Research Topics
Species | Jörg SchultzSummaryCountry: Germany Publications
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Publications
Heat shock protein-90-alpha, a prolactin-STAT5 target gene identified in breast cancer cells, is involved in apoptosis regulationChristian Perotti
Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
Breast Cancer Res 10:R94. 2008..We hypothesise that the identification of these genes should yield insights into the mechanisms by which prolactin participates in cancer formation or progression, and possibly how it regulates normal mammary gland development...
HMM Logos for visualization of protein familiesBenjamin Schuster-Böckler
Department of Mathematics and Computer Science, Freie Universitat Berlin, Germany
BMC Bioinformatics 5:7. 2004..Profile Hidden Markov Models (pHMMs) are a widely used tool for protein family research. Up to now, however, there exists no method to visualize all of their central aspects graphically in an intuitively understandable way...- A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the EukaryotaJörg Schultz
Department of Bioinformatics, University of Wurzburg, Biocenter, Am Hubland, D 97074 Wurzburg, Germany
RNA 11:361-4. 2005..In summary, our analysis strengthens the potential of ITS2 as a general phylogenetic marker and provides a data source for further ITS2-based analyses... 
HTTM, a horizontally transferred transmembrane domainJörg Schultz
Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
Trends Biochem Sci 29:4-7. 2004..Its occurrence in eukaryotes, bacteria and archaea is probably caused by horizontal gene transfer rather than by early evolution. The conservation of VKGC catalytic sites also indicates an enzymatic function for the other family members...- The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analysesJörg Schultz
Department of Bioinformatics, Biocenter, University of Würzburg Am Hubland, 97074 Wurzburg, Germany
Nucleic Acids Res 34:W704-7. 2006..The current version of the ITS2 database can be accessed via http://its2.bioapps.biozentrum.uni-wuerzburg.de... - The ITS2 Database III--sequences and structures for phylogenyChristian Koetschan
Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland 97074 Wuerzburg, Germany
Nucleic Acids Res 38:D275-9. 2010..Sequences can be searched for known and newly identified motifs. Together, the database and the web server build an exhaustive resource for ITS2 based phylogenetic analyses... - 4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editingPhilipp N Seibel
Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, Wurzburg, Germany
BMC Bioinformatics 7:498. 2006..g. the ITS2 Database), we are faced with the problem to handle sequences and their associated secondary structures synchronously... - The ITS2 Database II: homology modelling RNA structure for molecular systematicsChristian Selig
Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland 97074 Würzburg, Germany
Nucleic Acids Res 36:D377-80. 2008..These genera might have evolved an ITS2 structure diverging from the standard one. The current version of the ITS2 Database can be accessed via http://its2.bioapps.biozentrum.uni-wuerzburg.de... - Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structuresMatthias Wolf
Department of Bioinformatics, University of Wurzburg, Biocenter, Am Hubland, Germany
RNA 11:1616-23. 2005..bioapps.biozentrum.uni-wuerzburg.de... 
ProfDistS: (profile-) distance based phylogeny on sequence--structure alignmentsMatthias Wolf
Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, 97074 Wurzburg, Germany
Bioinformatics 24:2401-2. 2008..Moreover, ProfDistS can deal also with protein sequences...- Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic treesAlexander Keller
Department of Bioinformatics, University of Wurzburg, Am Hubland, 97074 Wurzburg, Germany
Biol Direct 5:4. 2010..In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking... - ITS2 database IV: interactive taxon sampling for internal transcribed spacer 2 based phylogeniesChristian Koetschan
Department of Bioinformatics, Biocenter, University Wurzburg, Germany
Mol Phylogenet Evol 63:585-8. 2012..Thus, the ITS2 Workbench enables a fast, interactive and iterative taxon sampling leading to more accurate ITS2 based phylogenies... - Distinguishing speciesTobias Müller
Department of Bioinformatics, Biocenter, University of Wurzburg, Germany
RNA 13:1469-72. 2007..Thus, a CBC in an ITS2 sequence-structure alignment is a sufficient condition to distinguish even closely related species... - 5.8S-28S rRNA interaction and HMM-based ITS2 annotationAlexander Keller
Department of Bioinformatics, University of Wurzburg, Biocenter, Am Hubland, 97074 Wurzburg, Germany
Gene 430:50-7. 2009..Sequences can be submitted to the following website for HMM-based ITS2 delineation: http://its2.bioapps.biozentrum.uni-wuerzburg.de... - When one plus one equals three: biochemistry and bioinformatics combine to answer complex questionsMatthias Kroiss
Theodor Boveri Institute, Biocenter, Wurzburg, Germany
Fly (Austin) 3:210-2. 2009..As a tool to better understand the function of individual proteins in multimeric molecular machineries, we therefore advocate iterative combination of bioinformatics with biochemical or functional assessment... - A novel conserved family of nitric oxide synthase?Tomasz Zemojtel
