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Click here to read the Winter 2014 ICM eNews.

New Tool May Help Researchers Develop Ebola Treatments

Date: November 25, 2014

The lab of William R. Brody Faculty Scholar Rachel Karchin, associate professor of biomedical engineering and ICM core faculty member, has collaborated with bioinformatics software firm in Silico Solutions and the UC Santa Cruz Ebola Genome Portal to develop MuPIT Ebola Edition, a free, browser-based online tool that enables researchers to visualize Ebola gene mutations in the context of three-dimensional protein structures. Dr. David Haussler, a researcher at UCSC and longtime collaborator of Dr. Karchin, suggested that her team create an add-on to UCSC’s new Human Genome Browser, which offers researchers detailed genetic information about the virus. The Karchin lab’s MuPIT Ebola Edition provides a 3-D view of Ebola’s proteins, making it easier to interpret the functional implications of mutations and their relationship to Ebola Virus Evolution and its potential vulnerabilities. According to Dr. Karchin, research suggests that mutations at the virus’s antibody-binding sites are important because they can provide clues about how effective a new antibody vaccine may be at combatting a disease such as Ebola. She added that because proteins are three-dimensional molecules, seeing their mutations and epitopes on-screen as 3-D structures can offer important details about their functional and clinical importance.

The MuPIT Ebola edition browser can be accessed at More information about this new tool can be found at

This illustration depicts the Ebola virus and proteins on its surface that may provide targets for new drugs that could help treat or prevent Ebola infections. Image: David Hopkins/Johns Hopkins Institute for Computational Medicine.

Cardiac modeling by Trayanova lab featured in IEEE Spectrum

Date: October 29, 2014

In a recent article featured in IEEE Spectrum, Dr. Natalia Trayanova, Murray B. Sachs Professor of Biomedical Engineering and ICM core faculty member, describes recent progress by her lab in the creation of custom virtual heart models for individual cardiac patients. These advances may fundamentally change the clinical approach to treating life-threatening heart conditions.

Dr. Trayanova and her colleagues are currently testing whether personalized heart models will serve as better predictors of a cardiac patient’s risk of developing a life-threatening arrhythmia. Such information will provide physicians with a noninvasive means to help determine whether implantation of a defibrillator is warranted. Implantation is the current standard treatment when a patient’s proportion of blood pumped out of the heart with each beat falls below 35 percent. However, follow-up studies indicate that only 5 percent of defibrillators implanted in such patients will provide a life-saving shock in the first year after the procedure. The virtual heart model is also expected to improve treatment of ventricular tachycardia by ablation, as the individualized simulations will provide cardiologists the ability to improve upon and narrow their target in such procedures. Dr. Trayanova and her lab expect that advances in computer-simulated heart models will “change the paradigm” of treatment and outcomes for heart patients of all ages.

To view the full story, click here.

Vogelstein and Ardekani join ICM Core Faculty

Date: October 7, 2014

The Institute for Computational Medicine is pleased to announce two recent additions to our core faculty. We’re confident that their professional and research contributions will further advance ICM’s mission to develop and apply individualized computational models of disease that enable physicians to deliver improved patient care. Please join us in welcoming the following distinguished colleagues:

Joshua Vogelstein, PhD PortraitJoshua Vogelstein joined the Department of Biomedical Engineering as an Assistant Professor in August of this year. His research focuses on the extension and application of scalable statistical inference methodologies to discover structure from multifarious data, namely relating brain structure and dynamics to behavior and cognition. Dr. Vogelstein followed the completion of his PhD in Johns Hopkins School of Medicine’s Department of Neuroscience with a fellowship in the lab of Dr. Carey Priebe of the Whiting School of Engineering’s Department of Applied Mathematics and Statistics. He comes to us most recently from Duke University, where held appointments as Senior Research Scientist in the Departments of Statistical Science and Mathematics and served as Senior Fellow at the Kenan Institute for Ethics. Dr. Vogelstein is a core faculty member of the Johns Hopkins Center of Imaging Science on the Homewood Campus and will hold a joint appointment in the Department of Neurology. Click Here to view view Dr. Vogelstein's Profile

Siamak Ardekani, PhD PortraitSiamak Ardekani was promoted in July 2014 to the rank of Assistant Research Professor of Biomedical Engineering. He will continue as core faculty of the Johns Hopkins Center for Imaging Science in addition to his expanded role in the ICM. His research areas of expertise include image-based shape and motion analysis of cardiac disease using mathematical models and analysis of the effect of radiation therapy on brain development using diffusion MRI and deformation-based morphometry. Prior to joining Johns Hopkins University in 2006, Dr. Ardekani received an MD from Shiraz University of Medical Sciences, a Master’s Degree from Drexel University, and a PhD in Biomedical Engineering from UCLA. Click Here to view view Dr. Ardekani's Profile.


