ICM has received a $2 million shared instrumentation grant from the NIH’s National Center for Research Resources
Date: July 16, 2008
The Institute for Computational Medicine (ICM) has received a $2 million shared instrumentation grant from the NIH’s National Center for Research Resources to acquire, at a minimum configuration, a 256 dual quad-core node cluster computer with 1 petabyte of storage. This computer will become the major shared computing resource used by the faculty, students, and staff of ICM in the three major areas of research taking place in the Institute: modeling of biological systems, computational anatomy, and mathematical bioinformatics. Dr. Raimond Winslow, the director of ICM, is the principle investigator of the grant.
For more information on this award, see the news releases below.
NIH-NCRR
Johns Hopkins University
EurekAlert
Information Week
Baltimore Business Journal
News-Medical.net
Newswise Science News
Medical News Today
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Congratulations to this year’s Raj and Neera Singh Undergraduate Fellows!
Date: April 25, 2008
Grace Tan will be mentored by Dr. Natalia Trayanova. Her project will focus on using a computational model of a three-dimensional cardiac tissue wedge to study how structural and biophysical remodeling that occurs in heart failure influences vulnerability of the heart to arrhythmic wave patterns . Grace is a rising junior in the Biomedical Engineering program.
Charlie Ouyang will be mentored by Dr. Rene Vidal. His project is titled "Nonlinear Filters for Tracing 3-D Purkinje Networks in Cardiac Images." Timothy is a rising junior in the Biomedical Engineering program.
These students are being awarded a $5000 stipend for a 10 week long research project, sponsored by a generous donation from Raj and Neera Singh.
Dr. Tilak Ratnanather and Shane Steinert-Threlkeld awarded fellowship.
Date: May 5, 2008
Congratulations to Dr. Tilak Ratnanather and undergraduate Mathematics/Philosophy student Shane Steinert-Threlkeld. They were awarded a Technology Fellowship from the Center for Educational Resources. They will be developing an on-line course titled "Introduction to Mathematical Methods for Computational Medicine". The project carries an award of $4,000 for Shane, and $1,000 to Dr. Ratnanather.
More information about the Technology Fellowship program can be found here (http://www.cer.jhu.edu/index.cfm?pageID=269).
Dr. Natalia Trayanova selected as a Fellow of the Heart Rhythm Society
Date: April 17, 2008
Dr. Natalia Trayanova has been selected as a Fellow of the Heart Rhythm Society. The most distinguished level of the society, Fellow status recognizes members who have realized significant professional achievement, provided exceptional service and are prominent in the field of cardiac arrhythmia research and treatment. Dr. Trayanova will be honored at the upcoming annual meeting, Heart Rhythm 2008, May 14-17 in San Francisco.
Please join us in congratulating her on this distinguished honor.
Dr. Rachel Karchin awarded "Susan B. Komen Investigator Initiated Research (IIR) Grant"
Date: April 3, 2008
Dr. Rachel Karchin has been awarded a Susan B. Komen Investigator Initiated Research (IIR) Grant that will provide three years of support to stimulate exploration of new ideas and novel approaches in breast cancer research and clinical practice that will lead to reductions in breast cancer incidence and mortality within the next decade.
Her team will be studying somatic mutations in the PI3 kinase gene, which are involved in 30% of breast cancers. The work will combine computational modeling of mutations, statistical learning methods, and experimental tests in cell culture, chicken embryo chorioallantoic membranes and nude mice, contributing to development of more specific inhibitors of PI3K.
Collaborators on the project are Drs. Saraswati Sukumar and Ben Ho Park of the Johns Hopkins Breast Cancer Center.
Congratulations to Dr. Karchin!
ICM Graduate Student Laura Doyle awarded "National Defense Science and Engineering Graduate (NDSEG) Fellowship"
Date: April 1, 2008
ICM Graduate student Laura Doyle has been awarded a 2008 National Defense Science and Engineering Graduate (NDSEG) Fellowship for heart failure research. Laura is currently implementing a model of the Rabbit myocyte with the goal of improving on its calcium handling. This model will be used in conjunction with wet lab data from collaborators to explore the role of altered metabolic pathways in heart failure. The NDSEG Fellowship will cover her tuition, required fees and a stipend for three years. Congratulations Laura!
ICM Graduate Student Hannah Carter awarded "National Defense Science and Engineering Graduate (NDSEG) Fellowship"
Date: April 1, 2008
ICM Graduate student Hannah Carter has been awarded a 2008 National Defense Science and Engineering Graduate (NDSEG) Fellowship for breast cancer research. Hannah will build a computational model to identify weak links in the PI3K/AKT pathway that can serve as drug targets in the prevention of breast cancer progression and metastasis and investigate the mechanisms behind cancer drug resistance. The NDSEG Fellowship will cover her tuition, required fees and a stipend for three years. Congratulations Hannah!
