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Two New Faculty Appointments at the Institute for Computational Medicine
Date: June 6, 2006
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| Dr. Natalia Trayanova |
Dr. Rachel Karchin |
The Johns Hopkins University's Institute for Computational Medicine is pleased to announce that two new faculty, Dr. Natalia Trayanova and Dr. Rachel Karchin, will be joining us in the next several months.
Natalia Trayanova, Ph.D. who is currently a Professor at Tulane University in the Department of Biomedical Engineering as well as the Director of the Computational Cardiac Electrophysiology Laboratory, will be joining the Institute in August, 2006 as a Professor in the Whiting School of Engineering's Department of Biomedical Engineering.
Dr. Trayanova is recognized internationally as a leader in the field of computational cardiac electrophysiology and research projects in her lab include arrhythmogenesis under the conditions of ischemia, mechano-electric feedback in the heart, mechanisms of ventricular defibrillation, the role of fibroblasts in conduction and defibrillation and arrhythmia induction due to electroporation caused by strong shocks in the heart.
Dr. Trayanova has over 100 peer-reviewed journal publications, book chapters and proceeding publications; was Elected Vice Chair for the 2007 and Chair for the 2008 Gordon Conference on Cardiac Arrhythmia Mechanisms; was an associate editor, IEEE Transactions on Biomedical Engineering; was appointed to the Editorial Board of the journal Heart Rhythm; received the Tulane University Award for Excellence in Research and Scholarship in 2005; was elected a Fellow of the American Institute for Medical and Biological Engineering in 2003; and was a Distinguished Fulbright Research Fellow at Oxford University.
Rachel Karchin, Ph.D., currently a Post Doctoral Fellow at the University of California, San Francisco, in the Department of Biopharmaceutical Sciences, will be joining the Institute in October 2006 as an Assistant Professor in the Whiting School of Engineering's Department of Biomedical Engineering.
Dr. Karchin's current research is focused on the problem of understanding and predicting the effect of point mutations on protein structure and function. Such information will provide insights into the functional mechanisms of proteins as well as their role in human disease and variation in drug response.
Dr. Karchin is a member of the International Society for Computational Biology and the Institute of Electrical and Electronics Engineers.
Institute for Computational Medicine's Summer Undergraduate Fellowship Winners
Date: June 6, 2006
Congratulations to students Laura Doyle and Andy Wong, the first recipients
of the Institute for Computational Medicine's Summer Undergraduate
Fellowship.
Each summer, the Institute for Computational Medicine (ICM), an Institute in
the Whiting School of Engineering and the School of Medicine, will sponsor
research fellowships for Johns Hopkins University undergraduate students.
Fellowships can be awarded in each of the areas of Biological Systems
Modeling, Computational Anatomy, and Bioinformatics.
Laura Doyle will be working with PostDoctoral Fellow Siamak Ardekani in the
area of Biological Systems Modeling. The goal of the project is the
registration of contrast MR images taken in one orientation on one scanner
with sodium MR images taken in a different orientation on a different
scanner in order to obtain information about the sodium ion distributions in
infarct regions of the heart. This process involves extracting the raw data
from the proprietary scanner formats, finding an affine transformation
matrix to describe the registration, implementing a MatLab function to
resample and transform the data, and finally performing LDDMM to match fine
details of the scans.
Andy Wong will be working with Dr. Rene Vidal in the area of Bioinformatics.
His project consists of implementing various image segmentation and
registration algorithms, like level-set based segmentation algorithms, in
C++ and to quantitatively compare the relative performance of different
algorithms against each other in the segmentation of CT scans and MRI heart
images.
Congratulations to both of our inaugural fellows!
ICM
Event: At the Heart of the New Medicine
Date: February 20, 2006
Click here for podcast
Click here to view the Power Point presentation from this event
ICM researchers use new imaging and analytical
methods to model the structure of the failing heart
Date: January 9, 2006
As described in an article published in the January 5th
issue of Circulation Research
(Helm
et. al. 2006. Evidence of structural remodeling in the dyssynchronous
failing heart. 98: 125), researchers at the Institute
for Computational Medicine and the Whitaker Biomedical Engineering
Institute performed diffusion tensor MRI in isolated perfusion-fixed
dog hearts to estimate the distributions of ventricular
myofiber and sheet orientations at sub-millimeter resolution.
The resulting large data sets were compared statistically
between normal and dysynchronous failing groups using novel
techniques from computational anatomy. These studies, let
by BME PhD Program student Patrick Helm, showed that early-activated
myocardial sites exhibit significant reorientation of myocardial
sheets whereas there was no change in late-activated sites.