ICM establishes ITCR Computational Medicine Core

Date: September 19, 2014

The Institute for Computational Medicine (ICM) is pleased to announce the establishment of a Computational Medicine Core. This new core, supported by NIH funding to the Institute for Clinical and Translational Research, will help faculty across the Johns Hopkins enterprise add computational modeling to their research endeavors.

The Computational Medicine Core was created to support innovative biomedical research programs at Johns Hopkins University. It offers services and consulting for investigators interested in mathematical modeling of complex biological systems in health and disease. Models may be used to achieve quantitative understanding of and to generate hypotheses about disease mechanisms and treatments that can then be tested in the laboratory and/or clinic.

For more information, Click Here.

Iraj Hosseini receives a 2015 Siebel Scholarship

Date: September 12, 2014

Iraj Hosseini, a Graduate Student in the lab of Feilim Mac Gabhann, Assistant Professor in the Department of Biomedical Engineering and Institute for Computational Medicine Core Faculty Member, has been awarded a 2015 Siebel Scholarship. Iraj received his M.Sc. and B.Sc. (with honors) from University of Alberta and Isfahan University, respectively. At JHU, Iraj has developed molecular-detailed multi-scale computational models of HIV infection to better understand HIV pathogenesis and design stem cell-based anti-HIV therapies. Iraj has co-authored over twenty peer reviewed journal articles and conference papers and received numerous awards including four international awards in RoboCup competitions, Alberta Ingenuity award, iCORE scholarship, Drescher scholarship and the Ruth Aranow fellowship in Computational Medicine. Beyond his academic achievements, Iraj leads novel efforts to reinvigorate PhD education and prepare students for alternative career opportunities. Iraj co-founded BME EDGE, obtaining $150,000 in competitive funding from the Provost's Office and matching funds from the BME department. At EDGE, Iraj co-chaired a team of 17 students and staff members to develop an integrated career pathway for graduate students through internships, professional development workshops, alumni speaker series, networking events and PhD-focused job fairs.

"The Siebel Scholars program was established in 2000 by the Siebel Foundation through grants to 17 of the most prestigious business, bioengineering, and computer science graduate programs. Each year, up to five graduate students from each partner institution are selected as Siebel Scholars to receive a $35,000 award for their final year of studies and join the vibrant community of leaders who collaborate, communicate, and institute meaningful change." Click here to read the full announcement on the Siebel Scholars Website. The news has also been covered on JHU's Hub news site.

Congratulations Iraj on your award!

Brian Lee awarded 2014-2015 David C. Gakenheimer Fellowship award

Date: September 8, 2014

Brian Lee, a second year BME Predoctoral Student in the lab of Dr. Michael Miller, Herschel and Ruth Seder Professor of Biomedical Engineering at Johns Hopkins, director of the university’s Center for Imaging Science, and core faculty member in the Institute for Computational Medicine, has been selected as the recipient of the Institute for Computational Medicine’s David C. Gakenheimer Fellowship, for the 2014-2015 academic year.

Dr. Gakenheimer, who holds a bachelor’s degree in engineering mechanics from Johns Hopkins University, generously funded this fellowship to provide support to a student conducting heart research in developing and advancing diagnostic methods such as detection, classification and treatment of rhythm disorders.

Congratulations Brian and good luck with your research!

Dr. Natalia Trayanova gives keynote lecture at 2014 SIAM Annual Meeting

Date: July 23, 2014

Natalia A. Trayanova, Murray B. Sachs Professor of Biomedical Engineering and the Institute for Computational Medicine, presented a keynote lecture at the 2014 SIAM Annual Conference of the Society for Industrial and Applied Mathematics. The conference was held July 7-11 in Chicago, Illinois. Natalia's presentation entitled “Virtual Electrophysiology Laboratory” was scheduled for Thurs, July 10.

