Jürgen Albert

Publications of Jürgen Albert

• Ancient Typefaces and Parametric Weighted Finite Automata.

  Authors: Jürgen Albert, German Tischler

  Rainbow of Computer Science - Dedicated to Hermann Maurer on the Occasion of His 70th Birthday; 01/2011

• On Succinct Representations of Textured Surfaces by Weighted Finite Automata.

  Authors: Jürgen Albert, German Tischler

  J. UCS. 01/2010; 16:586-603.

• Integrating color constancy into JPEG2000.

  Authors: Marc Ebner, German Tischler, Jürgen Albert

  IEEE transactions on image processing : a publication of the IEEE Signal Processing Society. 12/2007; 16(11):2697-706.

  The human visual system is able to perceive colors as approximately constant. This ability is known as color constancy. In contrast, the colors measured by a sensor vary with the type of illuminantThe human visual system is able to perceive colors as approximately constant. This ability is known as color constancy. In contrast, the colors measured by a sensor vary with the type of illuminant used. Color constancy is very important for digital photography and automatic color-based object recognition. In digital photography, this ability is known under the name automatic white balance. A number of algorithms have been developed for color constancy. We review two well-known color constancy algorithms, the gray world assumption and the Retinex algorithm and show how a color constancy algorithm may be integrated into the JPEG2000 framework. Since computer images are usually stored in compressed form anyway, little overhead is required to add color constancy into the processing pipeline.

• On Generalizations of Weighted Finite Automata and Graphics Applications.

  Authors: Jürgen Albert, German Tischler

  Algebraic Informatics, Second International Conference, CAI 2007, Thessaloniki, Greece, May 21-25, 2007, Revised Selected and Invited Papers; 01/2007

• Evolution of Vertex and Pixel Shaders.

  Authors: Marc Ebner, Markus Reinhardt, Jürgen Albert

  Genetic Programming, 8th European Conference, EuroGP2005, Lausanne, Switzerland, March 30 - April 1, 2005, Proceedings; 01/2005

• RIDOM: comprehensive and public sequence database for identification of Mycobacterium species.

  Authors: Dag Harmsen, Stefan Dostal, Andreas Roth, Stefan Niemann, Jörg Rothgänger, Michael Sammeth, Jürgen Albert, Matthias Frosch, Elvira Richter

  BMC infectious diseases. 12/2003; 3:26.

  BACKGROUND: Molecular identification of Mycobacterium species has two primary advantages when compared to phenotypic identification: rapid turn-around time and improved accuracy. The informationBACKGROUND: Molecular identification of Mycobacterium species has two primary advantages when compared to phenotypic identification: rapid turn-around time and improved accuracy. The information content of the 5' end of the 16S ribosomal RNA gene (16S rDNA) is sufficient for identification of most bacterial species. However, reliable sequence-based identification is hampered by many faulty and some missing sequence entries in publicly accessible databases. METHODS: In order to establish an improved 16S rDNA sequence database for the identification of clinical and environmental isolates, we sequenced both strands of the 5' end of 16S rDNA (Escherichia coli positions 54 to 510) from 199 mycobacterial culture collection isolates. All validly described species (n = 89; up to March 21, 2000) and nearly all published sequevar variants were included. If the 16S rDNA sequences were not discriminatory, the internal transcribed spacer (ITS) region sequences (n = 84) were also determined. RESULTS: Using 5'-16S rDNA sequencing a total of 64 different mycobacterial species (71.9%) could be identified. With the additional input of the ITS sequence, a further 16 species or subspecies could be differentiated. Only Mycobacterium tuberculosis complex species, M. marinum/M. ulcerans and the M. avium subspecies could not be differentiated using 5'-16S rDNA or ITS sequencing. A total of 77 culture collection strain sequences, exhibiting an overlap of at least 80% and identical by strain number to the isolates used in this study, were found in the GenBank. Comparing these with our sequences revealed that an average of 4.31 nucleotide differences (SD +/- 0.57) were present. CONCLUSIONS: The data from this analysis show that it is possible to differentiate most mycobacterial species by sequence analysis of partial 16S rDNA. The high-quality sequences reported here, together with ancillary information (e.g., taxonomic, medical), are available in a public database, which is currently being expanded in the RIDOM project http://www.ridom-rdna.de), for similarity searches.

• Digital extractor: analysis of digital differential display output.

  Authors: Michael Sammeth, Jörg Rothgänger, W. Esser, Jürgen Albert, Jens Stoye, Dag Harmsen

  Bioinformatics. 01/2003; 19:1592-1593.

• RIDOM: Ribosomal Differentiation of Medical Micro-organisms Database.

  Authors: Dag Harmsen, Jörg Rothgänger, Matthias Frosch, Jürgen Albert

  Nucleic acids research. 02/2002; 30(1):416-7.