ICM now accepting applications for the Raj and Neera Singh Summer Undergraduate Fellowship.
Date: March 31, 2008
The ICM announces the second annual Raj and Neera Singh Summer Undergraduate Fellowship. The Institute will sponsor competitive non-credit summer research fellowships for Johns Hopkins University undergraduate students in the Whiting School of Engineering. More Information...
ICM Graduate Student An-Chi Wei receives "Student Research Achievement Award"
Date: February 12, 2008
ICM Graduate Student An-Chi Wei receives "Student Research Achievement Award, Bio-Energetics Subgroup" for her research poster entitled "Modeling of Mitochondrial Energetics and Ion Dynamcs". This poster was presented at the 52nd Annual Meeting of the Biophysical Society at Long Beach, CA. View the poster PDF here.
NHLBI will support proposals for federating software tools or data sets through the CardioVascular Research Grid (CVRG) infrastructure.
Date: October 7, 2007
PAR Announcement
Application Instructions
ICM receives an NHLBI Exploratory Program in Systems Biology (R33) grant to study the systems biology of sudden cardiac death.
Date: August 20, 2007
Sudden Cardiac Death (SCD) remains a leading cause of death in the western world. Estimates suggest that roughly 10-20% of all annual mortality in the U.S. results from SCD and that approximately 5% of the middle-aged U.S. population has a significant predisposition to SCD. While implantable cardioverter defibrillators (ICDs) are proving to be effective in reducing the occurrence of SCD, wholesale deployment of ICDs is impractical economically and ignores the facts that the majority of patients with ICDs are likely never to require them and that there are as yet no effective means for identifying patients at highest risk for SCD.
ICM has received an award for $854,394 over 3 years from the NHLBI to investigate the causes of SCD. Working both from the top-down (whole heart optical mapping, anatomical reconstruction and simulation) and from the bottom up (mitochondrial and cellular imaging and modeling), this research project seeks to achieve an unprecedented level of integration of structure and function in order to understand and model the ways in which coupling between metabolic and electrophysiological processes in the myocyte contribute to risk of cardiac arrhythmias under conditions of metabolic stress. Dr. Raimond L. Winslow is the project principal investigator. Drs. Brian O’Rourke and Gordon Tomaselli direct cluster projects 1 and 2, and Dr. Winslow directs cluster project 3. Cluster Project 1 will test the hypothesis that metabolic sinks may be formed by producing local regions of IKATP activation in the intact-perfused guinea pig (GP) heart and will assess their impact on ventricular conduction and arrhythmia generation. Cluster Project 2 will test the hypothesis that metabolically stressed myocardium is particularly susceptible to formation of metabolic sinks leading to arrhythmia in the setting of heart failure. Cluster Project 3 will develop novel biophysically, metabolically and anatomically detailed computational models of electrical conduction and, in conjunction with Cluster Projects 1 & 2, test hypotheses regarding the ways in which the interplay between metabolic and electrophysiological function contributes to generation of arrhythmias under conditions of metabolic stress.
ICM Moves to a New Home!
Date: August 7, 2007
On August 7, the Institute for Computational Medicine moved into its home in the newly constructed Computational Sciences and Engineering Building at the JHU Homewood campus. Located on the second and third floor of CSEB, this new space provides the ICM space for new faculty, students, and staff. The space also includes a state of the art machine room in which the Institute's computing infrastructure will be located. All members of the ICM wish to thank Dean Nicholas Jones, Vice Dean of Research Marc Donohue, Vice Dean for Faculty Andrew Douglas, and project Program Manager Travers Nelson for making this possible.
Stephen Granite presents at Microsoft Research Faculty Summit 2007
Date: July 17, 2007
Stephen Granite, Director of Database/Software Development for the CCBM, recently presented at the Microsoft Research Faculty Summit 2007. The title of his talk was “The Cardiovascular Research Grid: A National Infrastructure for Representing, Sharing, Analyzing and Modeling Cardiovascular Data.” The Cardiovascular Research Grid (CVRG) will develop tools for representing, managing and sharing multi-scale data related to Sudden Cardiac Death (SCD), and will then use that multi-scale data to discover biomarkers that predict need for Implantable Cardioverter Defibrillator (ICD) placement. The CVRG is establishing working groups to create a mechanism for community input on the CVRG itself and undertaking outreach efforts to inform, train and support researchers in its use.
