin
Director of Physical Biosciences Division at Lawrence Berkeley National Laboratory
Dean A. Richard Newton Memorial Professor, Dept of Bioengineering, University of California, Berkeley
"Changing Chasses and Inventing Elements: Developing a combined systems biology and engineering approach to designing complex function in cells."
Date: Wednesday, April 25, 2012
Time: 12:00 PM
Location: PCTB Mountcastle Auditorium (SOM)
Hosted by: Dr. Feilim Mac Gabhann
Abstract:
To meet the goal of creating reliable, predictable, efficient, and transparent methods to harness cellular capabilities for human benefit, it is necessary both to have standard libraries of elements from which useful pathways can be constructed and an understanding of the how host physiology and the environment impacts the functioning of these heterologous circuits. We show how variations in cellular and environmental context affect the operation of the basic central dogma functions underlying gene expression. Then we describe progress on creating a complete, scalable, and relatively homogeneous and designable sets of part families that can control central dogma function predictably in the face of varying configurations, genetic contexts, and environments.
Bio:
Dr. Adam ArkinArkin is Division Director of the Physical Biosciences Division at the Lawrence Berkeley National Laboratory and a Full Professor in the Department of Bioengineering, U.C. Berkeley. He is Director of the Synthetic Biology Institute launched this year at Berkeley and Co-Director of the BIOFAB: International Open Facility Advancing Biotechnology (BIOFAB). In addition, he directs the Joint Bioenergy Institute’s Bioinformatics Group and Berkeley Lab’s Virtual Institute of Microbial Stress. He is a Professor of Bioengineering at the University of California (UC), Berkeley and was an investigator with the Howard Hughes Medical Institute (HHMI) until 2007. Prof. Arkin has served on many academic and government committees including the US Air Force Science Advisory Board and the Defense Science Study Group.
The thrust of Arkin’s research has focused on developing the physical theory, computational tools and experimental approaches for understanding cellular processes critical to life. The goal is to provide a framework that will facilitate the design and engineering of new functions and behaviors in cells through synthetic and systems biology.
Last year Prof. Arkin led the launch of the Synthetic Biology Institute (SBI) with Agilent as the Founding Industrial Partner. SBI brings together scientists working on the foundations and applications of biological design from the University and National Laboratory. He developed and co-taught an Introduction to Synthetic Biology course with Ron Weiss from MIT, which was video linked between the two campuses. The course was so popular it has been picked up by a consortium of 10 schools who will also receive the video feed while Profs. Arkin and Weiss teach. In 2010/11, Arkin published 14 papers laying an initial foundation for predictable programmable gene expression engineering in bacteria with advanced simulation, molecular characterization, and novel molecular “components” similar, in spirit to gate logics in electronics.
Note: Light lunch will be served starting at 11:45am.
March 2012
ICM Distinguished Seminar Series
Feilim Mac Gabhann
Assistant Professor, Department of Biomedical Engineering
Institute for Computational Medicine
"On Growth Factors and Vascular Form: the VEGF Family in Angiogenesis and Arteriogenesis"
Date: Tuesday, March 6, 2012
Time: 1:30 PM
Location: Hackerman Hall Basement Auditorium
Abstract:
Like most complex morphogenesis processes, the growth and remodeling of blood vessel networks is directed by the concentration gradients of secreted growth factors. Our laboratory uses a combination of computational and experimental techniques to determine how the endothelial cells that line the vasculature 'see' and respond to growth factors. In particular, we study the vascular endothelial growth factor (VEGF) family. The complexity of this family makes it an ideal subject for quantitative computational modeling: five genes each encode multiple splice-isoform ligands that can bind to three receptor tyrosine kinases and two non signaling co-receptors. Using a broad range of experimental data at the molecular, cellular and tissue levels, we develop biophysically and physiologically realistic multi-scale simulations of growth factor transport and therapeutic interventions.
Bio:
Feilim Mac Gabhann graduated from University College Dublin with a Bachelors in Chemical Engineering. He completed his PhD in Biomedical Engineering in 2007 at Johns Hopkins University, working with Aleksander S. Popel to create mathematical models of growth factor networks. The models built using this work are harnessed to understand both positive and negative regulation of blood vessel growth, which makes them applicable to diseases as diverse as peripheral artery disease and cancer. Dr. Mac Gabhann moved to the University of Virginia as a postdoctoral fellow in the Department of Biomedical Engineering and the Cardiovascular Research Center. Working with Shayn M. Peirce and Thomas C. Skalak, he conducted experimental research on microvascular remodeling in mouse skeletal muscle.
Dr. Mac Gabhann joined Johns Hopkins University as an Assistant Professor in 2009. As well as being a part of the Department of Biomedical Engineering, the lab is in the Institute for Computational Medicine, a world's-first institute focused on the application of mathematical modeling to the understanding and treatment of human disease. The Mac Gabhann lab studies mathematical models of disease and therapeutics, including peripheral artery disease, cancer, ALS, pre-eclampsia and HIV. The experimental side of the lab conducts independent studies of vascular remodeling in mice, protein transport in microfluidic cell culture devices and cell behavior novel scaffold constructs. In addition, tissue imaging and other experiments are conducted to generate parameters for the models and to validate mathematical predictions.
Dr. Mac Gabhann is a Sloan Research Fellow, as well as being the recipient of a K99/R00 NIH Pathway to Independence Award, the 2010 August Krogh Young Investigator Award from the Microcirculatory Society, and the 2012 Arthur C. Guyton Award for Excellence in Integrative Physiology from the American Physiology Society. He is the author of 35 peer-reviewed papers, and is an Associate Editor for PLoS Computational Biology and BMC Physiology.
Note: Light lunch will be served starting at 1:00pm. The presentation will begin at 1:30pm.
February 2012
ICM Distinguished Seminar Series
Brian Litt
Translational Neuroengineering Litt Lab, Department of Bioengineering, Upenn
"Multiscale Electrophysiology in Human Epileptic Networks and Flexible Brain-Computer Interfaces for Epilepsy"
Date: Tuesday, February 7, 2012
Time: 1:00 PM
Location: Hackerman Basement Auditorium
Hosted by: Dr. Sridevi Sarma
Abstract:
Recent evidence demonstrates that seizures may be generated by submilimeter domains in neocortex that are not imaged by standard clinical electrodes. In the search to localize epileptic networks for surgery or antiepileptic devices the technical challenge is clear: how can we map and decode 100 micron scale electrophysiology in human brain over regions spanning tens of square centimeters or more. In this seminar I will review recent studies of seizure generation in human neocortex, and present a new brain-computer interface platform we have developed to map and modulate this activity at high resolution in-vivo. The platform is composed of active, flexible, conformable electronics developed in collaboration with John Rogers at the University of Illinois, and Jonathan Viventi and NYU/ POLY. I will present high-resolution cortical surface recordings of epileptiform activity recorded with these devices from an acute feline seizure model and their implications for translation to human therapy.
Note: Light lunch will be served starting at 1:00pm. The presentation will begin at 1:30pm.
