The rapid progress within the areas of bioinformatics
and systems biology gives rise to numerous image analysis
problems. We collaborate with a number of researchers at
Saarland University and other research institutes in order
to address these problems.
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Antibody Profiling for Early Cancer Diagnosis.
Recent results indicate that blood sera screening can be
very useful for the early diagnosis of certain cancer types.
In collaboration with the Bioinformatics Chair of Professor
Hans-Peter Lenhof and the Machine
Learning Group of Professor
Matthias Hein, we have
developped an image processing pipeline for eavluating
autoantibody fingerprints in blood sera. It allows to
extract fairly reliable diagnostic information for
detecting different cancer types and inflammatory
diseases at an early stage [1].
One example are so-called glioma, the most common
primary brain tumor [2].
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Moment Invariants for Comparing Protein Binding Sites.
In collaboration with the Computational Biology and Applied Algorithmics
Group of Dr.
Ingolf Sommer (Max Planck Institute for Computer Science)
we have analysed the geometric shape of
protein-protein binding sites by computing feature
vectors of the 3D moment invariants of Mamistvalov.
The similarity of these feature vectors is used as an
indicator for the similarity of the binding sites. This
approach has been succesfully evaluated for a representative
set of the SCOPPI database consisting of 2819 binding
sites.
[3].
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Denoising of 3-D Cryo-Electron Tomograms.
Cryo-Electron Tomography is a modern 3-D imaging method
that allows investigations down to a biomolecular level,
e.g. in order to study actin filaments and cell membranes.
Unfortunately, these data sets are severely degraded by
noise.
In collaboration with the group of Professor
Hans-Christian Hege
(Zuse Institute Berlin) we have applied 3-D variants of
nonlocal means filters for denoising such data sets. The
data have been provided by the
Max Planck Institute of Biochemistry in Martinsried near Munich.
[4], [5].
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Analysis of Particle Transport in Lung Tissue.
Understanding the particle transport in lung tissue is
of importance for the study of the intake of harmful
particles as well as of useful medical substances.
In collaboration with the Chair of Professor
Claus Michael Lehr (Dept. of Biopharmaceutics and
Parmaceutical Technology) we have evaluated the usefulness of 12
different motion estimation algorithms for automising
the analysis of transport phenomena in tracheal tissue.
[6].
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Intracellular Transport of Nanoparticles.
Nanoparticles are becoming more and more important in numerous
applications, but their inflammatory and toxicological effects in
human cells are hardly understood. In collaboration with research
groups from
pharmaceutical biology
(Professor Alexandra Kiemer),
materials science
(Professors Annette Kraegeloh and Eduard Arzt) and
theoretical physics (Professor Ludger Santen),
an integrated approach to trace and model the intracellular transport of
nanoparticles is being developped. This will allow to relate the structural
properties of the nanoparticles with their subcellular distribution,
and to optimise the structural properties of nanoparticles such that
their inflammatory response is minimised. This project has just started
and is funded by the State of Saarland.
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A. Keller, N. Ludwig, S. Heisel, P. Leidinger, C. Andres, W.-I. Steudel,
H. Huwer, B. Burgeth, M. Hein, J. Weickert, E. Meese, H.-P. Lenhof:
Large-scale antibody profiling of human blood sera: The future of molecular
diagnosis..
Informatik Spektrum, Vol. 32, No. 4, 332-338, 2009.
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N. Ludwig, A. Keller, S. Heisel, P. Leidinger, V. Klein, S. Rheinheimer,
C. Andres, B. Stephan, W. I. Steudel, N. Graf, B. Burgeth, J. Weickert,
H.-P. Lenhof, E. Meese:
Improving seroreactivity based detection of glioma.
Neoplasia, Vol. 11, No. 12, 1383-1389, December 2009.
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I. Sommer, O. Müller; F. S. Domingues, O. Sander, J. Weickert,
T. Lengauer:
Moment invariants as shape recognition technique for comparing protein
binding sites.
Bioinformatics, Vol. 23, No. 23, 3139-3146, 2007.
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M. Portz:
Denoising of a 3-D Cryo-Electron-Tomogram via Non-Local Means.
Diploma Thesis, Dept. of Computer Science, Saarland University,
Saarbrücken, Germany, 2008.
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D. Günther, S. Prohaska, M. Portz, H.-C. Hege, J. Weickert:
Nonlocal means filtering for reconstructing actin filaments from
cryo-electron tomograms.
Preprint, 2008.
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C. Kariger:
Bewegungsanalyse von Nanopartikeln im Trachealgewebe von
Hühnerembryonen.
Diploma Thesis, Dept. of Computer Science, Saarland University,
Saarbrücken, Germany, 2008.
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