Click Here to view a pdf of the full presentation.
ICM PostDoctoral Fellow Dr. Viatcheslav Gurev Receives American Heart Association Fellowship
Date: July 10, 2007
ICM Postdoctoral Fellow Dr. Viatcheslav Gurev has received a prestigious American Heart Association Fellowship from the Mid-Atlantic Affiliate Research Committee of the AHA. His research project is entitled "Defibrillation mechanisms in ventricular dilatation: the role of active deformation" and he will be mentored by Dr. Natalia Trayanova. His research abstract is as follows:
Abstract:
The overall objective of this research is to provide an understanding of the mechanisms of decreased defibrillation efficacy under the conditions of ventricular dilatation. We propose to develop for the first time a dynamic model of combined mechanical and electrical activity in the rabbit ventricles, and to use this model to provide insight into the mechanisms that govern post-shock behavior and the outcome of a defibrillation shock under the conditions of ventricular dilatation. Specifically, the aims of the research are 1) to develop a detailed high-resolution 3D anatomically-accurate bidomain model of electro-mechanical activity in the intact rabbit ventricles that is capable to represent mechano-electric feedback arising from tissue deformation caused by the active tension in the ventricular wall; 2) characterize the distribution of transmembrane potential induced by a defibrillation shock and the post-shock propagation pattern that arises from it under the conditions of left or right ventricular dilatation; and 3) to determine how changes in the post-shock propagation pattern under the conditions of ventricular dilatation result in changes in the upper limit of vulnerability and defibrillation threshold. The working hypothesis in this research is that elevation of defibrillation threshold under the conditions of ventricular dilatation is due to the local mechanical deformations and rearrangement of fiber architecture following the increase of active tension in the ventricular wall. The new mechanistic insights to be acquired under the auspices of this award are expected to guide experimental design and interpretation of experimental findings, and to ultimately lead to rational rather than trial-and-error advancements in defibrillation procedure in patients with heart failure.
ICM PostDoctoral Fellow Dr. Siamak Ardekani Receives American Heart Association Fellowship
Date: May 25, 2007
ICM Postdoctoral Fellow Dr. Siamak Ardekani has received a prestigious American Heart Association Fellowship from the Mid-Atlantic Affiliate Research Committee of the AHA. His research project is entitled "Algorithms for Detecting Changes in Heart Shape and Motion That Are Indicative of Disease State and Arrhythmia Risk" and he will be mentored jointly by Drs. Michael I Miller and Raimond L. Winslow. His research abstract is as follows:
Abstract:
Cardiac disease is often accompanied by ventricular remodeling, a process by which mechanical, neurohormonal, and genetic factors alter ventricular size, shape and function. A detailed knowledge of ventricular remodeling therefore has fundamental importance to our understanding of disease processes and to the development of new treatment strategies. The emerging discipline of Computational Anatomy (CA) is building a mathematical framework for describing anatomic variability and for performing statistical inference and hypothesis testing on disease-induced anatomic changes. In prior work, we used methods of CA to identify the nature of anatomic remodeling in the canine tachycardia pacing-induced model of heart failure by imaging and analyzing excised canine heart (sect. B & C). Results suggest the hypothesis that these analytical methods may be applied to in-vivo analysis of disease-induced changes of both heart structure and motion in a quantitative and objective fashion. If this hypothesis proves to be true, then a broad range of significant clinical applications would be possible. As but one example, an ongoing project in the D. W. Reynolds Cardiovascular Clinical Research Center at JHU is imaging heart shape and motion in a large cohort of patients with left ventricular (LV) dysfunction and who have received Implantable Cardioverter Defibrillator (ICD) therapy for primary prevention of sudden cardiac death (SCD). Quantitative cardiac shape and motion analysis may be useful in revealing those patients who are at highest risk for SCD and who therefore are in greatest need for ICD therapy.