Click here to view more information about the SIAM conference.

To view the abstract from Dr. Trayanova's presentation, click here.

Daniel Tward awarded at 2014 XSEDE Conference for best "lightning talk"

Date: July 21, 2014

BME PhD student Daniel Tward attended the 2014 Extreme Science and Engineering Discovery Environment (XSEDE) conference in Atlanta, Georgia and received a prize for the best "Lightning Talk". His presentation "Computational Anatomy Gateway: Leveraging XSEDE Computational Resources for Shape Analysis" was authored with Saurabh Jain, David Lee, Anthony Kolasny, Timothy Brown, Tilak Ratnanather, Laurent Younes and Michael Miller.

Computational Anatomy (CA) is a discipline focused on the quantitative analysis of the variability in biological shape. The Large Deformation Diffeomorphic Metric Mapping (LDDMM) is the key algorithm which assigns computable descriptors of anatomical shapes and a metric distance between shapes. This is achieved by describing populations of anatomical shapes as a group of diffeomorphic transformations applied to a template, and using a metric on the space of diffeomorphisms. LDDMM is being used extensively in the neuroimaging ( and cardiovascular imaging ( communities. There are two major components involved in shape analysis using this paradigm. First is the estimation of the template, and second is calculating the diffeomorphisms mapping the template to each subject in the population. Template estimation is a computationally expensive problem, which involves an iterative process, where each iteration calculates one diffeomorphism for each target. These can be calculated in parallel and independently of each other, and XSEDE is providing the resources, in particular those provided by the cluster Stampede, that make these computations for large populations possible. Mappings from the estimated template to each subject can also be run in parallel. In addition, the use of NVIDIA Tesla GPUs available on Stampede present the possibility of speeding up certain convolution-like calculations which lend themselves well to the General Purpose GPU computation model. We are also exploring the use of the available Xeon Phi Co-processors to increase the efficiency of our codes. This will have a huge impact on both the neuroimaging and cardiac imaging communities as we bring these shape analysis tools online for use by these communities through our webservice (, with the XSEDE Computational Anatomy Gateway providing the resources to handle the computational demands for large populations.

To view other lightning talks and link to more information about the XSEDE conference, visit their site at

Congratulations Daniel!

Student work overseen by Dr. Tilak Ratnanather featured in WSE Summer News

Date: June 17, 2014

An article in the Summer 2014 issue of JHU Engineering Magazine highlights a promising iPad app designed by Hopkins undergrads to help train deaf adults with cochlear implants (CI) to understand speech from the electrical signals that CI devices provide. Student team members include Margo Heston, Rohit Bhattacharya, and Joanne Song, all of the Department of Biomedical Engineering. Their work is overseen by Dr. Tilak Ratnanather, an associate research professor in the Center for Imaging Science and ICM core faculty member.

According to Heston, the app – named Speech Banana after the term specialists use to describe the area where all human speech appears on an audiogram – is not intended to replace traditional in-person auditory training, “But we want to supplement it.”

To read the entire article, click here.

Prof. René Vidal elected to the 2014 Class of IEEE Fellows

Date: June 13, 2014

Dr. René Vidal receives award in Florence, Italy
Dr. René Vidal receives award in Florence, Italy

René Vidal has been named to the 2014 class of IEEE Computer Society Fellows. The IEEE Grade of Fellow recognizes unusual distinction in the profession and is conferred by the IEEE Board of Directors upon a person of outstanding and extraordinary qualifications and experience in IEEE-designated fields, and who has made important individual contributions to one or more of these fields. Dr. Vidal has been recognized for contributions to subspace clustering and motion segmentation in computer vision. He was presented with the award at the IEEE International Conference on Acoustics, Speech and Signal Processing in Florence, Italy, on Tuesday, May 6, 2014.

Dr. Vidal is an Associate Professor in the Department of Biomedical Engineering of Johns Hopkins University, with joint appointments in Computer Science, Electrical and Computer Engineering, and Mechanical Engineering. He is the director of the Vision Dynamics and Learning Lab, and a faculty member in the Center for Imaging Science (CIS), the Institute for Computational Medicine (ICM), and the Laboratory for Computational Sensing and Robotics (LCSR). For more information on his research, please see

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