Jörg Schultz

Summary

Country: Germany

Publications

  1. doi request reprint ISAAC - InterSpecies Analysing Application using Containers
    Herbert Baier
    Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, Würzburg 97074, Germany
    BMC Bioinformatics 15:18. 2014
  2. pmc The bilaterian roots of cordon-bleu
    Jörg Schultz
    Department of Bioinformatics, Biocenter, University Wurzburg, Am Hubland, Würzburg 97074, Germany
    BMC Res Notes 6:393. 2013
  3. pmc Structural genomics of human proteins--target selection and generation of a public catalogue of expression clones
    Konrad Büssow
    Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
    Microb Cell Fact 4:21. 2005
  4. pmc Heat shock protein-90-alpha, a prolactin-STAT5 target gene identified in breast cancer cells, is involved in apoptosis regulation
    Christian Perotti
    Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
    Breast Cancer Res 10:R94. 2008
  5. pmc HMM Logos for visualization of protein families
    Benjamin Schuster-Böckler
    Department of Mathematics and Computer Science, Freie Universitat Berlin, Germany
    BMC Bioinformatics 5:7. 2004
  6. pmc A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota
    Jörg Schultz
    Department of Bioinformatics, University of Wurzburg, Biocenter, Am Hubland, D 97074 Wurzburg, Germany
    RNA 11:361-4. 2005
  7. ncbi request reprint HTTM, a horizontally transferred transmembrane domain
    Jörg Schultz
    Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    Trends Biochem Sci 29:4-7. 2004
  8. pmc The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses
    Jörg Schultz
    Department of Bioinformatics, Biocenter, University of Würzburg Am Hubland, 97074 Wurzburg, Germany
    Nucleic Acids Res 34:W704-7. 2006
  9. pmc The ITS2 Database III--sequences and structures for phylogeny
    Christian Koetschan
    Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland 97074 Wuerzburg, Germany
    Nucleic Acids Res 38:D275-9. 2010
  10. ncbi request reprint Modelling interaction sites in protein domains with interaction profile hidden Markov models
    Torben Friedrich
    Bioinformatik, Biozentrum, Am Hubland, Universität Würzburg 97074 Würzburg, Germany
    Bioinformatics 22:2851-7. 2006

