A Message From the Director

Welcome to the first in a series of quarterly E-news letters presenting the latest news and developments in the Institute for Computational Medicine. Chartered in 2005 as an institute in both the Whiting School of Engineering and the School of Medicine, the mission of the Institute is to understand the mechanisms, and to improve the diagnosis, prediction and treatment of disease through the development of mathematical and computational models of disease processes.
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Computational Science &
Engineering Building

Installation complete on largest single high performance computer cluster currently at Hopkins

These new computational resources are the largest single high performance computer cluster currently at JHU and will be dedicated to the ICM’s three areas of research focus: modeling of biological systems, computational anatomy and mathematical bioinformatics.
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Dr. Rachel Karchin receives CAREER Award...

Dr. Rachel Karchin, a tenure-track Assistant Professor received the CAREER award to support Modeling Missense Mutation Research. The award totaling $518,182 over a five year period, will contribute to Dr. Karchin’s work in computational research in public health (genetic components of disease), agriculture and ecology. As part of her CAREER plan, Dr. Karchin will introduce high school students from groups underrepresented in Science, to computational biology. A unique approach to this activity is a molecular evolution computer game she has designed for high school students.
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GRACE TAN wins 1st place at Gordon Conference in Italy...

Grace Tan, a senior in the BME undergraduate program, received first prize (tissue-level category) in the trainee poster competition at the Gordon Research Conference on Cardiac Arrhythmias Mechanisms, held in Il Ciocco, Barga, Italy, Feb. 15-20, 2009.
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Welcome to ICM!

Dr. Rajat Mittal,
Professor, Department of Mechanical Engineering

Dr Mittal's research interests include computational fluid dynamics, biomedical engineering, bioinspired engineering and flow control.

Dr. Feilim Mac Gabhann,
Assistant Professor

Feilim’s research takes a combined experimental-computational approach to generating novel therapeutic strategies to major human diseases, including cancer, peripheral artery disease, and HIV.

Dr. Sridevi Sarma,
Assistant Professor

Sri’s research interests include control of constrained and defective systems (applications in neuroscience) and large-scale optimization.

Q&A with Dr. Joseph Greenstein

Dr. Joseph Greenstein’s area of expertise is in the development of computational models that can simulate heart function in both health and disease. His focus is on revealing and understanding integrative mechanisms of heart function across a range of biological scales from molecular interactions to whole-cell and tissue phenomena. One goal of his research is to help in the treatment of cardiovascular disease by identifying therapeutic targets that could reduce the likelihood of cardiac arrhythmia. Click here to read the Q&A with Joe!

Accolades

Awards

Rene Vidal, 2009 Received the Sloan Research Fellowship.
WSE Team Receives 2008 ICMLA Award. Dr. Dan Naiman and Dr. Don Geman along with grad student Bahman Asari and former postdoc Aik Choon Tan were named the winners of the ICMLA microarray clsassification algorithm competition.

Carolyn J. Park and BaoLuo Sun have been selected to receive the Summer 2009 Provost’s Undergraduate Research Award. Carolyn and BaoLuo will work with Drs. Trayanova and Winslow, respectively.

Yasmin Hashambhoy won second place in her category at the Graduate Students Association Poster Competition held at Johns Hopkins University, April 2009.

Papers Published

Carter H., S. Chen, L. Isik, S. Tyekucheva, V.E. Velculescu, K.W. Kinzler, B. Vogelstein, R. Karchin (2009)
Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Cancer Research, Aug 15; 69(16):6660-7.

Hashambhoy, Y.L., Winslow, R.L. and Greenstein, J.L. (2009) CaMKII-Induced Shift in Modal Gating Explains L-type Ca Current Facilitation: A Modeling Study.
Biophys. J. 2009 Mar 4;96(5):1770-85.

Pieper U.,Eswar, N., Webb, B., Eramian D., Kelly L., Barkan D., Carter, H., Mankoo, P.K., Karchin, R., Marti-Renom, M., Davis, F. and Sali, A. (2008) MODBASE: A database of annotated comparative structure models, and associated resources.
Nucleic Acids Research. 2009 Jan;37(Database issue):D347-54. Epub 2008 Oct 23.

Presentations

An-Chi Wei, Poster Presentation "Modeling and Experimental Studies of Mitochondrial Energetics and Ion Dynamics" 2009 BMES Annual Meeting, Pittsburg, PA, October 2009.

An-Chi Wei, Poster Presentation “Mitochondrial Energetics During Transients Following Substrate and Ca2+ Additions. Modeling and Experimental Studies” Biophysical Society 53rd Annual Meeting, Boston, MA, March 2009.

Yasmin Hashambhoy, Poster Presentation “A Mechanistic, Minimal Model of Ca2+/Calmodulin Dependent Kindase II Signaling in the Cardiac Myocyte” and “CaMKII-Induced Shift in Modal Gating Explains L-type Ca2+ Current Facilitation: A Modeling Study” Biophysical Society 53rd Annual Meeting, Boston, MA, March 2009.