News Story
Faculty Spotlight: Stefan Birmanns, PhD
Researcher creates 3D images with innovative approach to computational modeling
Published February 08, 2010 by Rachel Christianson
Stefan Birmanns, PhD, joined The University of Texas School of Health
Information Sciences at Houston (SHIS) in 2003 as a post-doctoral
research associate. In the seven years since, he became part of
the school's faculty and runs his own lab. 
Originally from Germany, Birmanns
received his Master's and Doctoral degrees from the University of
Aachen. During this time he collaborated with groups in Illinois and
California. After receiving his PhD, he then decided to move to the U.S.
permanently, where he first worked as a post-doctoral research
associate at the Scripps Research Institute in California. Shortly
thereafter, Birmanns came to Houston when he followed a faculty mentor
to SHIS.
"The School of Health Information Sciences was an
attractive opportunity, especially for me as an interdisciplinary
researcher," said Birmanns. "A school devoted to biomedical
informatics, situated in the largest medical center in the world."
In
2006 Birmanns became a faculty member at SHIS and less than a year
later he took over the Laboratory for Integrative Structural
Bioinformatics, which focuses on two key areas of research.
The
first is analyzing data from electron microscopy and tomography, which
are low resolution, volumetric images of atomic structures. Researchers
often look at these images to get a better understanding of molecules,
viruses and other systems throughout the body. However, these
images don't provide an atomic level of detail, which makes a
computer-based simulation of the dynamics of the molecule impossible. By
using data from other experiments, Birmanns is able to develop
algorithms that determine a high-resolution reconstruction of the
volumetric information of the structure.
This leads to Birmann's
second area of research. After creating the algorithms, Birmann?s
and his lab team are able to create interactive 3-D renderings of these
complex systems. They develop the molecular modeling and visualization
software "Sculptor," which uses state of the art, programmable computer
graphics cards to display the large macromolecular systems.
"We put the glasses on and see," said Birmanns.
Through
this visualization, millions of atoms are rendered and scientists are
able to see much more detail than ever before. The challenge is
developing meaningful visual renderings that can actually help
researchers detect unknown features in data.
To augment the
visual sense, Birmanns' team also uses haptic rendering to represent
these complex 3D relationships and shapes. A haptic device is employed
to create an artificial tactile sensation. It applies forces,
vibrations and motions upon the user.
This type of research is of
significant importance for the better understanding of the body's
complex systems at a molecular level. For example, glycosis is a process
that produces energy for the body. It is also known that tumor cells,
like those in cancer, have a very high glycosis rate. This is known as
the Warburg effect. If glycosis is better understood at the molecular
level, researchers might be able to block a molecular system in the
glycolytic pathway and thereby potentially stop or even reverse tumor
growth.
In the future, Birmann's research may be able to help in
the process of rational drug design. Although his research occurs
before actual drug development, it can help accelerate the process by
suggesting leads, which makes it more efficient and cost effective.
As
one of the relatively few places in the world like it, the lab is
routinely used by scientists from the Texas Medical Center for modeling
and rendering of large biomedical data sets. Birmanns also has
national and international collaborations with scientists from the
University of Vermont, Weill College of Medicine, Penn State University
and the Research Center in Juelich, Germany.
Birmann's vision
for the lab is to integrate more experimental methods in order to be
able to analyze data from images with lower and lower resolutions.
"A
long term goal would be the development of an interactive 3D
multi-resolution atlas of the cell," said Birmanns, "seamlessly
combining experimental data from various sources and levels of
resolution, at the same time displaying it using cutting-edge,
multi-modal rendering techniques."
With this, he hopes the lab
will continue to grow through the addition of more students and
researchers.
Additionally, Birmanns teaches several courses at
SHIS and won the John P. McGovern Outstanding Teacher Award in
2008.
by Rachel Christianson, School of Health Information Sciences
