Roland Schwarz's Publications List

Staphylococcus aureus physiological growth limitations: insights from flux calculations built on proteomics and external metabolite data.

2011-08-26T16:03:30Z

Comparing proteomics and metabolomics allows insights into Staphylococcus aureus physiological growth. We update genome and proteome information and deliver strain-specific metabolic models for three S. aureus strains (COL, N315, and Newman). We find a number of differences in metabolism and enzymes. Growth experiments (glucose or combined with oxygen limitation) were conducted to measure external...

Chunguang Liang, Manuel Liebeke, Roland Schwarz, Daniela Zühlke, Stephan Fuchs, Leonhard Menschner, Susanne Engelmann, Christiane Wolz, Sarah Jaglitz, Jörg Bernhardt, Michael Hecker, Michael Lalk, Thomas Dandekar (2011) Proteomics 11: 10 1915-1935

Characterization of FarR as a highly specialized, growth phase-dependent transcriptional regulator in Neisseria meningitidis.

2011-02-21T18:06:00Z

Transcriptional regulators play an important role for the survival of Neisseria meningitidis within its human host. We have recently shown that FarR acts as transcriptional repressor of the adhesin nadA in N. meningitidis. Here, we examined the FarR regulon by microarray analyses, qRT-PCR, and electrophoretic mobility shift assays, revealing that FarR is a highly specific repressor of nadA. We dem...

Stephanie Schielke, Carolin Spatz, Roland Felix Schwarz, Biju Joseph, Christoph Schoen, Sabine Marita Schulz, Kerstin Hubert, Matthias Frosch, Alexandra Schubert-Unkmeir, Oliver Kurzai (2011) Int J Med Microbiol :

Virulence Evolution of the Human Pathogen Neisseria meningitidis by Recombination in the Core and Accessory Genome.

2011-05-17T21:42:41Z

Neisseria meningitidis is a naturally transformable, facultative pathogen colonizing the human nasopharynx. Here, we analyze on a genome-wide level the impact of recombination on gene-complement diversity and virulence evolution in N. meningitidis. We combined comparative genome hybridization using microarrays (mCGH) and multilocus sequence typing (MLST) of 29 meningococcal isolates with computati...

Biju Joseph, Roland F Schwarz, Burkhard Linke, Jochen Blom, Anke Becker, Heike Claus, Alexander Goesmann, Matthias Frosch, Tobias Müller, Ulrich Vogel, Christoph Schoen (2011) PLoS One 6: 4

Evaluation of one- and two-color gene expression arrays for microbial comparative genome hybridization analyses in routine applications.

2010-07-23T16:08:45Z

DNA microarray technology has already revolutionized basic research in infectious diseases, and whole-genome sequencing efforts have allowed for the fabrication of tailor-made spotted microarrays for an increasing number of bacterial pathogens. However, the application of microarrays in diagnostic microbiology is currently hampered by the high costs associated with microarray experiments and the s...

Roland Schwarz, Biju Joseph, Gabriele Gerlach, Anja Schramm-Glück, Kathrin Engelhard, Matthias Frosch, Tobias Müller, Christoph Schoen (2010) J Clin Microbiol :

Evolutionary distances in the twilight zone-a rational kernel approach.

2011-01-13T09:57:41Z

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologi...

Roland F Schwarz, William Fletcher, Frank Förster, Benjamin Merget, Matthias Wolf, Jörg Schultz, Florian Markowetz (2010) PLoS One 5: 12

Comparative genome biology of a serogroup B carriage and disease strain supports a polygenic nature of meningococcal virulence.

2010-08-23T10:25:40Z

Neisseria meningitidis serogroup B strains are responsible for most meningococcal cases in the industrialized countries, and strains belonging to the clonal complex ST-41/44 are among the most prevalent serogroup B strains in carriage and disease. Here we report the first genome and transcriptome comparison of a serogroup B carriage strain from the clonal complex ST-41/44 with the serogroup B dise...

Biju Joseph, Susanne Schneiker-Bekel, Anja Schramm-Glück, Jochen Blom, Heike Claus, Burkhard Linke, Roland F Schwarz, Anke Becker, Alexander Goesmann, Matthias Frosch, Christoph Schoen (2010) J Bacteriol :

A probabilistic model of cell size reduction in Pseudo-nitzschia delicatissima (Bacillariophyta).

2009-04-23T12:45:50Z

The pennate planktonic diatom Pseudo-nitzschia delicatissima is very common in temperate marine waters and often responsible for blooms. Due to its surrounding rigid silicate frustrule the diatom undergoes successive size reduction as its vegetative reproduction cycle proceeds. Since a long time the life cycle of diatoms has raised scientific interest and some years ago extensive samples of Pseudo...

Schwarz, Wolf, Müller (2009) J Theor Biol :

Detecting species-site dependencies in large multiple sequence alignments.

2009-08-18T10:01:03Z

Multiple sequence alignments (MSAs) are one of the most important sources of information in sequence analysis. Many methods have been proposed to detect, extract and visualize their most significant properties. To the same extent that site-specific methods like sequence logos successfully visualize site conservations and sequence-based methods like clustering approaches detect relationships betwee...

Schwarz, Seibel, Rahmann, Schoen, Huenerberg, Müller-Reible, Dandekar, Karchin, Schultz, Müller (2009) Nucleic Acids Res :

The ITS2 Database III--sequences and structures for phylogeny.

2009-11-23T16:50:19Z

The internal transcribed spacer 2 (ITS2) is a widely used phylogenetic marker. In the past, it has mainly been used for species level classifications. Nowadays, a wider applicability becomes apparent. Here, the conserved structure of the RNA molecule plays a vital role. We have developed the ITS2 Database (http://its2.bioapps.biozentrum.uni-wuerzburg.de) which holds information about sequence, str...

