Matthias Wolf

Summary

Country: Germany

Publications

  1. doi request reprint ITS2, 18S, 16S or any other RNA - simply aligning sequences and their individual secondary structures simultaneously by an automatic approach
    Matthias Wolf
    Department of Bioinformatics, Biocenter, University of Wurzburg, 97074 Wurzburg, Germany Electronic address
    Gene 546:145-9. 2014
  2. pmc Compensatory base changes in ITS2 secondary structures correlate with the biological species concept despite intragenomic variability in ITS2 sequences--a proof of concept
    Matthias Wolf
    Department of Bioinformatics, Biocenter, University of Wurzburg, Wurzburg, Germany
    PLoS ONE 8:e66726. 2013
  3. pmc Congruence of chloroplast- and nuclear-encoded DNA sequence variations used to assess species boundaries in the soil microalga Heterococcus (Stramenopiles, Xanthophyceae)
    Nataliya Rybalka
    Experimental Phycology and Culture Collection of Algae SAG, Georg August University Gottingen, Untere Karspüle 2a, Gottingen, 37073, Germany
    BMC Evol Biol 13:39. 2013
  4. pmc ITS2 secondary structure improves phylogeny estimation in a radiation of blue butterflies of the subgenus Agrodiaetus (Lepidoptera: Lycaenidae: Polyommatus )
    Martin Wiemers
    Department of Animal Biodiversity, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Wien, Austria
    BMC Evol Biol 9:300. 2009
  5. 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
  6. ncbi request reprint A java applet for exploring the new higher level classification of eukaryotes with emphasis on the taxonomy of protists
    Matthias Wolf
    Department of Bioinformatics, Biocenter, University of Wurzburg, D 97074 Wurzburg, Germany
    J Eukaryot Microbiol 53:315. 2006
  7. pmc A molecular phylogeny of Hypnales (Bryophyta) inferred from ITS2 sequence-structure data
    Benjamin Merget
    Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, 97074 Wurzburg, Germany
    BMC Res Notes 3:320. 2010
  8. 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
  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. 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