Collaborators

Detail Information

Publications35

  1. doi request reprint ISAAC - InterSpecies Analysing Application using Containers
    Herbert Baier
    Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, Würzburg 97074, Germany
    BMC Bioinformatics 15:18. 2014
    ..Mostly, they search for enrichments of specific features. But, these tools do not allow an explorative walk through different views and to change the gene lists according to newly upcoming stories...
  2. pmc The bilaterian roots of cordon-bleu
    Jörg Schultz
    Department of Bioinformatics, Biocenter, University Wurzburg, Am Hubland, Würzburg 97074, Germany
    BMC Res Notes 6:393. 2013
    ..The emergence of new actin fibers is initiated by actin nucleators. Whereas most of them are evolutionary old, the cordon-bleu actin nucleator is classified as vertebrate specific...
  3. pmc Structural genomics of human proteins--target selection and generation of a public catalogue of expression clones
    Konrad Büssow
    Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
    Microb Cell Fact 4:21. 2005
    ..139 human proteins (18%) could be expressed and purified in soluble form and with the expected size. All E. coli expression clones are publicly available to facilitate further functional characterisation of this set of human proteins...
  4. pmc Heat shock protein-90-alpha, a prolactin-STAT5 target gene identified in breast cancer cells, is involved in apoptosis regulation
    Christian 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...
  5. pmc HMM Logos for visualization of protein families
    Benjamin 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...
  6. pmc A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota
    Jörg 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...
  7. ncbi request reprint HTTM, a horizontally transferred transmembrane domain
    Jörg 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...
  8. pmc The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses
    Jörg 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...
  9. pmc The ITS2 Database III--sequences and structures for phylogeny
    Christian 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...
  10. ncbi request reprint Modelling interaction sites in protein domains with interaction profile hidden Markov models
    Torben Friedrich
    Bioinformatik, Biozentrum, Am Hubland, Universität Würzburg 97074 Würzburg, Germany
    Bioinformatics 22:2851-7. 2006
    ..As recently demonstrated, these sites are not trivial to detect because of a varying degree of conservation of their location and type within a domain family...
  11. pmc 4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing
    Philipp 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...
  12. pmc The ITS2 Database II: homology modelling RNA structure for molecular systematics
    Christian 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...
  13. pmc Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures
    Matthias Wolf
    Department of Bioinformatics, University of Wurzburg, Biocenter, Am Hubland, Germany
    RNA 11:1616-23. 2005
    ..bioapps.biozentrum.uni-wuerzburg.de...
  14. doi request reprint ProfDistS: (profile-) distance based phylogeny on sequence--structure alignments
    Matthias Wolf
    Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, 97074 Wurzburg, Germany
    Bioinformatics 24:2401-2. 2008
    ..Besides the huge amount of sequence data the structure is important in RNA alignment analysis and phylogenetic reconstruction...
  15. pmc Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees
    Alexander 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...
  16. doi request reprint ITS2 database IV: interactive taxon sampling for internal transcribed spacer 2 based phylogenies
    Christian 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...
  17. doi request reprint 5.8S-28S rRNA interaction and HMM-based ITS2 annotation
    Alexander 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...
  18. pmc Distinguishing species
    Tobias 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...
  19. ncbi request reprint When one plus one equals three: biochemistry and bioinformatics combine to answer complex questions
    Matthias 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...
  20. ncbi request reprint 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
  21. pmc Evolutionary flexibility of protein complexes
    Michael 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...
  22. doi request reprint ITS2 sequence-structure analysis in phylogenetics: a how-to manual for molecular systematics
    Jörg 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...
  23. pmc Protein interaction networks--more than mere modules
    Stefan 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...
  24. pmc Partially-supervised protein subclass discovery with simultaneous annotation of functional residues
    Benjamin 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...
  25. doi request reprint A kinome of 2600 in the ciliate Paramecium tetraurelia
    Felix 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...
  26. ncbi request reprint Evolution of the multifunctional protein tyrosine phosphatase family
    Birgit Pils
    Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
    Mol Biol Evol 21:625-31. 2004
    ....
  27. pmc Explorative data analysis of MCL reveals gene expression networks implicated in survival and prognosis supported by explorative CGH analysis
    Steffen 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...
  28. pmc Genome Expression Pathway Analysis Tool--analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context
    Markus 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...
  29. pmc 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...
  30. pmc Variation in structural location and amino acid conservation of functional sites in protein domain families
    Birgit 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...
  31. pmc Evolution of an RNP assembly system: a minimal SMN complex facilitates formation of UsnRNPs in Drosophila melanogaster
    Matthias 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...
  32. ncbi request reprint Inactive enzyme-homologues find new function in regulatory processes
    Birgit Pils
    Department of Bioinformatics, Wurzburg University, Biozentrum, Am Hubland, 97074 Wurzburg, Germany
    J Mol Biol 340:399-404. 2004
    ..This modification of existing modules is an efficient mechanism to evolve new functions. The invention of inactive enzyme-homologues in metazoa has thereby led to an enhancement of complexity of regulatory networks...
  33. doi request reprint Human HAD phosphatases: structure, mechanism, and roles in health and disease
    Annegrit Seifried
    Rudolf Virchow Center for Experimental Biomedicine, University of Wurzburg, Wurzburg, Germany
    FEBS J 280:549-71. 2013
    ..In this review, we discuss the structure and evolution of human HAD phosphatases, and summarize their known functions in health and disease...
  34. doi request reprint Positive selection in tick saliva proteins of the Salp15 family
    Petra 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...
  35. ncbi request reprint Prediction of structure and functional residues for O-GlcNAcase, a divergent homologue of acetyltransferases
    Jörg 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...