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Dr. Rachel Karchin invited to speak at Carnegie Mellon APGA 2013 Meeting May 3-5

Date: May 1, 2013

Dr. Rachel Karchin, Associate Professor in the Department of Biomedical Engineering and Institute for Computational Medicine, is scheduled to speak at APGA 2013. The meeting entitled "Automated Personal Genome Analysis for Clinical Advisors: Challenges and Solutions" will be held at the Hillman Center for Future-Generation Technologies in the School of Computer Science Complex at Carnegie Mellon University in Pittsburg, PA.

The future of personalized medicine is often envisaged as doctors interrogating a “Dr. in a Box” that integrates multiple streams of data – whole patient genomes, blood tests, scans, and other information – to detect anomalies, diagnose disease, monitor response to therapy, and track changes in health over time. Of particular importance will be the ability to predict disease risk and treatment responsiveness from personal genome information. Developing machine learning software to model the relationships between complex diseases and genome variation is a major challenge.

To read more about the meeting click here to visit the Carnegie Mellon webpage.

Center for Imaging Science Hosting Symposium to Celebrate its 15 Years of Science

Date: April 25, 2013

The Center for Imaging Science will be hosting a Symposium on May 17 & 18 to celebrate its 15 years of science. The event will begin Friday May 17th at 1:00 PM at the Sheraton Baltimore North, and will continue Saturday 9:00 AM on the Johns Hopkins University Homewood campus at the Hodson Hall Boardroom.

The Center's two days of celebrations will feature talks from leading scientists in Medical Imaging, Computational Vision and Computational Biology, three areas upon which the Center for Imaging Science has focused over its existence. Our renowned speakers include Nicholas Ayache from INRIA, Stuart Geman from Brown University, Richard Hartley from National ICT Australia, Alfred Hero from the University of Michigan, Alain Trouvé from Ecole Normale Supérieure, Cachan and Raimond Winslow of the Johns Hopkins University.

To view a pdf brochure for the symposium event with an itinerary and full list of speakers, click here.

BME Transition Generator receives $150,000 from JHU PII

Date: April 2, 2013

A proposal put forth by two BME students, Iraj Hosseini, a 4th year PhD Candidate in the Institute for Computational Medicine lab of Dr. Feilim Mac Gabhann, and Shiva Razavi, co-president of the BME PhD Council, was awarded $150,000 from the Office of the Provost, as part of its PhD Innovation Initiative (PII) to support bold, creative, culture‐changing ideas for transforming PhD education at Johns Hopkins. The winning proposal, titled "BME Transition Generator" was the result of multi-faceted teamwork between BME PhD students, the faculty and the staff. Iraj Hosseini and Shiva Razavi led the efforts that shaped this proposal. Dr. Elliot McVeigh and Dr. Youseph Yazdi served on the advisory panel, while Hong Lan, Chuck Montague and Catherine Schoonover from the BME staff played an instrumental role. The valuable feedback received from surveying the BME PhD student body was a critical basis for their success.

From the proposal abstract:

“Traditionally, the mission of the doctoral programs has been to train future university faculty; however, there is increasing enthusiasm among PhD students to pursue careers in industry, entrepreneurship and consulting. As of 2012, about 26% of biomedical PhDs have tenured or tenure-track faculty positions, compared to 34% in 1993. It is therefore essential for our educational institutions to accept this shift in the academic market and offer our students additional mentorship and training that will make them competitive.

The gap between current training objectives and career outcomes brings into stark relief the need for a proactive role that universities need to pursue in preparing PhD students for both academic and alternative career paths. The JHU Department of Biomedical Engineering proposes to achieve this additional training by establishing a new departmental center, the BME Transition Generator. This center will serve two primary functions: (i) facilitating internships for the current PhD students; (ii) providing additional training opportunities to address the need for developing professional skills.”

Congratulations to the BME PII team on their outstanding achievement!

Dr. Michael Miller to receive McDonald Mentoring Award

Date: March 29, 2013

Dr. Michael Miller will receive the Capers and Marion McDonald Award for Excellence in Mentoring and Advising from the Whiting School of Engineering at May 6th Convocation. Often referred to simply as the "McDonald Mentoring Award," this program recognizes and honors diverse professionals in engineering and the applied sciences who, as exemplary mentors and advisors, have significantly and consistently supported the personal and professional development of others. In a university setting, these efforts will have included students and colleagues. In industry, government, or service organizations, they may have included a variety of developing personnel.

