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Click here to read the Winter 2014 ICM eNews.

Research from Dr. Karchin's lab featured in Winter JHU Engineering News

Date: January 13, 2015

Dr. Rachel Karchin, Associate Professor of Biomedical Engineering and core faculty member of the Institute for Computational Medicine, is featured in the winter 2015 edition of The Johns Hopkins Whiting School's Engineering Magazine. "Pinpointing Cystic Fibrosis Severity" focuses on research in Dr. Karchin's lab towards predicting the severity of individual's likely symptoms of cystic fibrosis from their genetic code.

As stated in the article, "The researchers have used a large array of clinical and genetic data from CF patients to "teach" the Karchin lab computer algorithm to think like a doctor—making highly accurate diagnoses of specific symptoms and disease severity, based on the presence of these rare CFTR mutations."

To read the entire article at the Johns Hopkins winter 2015 Engineering Magazine, click here.

Mark Walker’s Multimedia Publication Makes Sparks Fly in the Winslow Lab

Date: December 16, 2014

In this year’s final issue of Biophysical Journal, BME predoctoral student Mark Walker, a member of the Winslow lab, has achieved a rare trifecta. In addition to the publication of his article entitled “Superresolution Modeling of Calcium Release in the Heart”, the journal features his artistic rendering of a model Ca2+ spark on the cover, features a video clip of a model-generated Ca2+ spark on its homepage, and features a New and Notable article about his work entitled “The Ryanodine Receptor Patchwork: Knitting Calcium Spark Dynamics”. In this editorial, Eric Sobie describes the work of Walker et al as having potentially similar long-term impact as a couple of the most highly lauded landmark publications in this field over the last quarter century. Mark’s novel simulations bring together the fine geometrical details of the Ca2+ release unit with a contemporary mechanistic model of Ca2+-release channel gating. The results reveal new insight into the roles of Ca2+-store mediated channel regulation and release channel cluster shape on Ca2+ sparks, and hence lead the way for predicting how cardiac cell contraction will be altered in diseases where these mechanisms and structures are disturbed.

To view the feature video full-size on YouTube, click here.

Sri Sarma named inaugural recipient of the Krishna Kumar Award

Date: December 16, 2014

The North American Neuromodulation Society (NANS) awarded Dr. Sridevi Sarma, Assistant Professor of Biomedical Engineering and ICM core faculty member the first Krishna Kumar Award at their Dec 12, 2014 annual meeting held in Las Vegas. Dr. Sarma set the bar high for subsequent recipients by addressing the 2000 or so attendees with a talk that managed to make complicated modeling approachable and significant for everyone in the audience. The North American Neuromodulation Society (NANS) is dedicated to promoting multidisciplinary collaboration among clinicians, scientists, engineers, and others to advance neuromodulation through education, research, innovation and advocacy.

Congratulations Sri!

Trayanova Lab Research Published in PLOS Computational Biology

Date: December 15, 2014

In a research paper available today, Dr. Natalia Trayanova, Murray B. Sachs Professor of Biomedical Engineering and ICM core faculty member, BME grad student Kelly Chang and researcher Jason Bayer reveal insights into the mechanisms of proarrhythmic alternans — electrical signals in the heart that alternate from beat to beat— and the role they play in atrial fibrillation. The study, entitled “Disrupted Calcium Release as a Mechanism for Atrial Alternans Associated with Human Atrial Fibrillation,” was published by PLOS Computational Biology. In this study the researchers use computational models to conduct a detailed examination of the causes and contributors to alternans associated with human atrial fibrillation.

Christopher Douville awarded NRSA Fellowship

Date: December 5, 2014

Christopher Douville, a fourth-year BME PhD student in the lab of Dr. Rachel Karchin, associate professor of Biomedical Engineering and ICM core faculty member, has been awarded a National Research Service Award from the NIH’s National Human Genome Research Institute. The award will support his project “Predicting Impact of Genetic Variation on Splicing”, which aims to substantially improve the ability to interpret the consequences of exonic mutations on pre-mRNA splicing, as the impact of genetic variation on splicing is not well understood. The fellowship will provide three years of support for Christopher’s research training.

Congratulations, Christopher!

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!

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