This remodeling is likely to have significant effects on
regional wall mechanics and electrical conduction. This
issue of Circulation Research includes cover illustrations
from Dr. Helms work and an editorial comment on this work
written by Drs. Andrew McCulloch and Jeffrey Omens of UCSD
(Myocyte
shearing, myocardial sheet and microtubules. 2006. 98:1)
Graduate Student Yasmin Hashambhoy to Present at Conference on Decision and Control
Date: December 7, 2005
ICM Graduate Student Yasmin Hashambhoy will be giving
a presentation on a paper regarding identifying hybrid
systems in a recursive manner, titled "Recursive
Identification of Switched ARX Models with Unknown Number
of Models and Unknown Orders." She is the co-author
of the paper along with Dr. Rene Vidal of the Johns Hopkins
University Center for
Imaging Science. She will be presenting at the Conference
on Decision and Control in Seville, Spain, on December
14, 2005.
ICM awarded grant through the IBM Shared
University Research (SUR) program
Date: October 27, 2005
The Institute for Computational Medicine has been awarded
a grant through the IBM Shared University Research (SUR)
program. This grant will be used to purchase IBM equipment
in support for the Research Grid for Computational Medicine
in Cardiovascular Applications (CardioVascular Research
Grid CVRG) project. This award is being funded by IBM
Healthcare and Life Sciences as a joint research project
between the Institute for Computational Medicine and IBM.
This grant recognizes the high quality of the research
and educational programs being pursued at Johns Hopkins.
The IBM SUR program provides equipment to universities
in order to promote collaborative research in areas of
mutual interest, and strives to establish or strengthen
long term relationships between university faculty/personnel
and the IBM research, development and solutions provider
communities.
The Institute for Computational Medicine Is
Officially Launched!
Date: October 12, 2005
Professor Raimond L. Winslow (Biomedical Engineering)
will direct a new institute that will address important
health problems by using powerful information management
and computing technologies to produce a better understanding
of the origins of human disease. The Institute for Computational
Medicine will involve a close collaboration with researchers
at the School of Medicine.
Read the press release from the Johns Hopkins University here.
Read the article from The Washington Post here.
Read the article from Newswise here.
Read the article from the Baltimore Business Journal here.
Yang, Doyle and Helm Present at BMES
Laboratory Technician Jason Yang
Date: October 10, 2005
Jason Yang, Laura Doyle, Dr. Joseph Greenstein, and Dr.
Patrick Helm of the Center for Cardiovascular Bioinformatics
and Modeling attended the 2005
Annual Biomedical Engineering Society Fall Meeting.
Doyle and Helm gave a presentation on "Virtually
Unwrapping The Cardiac Ventricles." Yang and Helm
presented the poster "Ex Vivo 3D DTMRI Of Human Myocardium."
Greenstein presented "Multi-Scale Modeling Of Ca2+-Induced
Ca2+ Release."
ICM/CCBM Announces Availability of Version 2.0 of
the Protein-DB2 Database/Web Interface System
Date: October 3, 2005
Version 2.0 of the Protein-DB2 database/web interface
system is now available for immediate download via the
CCBM website. An Apache/PHP system was the development
platform for version 1.0 of the web interface; version
2.0 centers its functionality on a Java Application/JSP
server, namely IBM Websphere v5.1. In addition to the
structural changes to the web interface portion, version
2.0 contains several expansions in functionality. They
include the following:
1) Upload and query interfaces for Difference-In Gel
Electrophoresis (DIGE) gel image and analysis software
files,
2) The ability to upload and convert raw MS data files
produced by Shimadzu Axima, Applied Biosystems Voyager,
ThermoFinnigan LCQ and LTQ, and ABI/SCIEX QStar to mzXML
files,
3) Upload and query interfaces for Mascot Mass Spectrometry
(MS) Results HTML and XML files,
4) The ability to associate Two-dimensional Polyacrylamide
Gel Electorphoresis (2D-PAGE), DIGE, MS, and MS results
data to a specific experiment, and
5) User creation and querying interfaces for administrators
to manage access to the system.
Version 2.0 also includes several database schema changes;
a visual display of the database schema is available here.
They include the addition of tables for DIGE analysis
storage, as well as the addition of an alternative protein
hit table, to expand upon the MS Results storage.
Comprehensive system installation documentation, database
creation scripts, and web interface/data processing application
source code are all available here (Registration Required).
Bazzazi Awarded Grant
Date: September 21, 2005
Congratulations to Graduate Student Hojjat Bazzazi who
was awarded a $700 grant toward travel expenses for the Workshop
on Applications of Methods of Stochastic Systems and Statistical
Physics in Biology. The Workshop will be held at the
University of Notre Dame from October 28 - 30, 2005.