  The ribosomal differentiation of medical micro-organisms (RIDOM) web server, first described by Harmsen et al. [Harmsden,D., Rothganger,J., Singer,C., Albert,J. and Frosch,M. (1999) Lancet, 353,The ribosomal differentiation of medical micro-organisms (RIDOM) web server, first described by Harmsen et al. [Harmsden,D., Rothganger,J., Singer,C., Albert,J. and Frosch,M. (1999) Lancet, 353, 291], is an evolving electronic resource designed to provide micro-organism differentiation services for medical identification needs. The diagnostic procedure begins with a specimen partial small subunit ribosomal DNA (16S rDNA) sequence. Resulting from a similarity search, a species or genus name for the specimen in question will be returned. Where the first results are ambiguous or do not define to species level, hints for further molecular, i.e. internal transcribed spacer, and conventional phenotypic differentiation will be offered ('sequential and polyphasic approach'). Additionally, each entry in RIDOM contains detailed medical and taxonomic information linked, context-sensitive, to external World Wide Web services. Nearly all sequences are newly determined and the sequence chromatograms are available for intersubjective quality control. Similarity searches are now also possible by direct submission of trace files (ABI or SCF format). Based on the PHRED/PHRAP software, error probability measures are attached to each predicted nucleotide base and visualised with a new 'Trace Editor'. The RIDOM web site is directly accessible on the World Wide Web at http://www.ridom.de/. The email address for questions and comments is webmaster@ridom.de.

• On The Use Of Negative Selection In An Artificial Immune System.

  Authors: Marc Ebner, Hans-Georg Breunig, Jürgen Albert

  GECCO 2002: Proceedings of the Genetic and Evolutionary Computation Conference, New York, USA, 9-13 July 2002; 01/2002

• Coevolution Produces an Arms Race among Virtual Plants.

  Authors: Marc Ebner, Adrian Grigore, Alexander Heffner, Jürgen Albert

  Genetic Programming, 5th European Conference, EuroGP 2002, Kinsale, Ireland, April 3-5, 2002, Proceedings; 01/2002

• Diagnostics of Neisseriaceae and Moraxellaceae by Ribosomal DNA Sequencing: Ribosomal Differentiation of Medical Microorganisms

  Authors: Dag Harmsen, Christian Singer, Jörg Rothgänger, Tone Tønjum, Gerrit Sybren de Hoog, Haroun Shah, Jürgen Albert, Matthias Frosch

  Fast and reliable identification of microbial isolates is a fundamental goal of clinical microbiology. However, in the case of some fastidious gram-negative bacterial species, classical phenotypeFast and reliable identification of microbial isolates is a fundamental goal of clinical microbiology. However, in the case of some fastidious gram-negative bacterial species, classical phenotype identification based on either metabolic, enzymatic, or serological methods is difficult, time-consuming, and/or inadequate. 16S or 23S ribosomal DNA (rDNA) bacterial sequencing will most often result in accurate speciation of isolates. Therefore, the objective of this study was to find a hypervariable rDNA stretch, flanked by strongly conserved regions, which is suitable for molecular species identification of members of the Neisseriaceae and Moraxellaceae. The inter- and intrageneric relationships were investigated using comparative sequence analysis of PCR-amplified partial 16S and 23S rDNAs from a total of 94 strains. When compared to the type species of the genera Acinetobacter, Moraxella, and Neisseria, an average of 30 polymorphic positions was observed within the partial 16S rDNA investigated (corresponding to Escherichia coli positions 54 to 510) for each species and an average of 11 polymorphic positions was observed within the 202 nucleotides of the 23S rDNA gene (positions 1400 to 1600). Neisseria macacae and Neisseria mucosa subsp. mucosa (ATCC 19696) had identical 16S and 23S rDNA sequences. Species clusters were heterogeneous in both genes in the case of Acinetobacter lwoffii, Moraxella lacunata, and N. mucosa. Neisseria meningitidis isolates failed to cluster only in the 23S rDNA subset. Our data showed that the 16S rDNA region is more suitable than the partial 23S rDNA for the molecular diagnosis of Neisseriaceae and Moraxellaceae and that a reference database should include more than one strain of each species. All sequence chromatograms and taxonomic and disease-related information are available as part of our ribosomal differentiation of medical microorganisms (RIDOM) web-based service (http://www.ridom.hygiene.uni-wuerzburg.de/). Users can submit a sequence and conduct a similarity search against the RIDOM reference database for microbial identification purposes.

• QAlign: quality-based multiple alignments with dynamic phylogenetic analysis

  Authors: Michael Sammeth, Jörg Rothgänger, Wolfram Eßer, Jürgen Albert, Jens Stoye, Dag Harmsen

  Bioinformatics, 19(12), pp. 1592-1593.

  Integrating different alignment strategies, a layout editor and tools deriving phylogenetic trees in a 'multiple alignment environment' helps to investigate and enhance results of multiple sequenceIntegrating different alignment strategies, a layout editor and tools deriving phylogenetic trees in a 'multiple alignment environment' helps to investigate and enhance results of multiple sequence alignment by hand. QAlign combines algorithms for fast progressive and accurate simultaneous multiple alignment with a versatile editor and a dynamic phylogenetic analysis in a convenient graphical user interface.