A5103123664- Particle Detector Development and Performance
- Radiation Detection and Scintillator Technologies
- Bacterial Genetics and Biotechnology
- Clostridium difficile and Clostridium perfringens research
- Protein Structure and Dynamics
- Biofuel production and bioconversion
- CCD and CMOS Imaging Sensors
- Enzyme Structure and Function
- Machine Learning in Bioinformatics
- Advanced Proteomics Techniques and Applications
- Dark Matter and Cosmic Phenomena
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Nuclear Physics and Applications
- Bioinformatics and Genomic Networks
- RNA modifications and cancer
- Microbial Metabolic Engineering and Bioproduction
- Solar and Space Plasma Dynamics
- RNA Research and Splicing
- Advanced Data Compression Techniques
- Distributed and Parallel Computing Systems
- Yersinia bacterium, plague, ectoparasites research
- X-ray Diffraction in Crystallography
- Vector-borne infectious diseases
- Molecular Junctions and Nanostructures
Ludwig-Maximilians-Universität München
2014-2023
University of Bonn
2018-2023
University of Salzburg
2008-2014
Max Planck Institute for Biophysical Chemistry
2014
Johannes Kepler University of Linz
2013
Max Planck Institute for Developmental Biology
2003-2008
Max Planck Society
2006
Abstract Motivation : Recent breakthroughs in protein residue–residue contact prediction have made reliable de novo of structures possible. The key was to apply statistical methods that can distinguish direct couplings between pairs columns a multiple sequence alignment from merely correlated pairs, i.e. separate indirect effects. Two classes such exist, either relying on regularized inversion the covariance matrix or pseudo-likelihood maximization (PLM). Although PLM-based offer clearly...
REPPER (REPeats and their PERiodicities) is an integrated server that detects analyzes regions with short gapless repeats in protein sequences or alignments. It finds periodicities by Fourier Transform (FTwin) internal similarity analysis (REPwin). FTwin assigns numerical values to amino acids reflect certain properties, for instance hydrophobicity, gives information on corresponding periodicities. REPwin uses self-alignments displays reveal significant similarities. Both programs use a...
Yersinia enterocolitica is an enteric pathogen that exploits diverse means to survive in the human host. Upon Y. entry into host, bacteria sense and respond variety of signals, one which temperature. Temperature particular has a profound impact on gene expression, as most its virulence factors are expressed exclusively at 37 degrees C. These include two outer membrane proteins, YadA Ail, function adhesins complement resistance (CR) factors. Both Ail bind functionally active alternative...
Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such generally requires comprehensive searches in databases known by means appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable instantly matching large oligomers against the complete up-to-date database...
Mass spectrometry based proteomics is the method of choice for quantifying genome-wide differential changes protein expression in a wide range biological and biomedical applications. Protein need to be reliably derived from many measured peptide intensities their corresponding fold changes. These vary considerably given protein. Numerous instrumental setups aim reduce this variability, whereas current computational methods only implicitly account problem. We introduce new method, MS-EmpiRe,...
Every unit of the rRNA gene cluster Saccharomyces cerevisiae contains a unique site, termed replication fork barrier (RFB), where progressing forks are stalled in polar manner. In this work, we determined positions nascent strands at RFB nucleotide resolution. Within an HpaI-HindIII fragment essential for RFB, major and two closely spaced minor arrest sites were found. majority molecules, lagging strand was completely processed discontinuously synthesized extended three bases farther than...
One of the main obstacles preventing solventogenic clostridia from achieving higher yields in biofuel production is toxicity produced solvents. Unfortunately, regulatory mechanisms responsible for shock response are poorly described on transcriptomic level. Although strain
Abstract Summary: The database of known protein structures contains an overwhelming number structural similarities that frequently point to intriguing biological relationships. are often difficult spot, and once detected their comprehension needs proper visualization. Here we introduce the new concept a Fold Space Navigator, user interface enabling efficient navigation through fold space instantaneous visualization pairwise structure similarities. Availability: Navigator is accessible as...
Abstract Summary: The performance of sequence database search methods is usually judged by receiver operating characteristic (ROC) analysis. proper interpretation the results obtained and a fair comparison across different critically depends on properties data set used for such an analysis; in particular, each query must have same number true positives negatives. Here, we present novel web service based dataset specifically designed ROC analysis investigation alignment quality. derived from...
1 Abstract Mass spectrometry based proteomics is the method of choice for quantifying genome-wide differential changes proteins in a wide range biological and biomedical applications. Protein need to be reliably derived from large number measured peptide intensities their corresponding fold changes. These vary considerably given protein. Numerous instrumental setups aim reduce this variability, while current computational methods only implicitly account problem. We introduce new method,...
We report on the preparation of epitaxial MgO film GaAs(001) substrates by molecular beam epitaxy at growth temperature 20–200 °C. Reflection high energy electron diffraction, x-ray and resolution transmission microscopy reveal ordered crystalline cubic MgO(001) ∼200 °C with MgO(001)[100] || GaAs(001)[100] a 4 : 3 lattice registry. The surface films, characterized atomic force microscopy, exhibits root mean square roughness only 0.5 nm. In situ stress measurements tensile as low 1.7 GPa for...
X-ray polarimetry of solar flares is still a not well established field observation our star. Past polarimeters were able to measure with high significance the polarization in X-rays from flares. Moreover, they had no imaging capabilities and measured only by integrating on all image source. We propose mission concept based gas photoelectric polarimeter, coupled multilayer lobster-eye optics, perform imaging-spectro-polarimetry while monitoring entire disc.
ABSTRACT While absolute quantification is challenging in high-throughput measurements, changes of features between conditions can often be determined with high precision. Therefore, analysis fold the standard method, but often, a doubly differential required. Differential alternative splicing an example analysis, i.e. for different isoforms gene. EmpiRe quantitative approach various kinds omics data based on appropriate biological objects. Empirical error distributions these are estimated...
Summary Alternative splicing can substantially diversify biological cell states and influence cellular function. The functional impact of has to be estimated at protein level, typically by mass spectrometry (MS) -based proteomics. Although this technology measures increasingly large peptides sets, distinguishing isoform-specific are rare, limiting detection quantification splicing. We introduce MS-EmpiReS, a quantification-based computational approach for differential alternative in...
Abstract High precision experiments with muons and pions often require tracking charged particles O (100 μm) single-hit resolution, possibly particle identification capabilities, down to very low momenta ( p ≲ 100 MeV/ c ). In such conditions, the trajectories are strongly affected by interaction detector material, reconstruction of kinematic observables consequently deteriorates. A good compromise between resolution material budget can be obtained a Time Projection Chamber (TPC), if light...