Department of Bioinformatics, University of Wuerzburg, Am Hubland, D 97074 Wuerzburg, Germany
Trends Biochem Sci 29:224-6. 2004 - Evolutionary flexibility of protein complexesMichael F Seidl
Department of Bioinformatics, Biozentrum, University Wurzburg, Am Hubland, 97074 Wurzburg, Germany
BMC Evol Biol 9:155. 2009..Here, we analysed in a large scale approach whether this flexibility in evolution is only limited to a distinct number of complexes or represents a more general trend... - Protein interaction networks--more than mere modulesStefan Pinkert
Department of Bioinformatics, Biocenter, University of Wurzburg, Wurzburg, Germany
PLoS Comput Biol 6:e1000659. 2010..Thus, there is more structure in protein-interaction networks than cohesive modules alone and we believe this finding can significantly improve automated function prediction algorithms... - ITS2 sequence-structure analysis in phylogenetics: a how-to manual for molecular systematicsJörg Schultz
Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, D 97074 Wurzburg, Germany
Mol Phylogenet Evol 52:520-3. 2009..Moreover, compensatory base changes (CBCs) in ITS2 sequence-structure pairs are identified as a possible marker for distinguishing species... - Partially-supervised protein subclass discovery with simultaneous annotation of functional residuesBenjamin Georgi
Max Planck Institute for Molecular Genetics, Dept, of Computational Molecular Biology, Ihnestrasse 73, 14195 Berlin, Germany
BMC Struct Biol 9:68. 2009..The locations of putative functional residues in known protein structures provide insights into how different substrate specificities are reflected on the protein structure level... - A kinome of 2600 in the ciliate Paramecium tetraureliaFelix Bemm
Department of Bioinformatics, Biocenter, Am Hubland, 97074 Wurzburg, Germany
FEBS Lett 583:3589-92. 2009..tetraurelia. The kinases are embedded in only 40 domain architectures, contrasting 134 in human. This might indicate different mechanisms to achieve target specificity... - Explorative data analysis of MCL reveals gene expression networks implicated in survival and prognosis supported by explorative CGH analysisSteffen Blenk
Department of Bioinformatics, University of Wurzburg, Biozentrum, Am Hubland, D 97074 Wurzburg, Germany
BMC Cancer 8:106. 2008..Both gene expression and comparative genomic hybridization (CGH) data vary considerably between patients with implications for their prognosis... - Genome Expression Pathway Analysis Tool--analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic contextMarkus Weniger
Department of Bioinformatics, Biocenter, University of Wurzburg, Wurzburg, Germany
BMC Bioinformatics 8:179. 2007..Although programs for the statistical analysis of microarray data exist, most of them lack an integration of analysis results and biological interpretation... - Modelling interaction sites in protein domains with interaction profile hidden Markov modelsTorben Friedrich
Bioinformatik, Biozentrum, Am Hubland, , Germany
Bioinformatics 22:2851-7. 2006..The algorithm enhances the quality of interaction site predictions and is a suitable tool for large scale studies, which was already demonstrated for pHMMs. AVAILABILITY: The MATLAB-files are available on request from the first author... - Exonization of active mouse L1s: a driver of transcriptome evolution?Tomasz Zemojtel
Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D 14195 Berlin, Germany
BMC Genomics 8:392. 2007..Long interspersed nuclear elements (LINE-1s, L1s) have been recently implicated in the regulation of mammalian transcriptomes... - Variation in structural location and amino acid conservation of functional sites in protein domain familiesBirgit Pils
Department of Bioinformatics, University of Wurzburg, Biocenter, Am Hubland, 97074 Wurzburg, Germany
BMC Bioinformatics 6:210. 2005..In the analysis presented here, we have investigated the conservation of location and type of amino acids at functional sites, and compared the behaviour of functional sites between different protein domains... - Evolution of an RNP assembly system: a minimal SMN complex facilitates formation of UsnRNPs in Drosophila melanogasterMatthias Kroiss
Department of Biochemistry, Theodor Boveri Institute, Biocenter, Am Hubland, 97074 Wurzburg, Germany
Proc Natl Acad Sci U S A 105:10045-50. 2008..The evolution of the SMN complex is an interesting example of how the simplification of a biochemical process contributes to genome compaction... - Evolution of the multifunctional protein tyrosine phosphatase familyBirgit Pils
Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
Mol Biol Evol 21:625-31. 2004.... - Positive selection in tick saliva proteins of the Salp15 familyPetra Catalina Schwalie
Department of Bioinformatics, Biocenter, University of Wurzburg, Wurzburg, Germany
J Mol Evol 68:186-91. 2009..The identification of probably functionally relevant sites in the Salp15 family might direct the detailed experimental analysis of their interaction with human and bacterial proteins... - Prediction of structure and functional residues for O-GlcNAcase, a divergent homologue of acetyltransferasesJörg Schultz
Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany
FEBS Lett 529:179-82. 2002..Comparison with solved structures of different GNATs led to a reliable structure prediction and mapping of residues involved in binding of the GlcNAc-modified proteins and catalysis...