Beginning with the first award in April 2005, the program is designed to celebrate annually those who have enduringly engaged minds, elevated spirits, and stimulated best efforts. It also aspires to help spread the virtues of excellent mentoring and advising in the engineering and applied sciences community.

The program is endowed by Capers W. McDonald and Marion K. McDonald to operate through six supporting institutions. An international recognition is part of the annual society-level award programs of ASME. U. S. national honorees are recognized through the engineering honor society, Tau Beta Pi. Other outstanding mentors are selected annually through similarly-endowed institutional programs at Duke University, Harvard University, Johns Hopkins University, and Massachusetts Institute of Technology – universities where sponsor Capers McDonald has been privileged to have been a learner, either as a student or faculty member.

Dr. Natalia Trayanova’s recent application to NHLBI recommended for funding with percentile of 1%

Date: March 21, 2013

Dr. Natalia Trayanova’s recent application to the National Heart, Lung and Blood Institute, “Predicting the Optimal Ablation Targets for Infarct-related Ventricular Tachycardia” has been recommended for funding with the remarkable percentile of 1%. This caps a string of achievements in the past year for Dr. Trayanova, the Murray B. Sachs Professor of Biomedical Engineering and the Institute for Computational Medicine, who in February gave the Keynote Address for the Society for Industrial and Applied Mathematics Conference on Computational Science and Engineering, in Boston.

Congratulations Natalia!

Dr. Rachel Karchin promoted to Associate Professor with tenure

Date: March 11, 2013

Dr. Rachel Karchin

The Institute for Computational Medicine is pleased to announce that Dr. Rachel Karchin has been promoted to Associate Professor with tenure effective July 1, 2013. Dr. Karchin holds appointments with the Institute for Computational Medicine, the Department of Biomedical Engineering, and the Department of Computer Science in the Johns Hopkins Whiting School of Engineering, as well as with the Institute of Genetic Medicine in the Johns Hopkins School of Medicine. The focus of her research is the development of computational methods to assess the impact of DNA sequence variation on human health. In 2009, she received a National Science Foundation CAREER Award to support research in modeling missense mutation. In April of 2013 she will receive a National Science Foundation Advances in Biological Informatics Innovation Grant. This 3-year, $695K award will fund her research collaboration with Dr. Manel Camps of the University of California, Santa Cruz, to develop a new method to model higher order mutation interactions by combining evolutionary genetics, network models, and protein sequence analysis. Dr. Karchin has also received funding from the National Cancer Institute, the National Institute of Mental Health, the Susan G. Komen Foundation, and the Cystic Fibrosis Foundation, and she enjoys many productive collaborations with research faculty in the School of Medicine’s Department of Oncology and elsewhere within Johns Hopkins.

Dr. Raimond Winslow, Director of the Institute for Computational Medicine states "Dr. Karchin is blazing a new frontier of cancer biology in which computational modeling will be used to identify the gene mutations which drive tumor progression. Ultimately, this computational approach will lead to more personalized, precision cancer therapies. Her work is receiving international recognition, and we are all proud that she is a part of the Institute for Computational Medicine".

For more information on Dr. Karchin’s work, click here to view her profile.

Please join us in congratulating Rachel on this tremendous achievement!

Kathleen McDowell awarded for poster at Gordon Research Conference on Cardiac Arrhythmia Mechanisms

Date: February 28, 2013

Kathleen McDowell, a 5th year PhD Candidate in the lab of Dr. Natalia Trayanova, received 1st place in the Student/Trainee Poster Competition at the Gordon Research Conference on Cardiac Arrhythmia Mechanisms. She presented her research entitled, "Investigating the Arrhythmogenic Effects of Atrial Fibrosis in Patient-Specific Models". The 2013 Gordon Research Conference (GRC) on Cardiac Arrhythmia Mechanisms was held on February 17-22 and focused on integrating basic and translational science with clinically relevant topics. Click here to view more information on the conference.

Congratulations Kathleen!

