Stefan Kurtz

Summary

Affiliation: University of Hamburg
Country: Germany

Publications

  1. pmc LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons
    Sascha Steinbiss
    Center for Bioinformatics, University of Hamburg, 20146 Hamburg, Bundesstrasse 43, Germany
    Mob DNA 3:18. 2012
  2. pmc Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8
    Max Farnbacher
    Max von Pettenkofer Institute for Hygiene and Medical Microbiology, Ludwig Maximilian University Munich, 80336 Munich, Germany
    BMC Genomics 11:335. 2010
  3. pmc Selective regain of egfr gene copies in CD44+/CD24-/low breast cancer cellular model MDA-MB-468
    Konstantin Agelopoulos
    Department of Medicine, Hematology and Oncology, University of Muenster, Muenster, Germany
    BMC Cancer 10:78. 2010
  4. pmc CoCoNUT: an efficient system for the comparison and analysis of genomes
    Mohamed I Abouelhoda
    Faculty of Engineering, Cairo University, Giza, Egypt
    BMC Bioinformatics 9:476. 2008
  5. pmc Efficient computation of absent words in genomic sequences
    Julia Herold
    Center of Biotechnology, Bielefeld University, Postfach 10 01 31, 33501 Bielefeld, Germany
    BMC Bioinformatics 9:167. 2008
  6. pmc Fast index based algorithms and software for matching position specific scoring matrices
    Michael Beckstette
    International NRW Graduate School in Bioinformatics and Genome Research, Center for Biotechnology CeBiTec, Bielefeld University, D 33594 Bielefeld, Germany
    BMC Bioinformatics 7:389. 2006
  7. pmc FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context
    Malte Mader
    Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
    J Clin Bioinforma 1:20. 2011
  8. pmc A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes
    Stefan Kurtz
    Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
    BMC Genomics 9:517. 2008
  9. pmc Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns
    Fernando Meyer
    Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, Hamburg 20146, Germany
    BMC Bioinformatics 14:226. 2013
  10. pmc Fine-grained annotation and classification of de novo predicted LTR retrotransposons
    Sascha Steinbiss
    Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
    Nucleic Acids Res 37:7002-13. 2009