Koetschan, Förster, Keller, Schleicher, Ruderisch, Schwarz, Müller, Wolf, Schultz (2009) Nucleic Acids Res :

A kinome of 2600 in the ciliate Paramecium tetraurelia.

2009-10-22T17:00:52Z

Protein kinases play a crucial role in the regulation of cellular processes. Most eukaryotes reserve about 2.5% of their genes for protein kinases. We analysed the genome of the single-celled ciliate Paramecium tetraurelia and identified 2,606 kinases, about 6,6% of its genes, representing the largest kinome to date. A gene tree combined with human kinases revealed a massive expansion of the calci...

Bemm, Schwarz, Förster, Schultz (2009) FEBS Lett :

New trends in pharmacogenomic strategies against resistance development in microbial infections.

2009-04-23T12:45:13Z

This review summarizes some of the new trends in the fight against drug resistant bacteria. We review Gram-positive (e.g., S.aureus) and Gram-negative (e.g., Pseudomonas aeruginosa, Helicobacter pylori) bacteria, the current antibiotic resistance situation, as well as resistance spread and some recently discovered resistance mechanisms, such as those based on integrons and complex transposons. We ...

Knut Ohlsen, Gudrun Dandekar, Roland Schwarz, Thomas Dandekar (2008) Pharmacogenomics 9: 11 1711-1723

Modelling phagosomal lipid networks that regulate actin assembly.

2009-04-23T12:45:13Z

BACKGROUND: When purified phagosomes are incubated in the presence of actin under appropriate conditions, microfilaments start growing from the membrane in a process that is affected by ATP and the lipid composition of the membrane. Isolated phagosomes are metabolically active organelles that contain enzymes and metabolites necessary for lipid interconversion. Hence, addition of ATP, lipids, and a...

Mark Kühnel, Luis S Mayorga, Thomas Dandekar, Juilee Thakar, Roland Schwarz, Elsa Anes, Gareth Griffiths, Jens Reich (2008) BMC Syst Biol 2:

Unsupervised meta-analysis on diverse gene expression datasets allows insight into gene function and regulation

2009-05-08T08:30:56Z

Over the past years, microarray databases have increased rapidly in size. While they offer a wealth of data, it remains challenging to integrate data arising from different studies. Here we propose an unsupervised approach of a large-scale meta-analysis on Arabidopsis thaliana whole genome expression datasets to gain additional insights into the function and regulation of genes. Applying...

Julia C. Engelmann and Roland Schwarz and Steffen Blenk and Torben Friedrich and Philipp N. Seibel and Thomas Dandekar and Tobias Müller (2008) Bioinformatics and Biology Insights 2: 271-286

Integrated network reconstruction, visualization and analysis using YANAsquare.

2009-04-23T12:45:13Z

BACKGROUND: Modeling of metabolic networks includes tasks such as network assembly, network overview, calculation of metabolic fluxes and testing the robustness of the network. RESULTS: YANAsquare provides a software framework for rapid network assembly (flexible pathway browser with local or remote operation mode), network overview (visualization routine and YANAsquare editor) and network perform...

Roland Schwarz, Chunguang Liang, Christoph Kaleta, Mark Kühnel, Eik Hoffmann, Sergei Kuznetsov, Michael Hecker, Gareth Griffiths, Stefan Schuster, Thomas Dandekar (2007) BMC Bioinformatics 8:

13C isotopologue perturbation studies of Listeria monocytogenes carbon metabolism and its modulation by the virulence regulator PrfA.

2009-04-23T12:45:13Z

The carbon metabolism of Listeria monocytogenes (Lm) EGD and the two isogenic mutant strains LmDeltaprfA and LmDeltaprfApPRFA* (showing no or enhanced expression, respectively, of the virulence factor PrfA) was determined by 13C isotopologue perturbation. After growth of the bacteria in a defined medium containing a mixture of [U-13C6]glucose and glucose with natural 13C abundance (1:25, wt/wt), 1...

Wolfgang Eisenreich, Jörg Slaghuis, Ralf Laupitz, Johanna Bussemer, Jochen Stritzker, Christine Schwarz, Roland Schwarz, Thomas Dandekar, Werner Goebel, Adelbert Bacher (2006) Proc Natl Acad Sci U S A 103: 7 2040-2045

YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.

2009-04-23T12:45:13Z

BACKGROUND: A number of algorithms for steady state analysis of metabolic networks have been developed over the years. Of these, Elementary Mode Analysis (EMA) has proven especially useful. Despite its low user-friendliness, METATOOL as a reliable high-performance implementation of the algorithm has been the instrument of choice up to now. As reported here, the analysis of metabolic networks has b...

Roland Schwarz, Patrick Musch, Axel von Kamp, Bernd Engels, Heiner Schirmer, Stefan Schuster, Thomas Dandekar (2005) BMC Bioinformatics 6:

Pharmacogenomic strategies against resistance development in microbial infections.

2009-04-23T12:45:13Z

There are several promising new strategies against resistance development in microbial infections. This paper discusses typical experimental and bioinformatical strategies to study the impact of infectious challenges on host-pathogen interaction, followed by several novel approaches and sources for new pharmaceutical strategies against resistance development. Genomics reveals promising new targets...

Wilma Ziebuhr, Ke Xiao, Boubacar Coulibaly, Roland Schwarz, Thomas Dandekar (2004) Pharmacogenomics 5: 4 361-379