Suchi Saria and Joel Bader Join ICM Core Faculty

Date: February 21, 2013

The Institute for Computational Medicine is pleased to announce the appointments of Suchi Saria and Joel Bader to our core faculty, bringing the total number of ICM core faculty to 17. Their research and participation will further enrich the Institute's mission to develop and apply individualized computational models of disease that enable physicians to deliver improved patient care.

Suchi Saria, PhD PortraitSuchi Saria, PhD is an Assistant Professor in Computer Science in the Whiting School of Engineering and in Health Policy & Management in the Bloomberg School of Public Health. She is a founding faculty member of the Center for Population Health Information Technology (CPHIT) and is jointly appointed in the Division of Health Sciences & Informatics. Dr. Saria received her PhD in Computer Science with Dr. Daphne Koller from Stanford University. Prior to arriving at Johns Hopkins in 2012, she spent a year as a National Science Foundation Computing Innovation Fellow at the Boston Children’s Hospital and Harvard University. Her honors include a full undergraduate scholarship from Microsoft, a Rambus Fellowship, and an NSF Computing Innovation Fellowship. Her laboratory focuses on machine learning and novel decision support solutions that can improve the safety, quality and cost-effectiveness of the delivery of health care. Her work has led to the development of a fully non-invasive, inexpensive and rapid tool for risk prediction in premature infants that has shown to be significantly more accurate than the current standard of care. Her research has been featured on the cover of Science Translational Medicine (AAAS/Science press). Click Here to view view Dr. Saria's Profile

Dr. Joel S. Bader PortraitJoel Bader, PhD is an Associate Professor in the Johns Hopkins Department of Biomedical Engineering and the Bioinformatics and Computational Biology Lab. His research elucidates how networks of genes and proteins achieve their function. The biological significance of this work has been to predict gene function based on network context, to identify functionally distinct modules representing protein complexes and pathways, and to establish links between genes and disease. Hundreds of his lab’s computational predictions have been validated experimentally. Click Here to view view Dr. Bader's Profile

Welcome to the Institute, Suchi and Joel!

David C. Gakenheimer Funds New ICM Graduate Fellowship

Date: February 11, 2013

David C. Gakenheimer, PhD

Johns Hopkins Engineering alumnus, David C. Gakenheimer, PhD (MechE '65) has funded a fellowship within ICM to assist in developing and advancing heart research diagnostic methods such as detecting, classifying and treating heart rhythm disorders, including atrial fibrillation and atrial flutter.

Gakenheimer, who has a specific interest in atrial fibrillation, is the principal developer of the Logion Caries Detector, a groundbreaking image analysis software program, currently used in thousands of dental offices. Dr. Gakenheimer grew up in Baltimore and now resides in Rancho Palos Verdes, California. After receiving his undergraduate engineering degree at Hopkins, he achieved a Masters and PhD at the California Institute of Technology.

We thank Dr. Gakenheimer for his generous gift, which will be held in perpetuity to annually support an ICM fellow, starting with the 2013-2014 academic year.


Dr. Rachel Karchin awarded NSF ABI:Advances in Biological Informatics Grant

Date: February 4, 2013

A network model of antibiotic resistance mutation interactions in TEM Beta Lactamase. (click to view larger)

Assistant Professor Rachel Karchin of the Department of Biomedical Engineering and Institute for Computational Medicine recently received an award of $695K for 3 years from the National Science Foundation. The award, which is part of the NSF's Advances in Biological Informatics program is entitled "ABI Innovation: Predicting the combined impact of multiple mutations on protein functional adaptation" The study is a collaboration with Dr. Manel Camps of the Department of Environmental Toxicology at University of California, Santa Cruz.

From the Grant abstract:
"This work promotes close interaction between the computational sciences and biology communities: It combines expertise in computational/statistical modeling of mutations in proteins and applied evolutionary genetics in microbial systems. The broader use of this work will be to anticipate the emergence of drug resistance in clinically relevant proteins. It will also have great utility for protein engineers who seek to design proteins with new or improved functions. Furthermore, it will contribute to the design of therapeutic regimens for diseases driven by bacteria or viruses, in which the evolution of drug resistance is commonplace. The educational goals of the project include new course components for undergraduates and graduates at the universities where the project investigators teach and outreach to underrepresented minority students in science and engineering."

To see details on the full award, click here to view on the NSF website.

Congratulations, and good luck with your research!


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