Collaborators

Detail Information

Publications20

  1. pmc LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons
    Sascha Steinbiss
    Center for Bioinformatics, University of Hamburg, 20146 Hamburg, Bundesstrasse 43, Germany
    Mob DNA 3:18. 2012
    ..abstract:..
  2. pmc Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8
    Max Farnbacher
    Max von Pettenkofer Institute for Hygiene and Medical Microbiology, Ludwig Maximilian University Munich, 80336 Munich, Germany
    BMC Genomics 11:335. 2010
    ..In the current study the gerbil-adapted strain B8 was completely sequenced, annotated and compared to previous genomes, including the 73 supercontigs of the parental strain B128...
  3. pmc Selective regain of egfr gene copies in CD44+/CD24-/low breast cancer cellular model MDA-MB-468
    Konstantin Agelopoulos
    Department of Medicine, Hematology and Oncology, University of Muenster, Muenster, Germany
    BMC Cancer 10:78. 2010
    ..A deeper understanding of those marker events might improve early diagnosis of cancer in suspect lesions, early detection of cancer progression and the prediction of egfr targeted therapies...
  4. pmc CoCoNUT: an efficient system for the comparison and analysis of genomes
    Mohamed I Abouelhoda
    Faculty of Engineering, Cairo University, Giza, Egypt
    BMC Bioinformatics 9:476. 2008
    ..This area of research is driven by the large number of sequenced genomes and heavily relies on efficient algorithms and software to perform pairwise and multiple genome comparisons...
  5. pmc Efficient computation of absent words in genomic sequences
    Julia Herold
    Center of Biotechnology, Bielefeld University, Postfach 10 01 31, 33501 Bielefeld, Germany
    BMC Bioinformatics 9:167. 2008
    ..Relative to a random sequence of the same length, unique subsequences are overrepresented in real genomes. Shortest words absent from a genome have been addressed in two recent studies...
  6. pmc Fast index based algorithms and software for matching position specific scoring matrices
    Michael Beckstette
    International NRW Graduate School in Bioinformatics and Genome Research, Center for Biotechnology CeBiTec, Bielefeld University, D 33594 Bielefeld, Germany
    BMC Bioinformatics 7:389. 2006
    ..Searching with PSSMs in complete genomes or large sequence databases is a common, but computationally expensive task...
  7. pmc FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context
    Malte Mader
    Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
    J Clin Bioinforma 1:20. 2011
    ..abstract:..
  8. pmc A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes
    Stefan Kurtz
    Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
    BMC Genomics 9:517. 2008
    ....
  9. pmc Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns
    Fernando Meyer
    Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, Hamburg 20146, Germany
    BMC Bioinformatics 14:226. 2013
    ....
  10. pmc Fine-grained annotation and classification of de novo predicted LTR retrotransposons
    Sascha Steinbiss
    Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
    Nucleic Acids Res 37:7002-13. 2009
    ..Representative sequences from 41 of these 62 groups were matched to reference sequences with >80% global sequence similarity...
  11. doi request reprint AnnotationSketch: a genome annotation drawing library
    Sascha Steinbiss
    Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
    Bioinformatics 25:533-4. 2009
    ..To exemplify the use of AnnotationSketch in other languages, we provide bindings to the scripting languages Ruby, Python and Lua...
  12. pmc Structator: fast index-based search for RNA sequence-structure patterns
    Fernando Meyer
    Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
    BMC Bioinformatics 12:214. 2011
    ..Furthermore, established index data structures for fast sequence matching, like suffix trees or arrays, cannot benefit from the complementarity constraints introduced by the secondary structure of RNAs...
  13. pmc Significant speedup of database searches with HMMs by search space reduction with PSSM family models
    Michael Beckstette
    Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
    Bioinformatics 25:3251-8. 2009
    ..They provide sensitive family descriptors, and sequence database searching with pHMMs has become a standard task in today's genome annotation pipelines. On the downside, searching with pHMMs is computationally expensive...
  14. doi request reprint CASSys: an integrated software-system for the interactive analysis of ChIP-seq data
    Malik Alawi
    Center for Bioinformatics, University of Hamburg, Bundesstraße 43, D 20146 Hamburg, Germany
    J Integr Bioinform 8:155. 2011
    ..To demonstrate CASSys's functionality we used the system for the complete data analysis of a publicly available Chip-seq study that investigated the role of the transcription factor estrogen receptor-α in breast cancer cells...
  15. pmc Versatile and open software for comparing large genomes
    Stefan Kurtz
    Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
    Genome Biol 5:R12. 2004
    ..This allows other developers to contribute to the code base and freely redistribute the code. The MUMmer sources are available at http://www.tigr.org/software/mummer...
  16. pmc Readjoiner: a fast and memory efficient string graph-based sequence assembler
    Giorgio Gonnella
    Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
    BMC Bioinformatics 13:82. 2012
    ..An alternative framework of growing interest is the assembly string graph, not necessitating a division of the reads into k-mers, but requiring fast algorithms for the computation of suffix-prefix matches among all pairs of reads...
  17. pmc LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
    David Ellinghaus
    ZBH Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
    BMC Bioinformatics 9:18. 2008
    ..LTR retrotransposons, an important subclass of transposable elements, are well suited for computational identification, as they contain long terminal repeats (LTRs)...
  18. doi request reprint In situ chemistry and microbial community compositions in five deep-sea hydrothermal fluid samples from Irina II in the Logatchev field
    Mirjam Perner
    Molecular Biology of Microbial Consortia, University of Hamburg, Biocenter Klein Flottbek, Ohnhorststr 18, 22609, Hamburg, Germany
    Environ Microbiol 15:1551-60. 2013
    ..However, further studies are required to support this hypothesis...
  19. pmc Quantitative high-resolution genomic analysis of single cancer cells
    Juliane Hannemann
    Department of Tumor Biology, University Medical Center Hamburg Eppendorf, Hamburg, Germany
    PLoS ONE 6:e26362. 2011
    ..The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics...
  20. pmc RNA-related tools on the Bielefeld Bioinformatics Server
    Alexander Sczyrba
    Technische Fakultat, Universitat Bielefeld, Postfach 10 01 31, D 33501 Bielefeld Zentrum für Bioinformatik, Universitat Hamburg, Bundesstrasse 43, D 20146 Hamburg, Germany
    Nucleic Acids Res 31:3767-70. 2003
    ..All are available via the Bielefeld University Bioinformatics Server (http://bibiserv.techfak.uni-bielefeld.de)...