Collaborators

Detail Information

Publications31

  1. doi request reprint ITS2, 18S, 16S or any other RNA - simply aligning sequences and their individual secondary structures simultaneously by an automatic approach
    Matthias Wolf
    Department of Bioinformatics, Biocenter, University of Wurzburg, 97074 Wurzburg, Germany Electronic address
    Gene 546:145-9. 2014
    ..We further introduce a scaled down non-GUI version of 4SALE particularly designed for big data analysis, and available at: http://4sale.bioapps.biozentrum.uni-wuerzburg.de. ..
  2. pmc Compensatory base changes in ITS2 secondary structures correlate with the biological species concept despite intragenomic variability in ITS2 sequences--a proof of concept
    Matthias Wolf
    Department of Bioinformatics, Biocenter, University of Wurzburg, Wurzburg, Germany
    PLoS ONE 8:e66726. 2013
    ..In accordance with the CBC species concept, we could demonstrate that the probability that there is no intragenomic CBC is ∼0.99. ..
  3. pmc Congruence of chloroplast- and nuclear-encoded DNA sequence variations used to assess species boundaries in the soil microalga Heterococcus (Stramenopiles, Xanthophyceae)
    Nataliya Rybalka
    Experimental Phycology and Culture Collection of Algae SAG, Georg August University Gottingen, Untere Karspüle 2a, Gottingen, 37073, Germany
    BMC Evol Biol 13:39. 2013
    ..Despite the large number of species described exclusively using light microscopic morphology, the assessment of species diversity is hampered by extensive morphological plasticity...
  4. pmc ITS2 secondary structure improves phylogeny estimation in a radiation of blue butterflies of the subgenus Agrodiaetus (Lepidoptera: Lycaenidae: Polyommatus )
    Martin Wiemers
    Department of Animal Biodiversity, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Wien, Austria
    BMC Evol Biol 9:300. 2009
    ..Furthermore, we assess the use of compensatory base changes in ITS2 for the delimitation of species and discuss the prospects of ITS2 as a nuclear marker for barcoding studies...
  5. 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...
  6. ncbi request reprint A java applet for exploring the new higher level classification of eukaryotes with emphasis on the taxonomy of protists
    Matthias Wolf
    Department of Bioinformatics, Biocenter, University of Wurzburg, D 97074 Wurzburg, Germany
    J Eukaryot Microbiol 53:315. 2006
    ..The tree was made using the Prefuse Toolkit for interactive information visualization. All browsers capable of using Java applets will be able to view the tree. The applet is freely available for scientists, teachers, and students...
  7. pmc A molecular phylogeny of Hypnales (Bryophyta) inferred from ITS2 sequence-structure data
    Benjamin Merget
    Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, 97074 Wurzburg, Germany
    BMC Res Notes 3:320. 2010
    ..Therefore we used highly variable internal transcribed spacer 2 (ITS2) sequences and conserved secondary structures, as deposited with the ITS2 Database, simultaneously...
  8. 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...
  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. 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...
  11. 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...
  12. 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...
  13. 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...
  14. 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...
  15. 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...
  16. pmc ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales)
    Alexander Keller
    Department of Bioinformatics, University of Wurzburg, Am Hubland, 97074 Wurzburg, Germany
    BMC Evol Biol 8:218. 2008
    ....
  17. 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...
  18. ncbi request reprint Deep metazoan phylogeny
    Daniel Gerlach
    Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, D 97074 Wurzburg, Germany
    In Silico Biol 7:151-4. 2007
    ....
  19. 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...
  20. ncbi request reprint CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures
    Matthias Wolf
    Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, D 97074 Wurzburg, Germany
    In Silico Biol 5:291-4. 2005
    ..In this note we describe the features of the toolbox as well as application examples. The toolbox provides a graphical user interface. It is written in C++ and freely available at: http://cbcanalyzer.bioapps.biozentrum.uni-wuerzburg.de...
  21. 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...
  22. ncbi request reprint ProfDist: a tool for the construction of large phylogenetic trees based on profile distances
    Joachim Friedrich
    Department of Bioinformatics, Biocenter, University of Wurzburg, Germany
    Bioinformatics 21:2108-9. 2005
    ..It is a tool for reconstructing and visualizing large phylogenetic trees providing new and standard features with a special focus on time efficency, robustness and accuracy...
  23. ncbi request reprint ITS-2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae)
    Susanne Schmitt
    Research Center for Infectious Diseases, University of Wurzburg, Germany
    J Mol Evol 60:327-36. 2005
    ..The species concept for Aplysina sponges as well as a phylogenetic history with a possibly Tethyan origin is discussed...
  24. pmc Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta)
    Tobias Müller
    Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, D 97074 Wurzburg, Germany
    BMC Evol Biol 4:20. 2004
    ..We represent each subclade by a sequence profile and estimate evolutionary distances between profiles to obtain a matrix of distances between subclades...
  25. doi request reprint ITS2 Database V: Twice as Much
    Markus J Ankenbrand
    Department of Animal Ecology and Tropical Biology, Julius Maximilian University, Wurzburg, Germany
    Mol Biol Evol 32:3030-2. 2015
    ..Moreover, additional data has been added to underrepresented groups and some new groups have been added. The broader coverage across the tree of life improves phylogenetic analyses and the capability of ITS2 as a DNA barcode. ..
  26. ncbi request reprint Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data
    Matthias Wolf
    University of Wurzburg, Department of Bioinformatics, Biocenter, Am Hubland, 97074 Wurzburg, Germany
    Int J Syst Evol Microbiol 54:871-5. 2004
    ....
  27. pmc Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE
    Philipp N Seibel
    Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, Wurzburg, Germany
    BMC Res Notes 1:91. 2008
    ..The problem is both these tasks need to be performed simultaneously...
  28. doi request reprint A probabilistic model of cell size reduction in Pseudo-nitzschia delicatissima (Bacillariophyta)
    Roland Schwarz
    Department of Bioinformatics, University of Wurzburg, Am Hubland, 97074 Wurzburg, Germany
    J Theor Biol 258:316-22. 2009
    ..We thus propose a unique way to describe the stationary size distribution in a diatom population in terms of cell division and auxospore formation probabilities of its individuals...
  29. ncbi request reprint A new method for spherical object detection and its application to computer aided detection of pulmonary nodules in CT images
    Xiangwei Zhang
    University of Iowa, Iowa City, IA 52242, USA
    Med Image Comput Comput Assist Interv 10:842-9. 2007
    ..The proposed method was applied to computer aided detection of pulmonary nodules based on helical CT images. Experiments showed that this method attained a better performance compared to the original normal overlap technique...
  30. ncbi request reprint Ewald sphere correction for single-particle electron microscopy
    Matthias Wolf
    Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South Street, Waltham, MA 02454, USA
    Ultramicroscopy 106:376-82. 2006
    ..Either method applied to synthetic data representing a large virus yields a higher resolution reconstruction than a method lacking this correction...