Dilated cardiomyopathy (DCM) is one of the important causes of congestive heart failure (HF), the leading cause of hospitalization in older individuals in the United States. Regardless of type or cause of DCM, an initial insult that produces systolic dysfunction is followed by the initiation of processes designed to temporarily stabilize pump function. However, despite short-term benefits, these compensatory responses ultimately fail over the longer term. The majority of work has focused on characterizing the nature of end-stage DCM. Consequently, there is little information available regarding the time-evolution of anatomic and functional remodeling during DCM. Recently, Costandi et al examined the time course of global anatomical and functional changes that occur during transition to overt HF in a murine model (MLP knockout) of DCM. This study indicates that at the early stage of DCM, ventricular remodeling is mostly driven by myocardial hypertrophic growth. Shortly after this stage, the ventricles undergo a transient dilation followed by overt HF. While several factors, including a possible role of MLP abnormalities, have been attributed to human HF, the murine model of heart failure produces many of the clinical features of human DCM. The MLP deficient murine model of heart failure therefore provides us with a well-studied, controlled preparation with which we will develop, analyze and refine our computational algorithms for in-vivo characterization of changes in heart shape and motion. As our first major objective, we will test the hypothesis that methods of computational anatomy can be applied to in-vivo imaging data to detect functionally relevant changes in heart shape and motion in MLP knockout (MLPKO) murine model of DCM. To do this, we will develop new computational anatomy methods that, when applied to 3D time evolving heart imagery obtained from the MLPKO model of heart failure, enable us to detect statistically significant changes in heart shape and motion over time. As a second major objective, we will test the hypothesis that the analytical methods developed in the MLPKO study can be applied to in-vivo imaging data from a large cohort of patients who are at risk for SCD, who have received ICD placement and who are followed over time to determine those whose ICDs fire (high risk of SCD) and those whose ICDs do not fire (lower risk). We will attempt to find heart shape and motion changes that are predictive of those patients who are at high risk for SCD and thus who are best suited for ICD therapy.
Congratulations to this year’s Raj and Neera Singh Undergraduate Fellows!
Date: May 3, 2007
Ann Kennedy will be mentored by Dr. Michael Miller and Dr. Tilak Ratnanather. Her project will focus on computational neuroanatomy. Ann is a rising junior in the Biomedical Engineering program with a minor in Biology.
Timothy Law will be mentored by Dr. Raimond Winslow and Dr. Joseph Greenstein. His project’s focus is computational modeling of vascular endothelial cells. Timothy is a rising junior in the Biomedical Engineering program.
Linmiao Xu will be mentored by Dr. Natalia Trayanova. He will be working on defibrillation in a 2D computational model of calcium overload. Linmiao is a rising senior in the Biomedical Engineering program.
These students are being awarded a $5000 stipend for a 10 week long research project, sponsored by a generous donation from Raj and Neera Singh.
ICM article highlighted in Proteomics
Date: April 20, 2007
ICM graduate student Troy Anderson, along with ICM faculty Raimond Winslow and Don Geman, recently published an article in Proteomics titled “Discovering robust protein biomarkers for disease from relative expression reversals in 2-D DIGE data.” It was selected as one of 3 articles to highlight in the "In this issue" portion of the journal.
Click here for the full podcast.
ICM is awarded funding from NIH/NHLBI for a short course "Integrative Models of the Cardiac Myocyte"
Date: April 2, 2007
The short course "Integrative Models of the Cardiac Myocyte" will train biomedical researchers and clinician-scientists in how to develop and apply biophysically- and biochemically-detailed, experimentally-based computational models of the cardiac myocyte. Emphasis will be on modular development and testing of models using experimental data, numerical methods for solving model equations, mathematical techniques for developing and solving multi-scale models of the cell and methods for analyzing parameter sensitivity of models.
No date has been set for this course, but information will be posted as it becomes available.
The Institute for Computational Medicine Announces the Cardiovascular Research Grid
Date: March 1, 2007
Supported by an $8.5 million federal grant from NIH/NHLBI, leading researchers at three universities, including Johns Hopkins, are creating an ambitious digital network that will allow cardiovascular researchers worldwide to easily exchange data and expertise on heart-related illnesses. The project, called the Cardiovascular Research Grid, is expected to be a boon to the large community of heart researchers who will use these digital tools to find new ways to prevent, detect and treat life-threatening cardiac ailments.
Read the Headlines at Hopkins article here.
Read the JHU Gazette article here.
Read the Daily Record article here.
Read the Grid Today article here.
Read the Computerworld article here.
ICM Faculty featured in Johns Hopkins Engineering
Date: March 1, 2007
Dr. Raimond Winslow was featured on page 8 in the "R+D" section-short for the Latest Research and Developments from the Whiting School. Drs. Trayanova and Karchin were introduced on page 9 as new faculty members. Read the articles here.
Computer Tool Helps Pinpoint Risky Gene Mutations
Date: February 20, 2007
ICM Faculty member Rachel Karchin was featured in an article on the Headlines at Hopkins website. Dr. Karchin discusses using a computer tool to help identify genetic mutations that may lead to cancer. Read the article here.
Heart of the Matter Video
Date: June 29, 2006
ICM Director Dr. Raimond Winslow, along with ICM Affiliated Faculty member Dr. Eduardo Marbán are featured in this 8 minute mini movie, "The Heart of the Matter." Click here for the movie.
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