Sebastian Böcker

Summary

Affiliation: Friedrich Schiller University
Country: Germany

Publications

  1. doi request reprint Determination of glycan structure from tandem mass spectra
    Sebastian Böcker
    Faculty for Mathematics and Computer Science, Friedrich Schiller Universitat Jena, Ernst Abbe Platz 2, Jena 07743, Germany
    IEEE/ACM Trans Comput Biol Bioinform 8:976-86. 2011
  2. doi request reprint De novo analysis of electron impact mass spectra using fragmentation trees
    Franziska Hufsky
    Chair of Bioinformatics, Friedrich Schiller University, Ernst Abbe Platz 2, Jena, Germany
    Anal Chim Acta 739:67-76. 2012
  3. ncbi request reprint Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry
    Sebastian Böcker
    Friedrich Schiller University Jena Ernst Abbe Platz 2, 07743 Jena, Germany
    Bioinformatics 23:e5-12. 2007
  4. doi request reprint Combinatorial approaches for mass spectra recalibration
    Sebastian Böcker
    Friedrich Schiller Universitat Jena, Germany
    IEEE/ACM Trans Comput Biol Bioinform 5:91-100. 2008
  5. doi request reprint EPoS: a modular software framework for phylogenetic analysis
    Thasso Griebel
    Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany
    Bioinformatics 24:2399-400. 2008
  6. pmc On optimal comparability editing with applications to molecular diagnostics
    Sebastian Böcker
    Institut fur Informatik, Friedrich Schiller Universitat, Jena, Germany
    BMC Bioinformatics 10:S61. 2009
  7. doi request reprint Combinatorics of aliphatic amino acids
    Konrad Grützmann
    Jena Centre for Bioinformatics, Friedrich Schiller University Jena, Ernst Abbe Platz 2, 07743, Jena, Germany
    Naturwissenschaften 98:79-86. 2011
  8. doi request reprint Computing fragmentation trees from metabolite multiple mass spectrometry data
    Kerstin Scheubert
    Chair for Bioinformatics, Friedrich Schiller Universitat Jena, Jena, Germany
    J Comput Biol 18:1383-97. 2011
  9. pmc Computational mass spectrometry for small molecules
    Kerstin Scheubert
    Chair of Bioinformatics, Friedrich Schiller University, Ernst Abbe Platz 2, Jena, Germany
    J Cheminform 5:12. 2013
  10. pmc Swiftly computing center strings
    Franziska Hufsky
    Lehrstuhl für Bioinformatik, Friedrich Schiller Universitat Jena, Ernst Abbe Platz 2, Jena, Germany
    BMC Bioinformatics 12:106. 2011

Detail Information

Publications13

  1. doi request reprint Determination of glycan structure from tandem mass spectra
    Sebastian Böcker
    Faculty for Mathematics and Computer Science, Friedrich Schiller Universitat Jena, Ernst Abbe Platz 2, Jena 07743, Germany
    IEEE/ACM Trans Comput Biol Bioinform 8:976-86. 2011
    ..We generalize this result to count the number of (labeled) trees with bounded out degree, improving on results obtained using Pólya's enumeration theorem...
  2. doi request reprint De novo analysis of electron impact mass spectra using fragmentation trees
    Franziska Hufsky
    Chair of Bioinformatics, Friedrich Schiller University, Ernst Abbe Platz 2, Jena, Germany
    Anal Chim Acta 739:67-76. 2012
    ..This method will be very helpful in the automated analysis of metabolites that are not included in common libraries and it thus has the potential to support the explorative character of metabolomics studies...
  3. ncbi request reprint Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry
    Sebastian Böcker
    Friedrich Schiller University Jena Ernst Abbe Platz 2, 07743 Jena, Germany
    Bioinformatics 23:e5-12. 2007
    ....
  4. doi request reprint Combinatorial approaches for mass spectra recalibration
    Sebastian Böcker
    Friedrich Schiller Universitat Jena, Germany
    IEEE/ACM Trans Comput Biol Bioinform 5:91-100. 2008
    ..We compare our results to a computational geometry algorithm using a topological line-sweep...
  5. doi request reprint EPoS: a modular software framework for phylogenetic analysis
    Thasso Griebel
    Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany
    Bioinformatics 24:2399-400. 2008
    ..Implemented algorithms cover distance-based tree construction, consensus trees and various graph-based supertree methods. The rendering system can be customized for, say, different edge and node styles...
  6. pmc On optimal comparability editing with applications to molecular diagnostics
    Sebastian Böcker
    Institut fur Informatik, Friedrich Schiller Universitat, Jena, Germany
    BMC Bioinformatics 10:S61. 2009
    ..The task is to identify the minimum number of edge insertions or deletions to transform G into a transitive graph, that is, if edges (u, v) and (v, w) are present then edge (u, w) must be present, too...
  7. doi request reprint Combinatorics of aliphatic amino acids
    Konrad Grützmann
    Jena Centre for Bioinformatics, Friedrich Schiller University Jena, Ernst Abbe Platz 2, 07743, Jena, Germany
    Naturwissenschaften 98:79-86. 2011
    ..Thus, natural biological complexity arises from the multifarious combination of building blocks...
  8. doi request reprint Computing fragmentation trees from metabolite multiple mass spectrometry data
    Kerstin Scheubert
    Chair for Bioinformatics, Friedrich Schiller Universitat Jena, Jena, Germany
    J Comput Biol 18:1383-97. 2011
    ..Evaluation of our method on a dataset of 45 reference compounds showed that the quality of constructed fragmentation trees is improved by using MS(n) instead of MS² measurements...
  9. pmc Computational mass spectrometry for small molecules
    Kerstin Scheubert
    Chair of Bioinformatics, Friedrich Schiller University, Ernst Abbe Platz 2, Jena, Germany
    J Cheminform 5:12. 2013
    ..In addition, this review shortly covers the reconstruction of metabolic networks using MS data. Finally, we list available software for different steps of the analysis pipeline...
  10. pmc Swiftly computing center strings
    Franziska Hufsky
    Lehrstuhl für Bioinformatik, Friedrich Schiller Universitat Jena, Ernst Abbe Platz 2, Jena, Germany
    BMC Bioinformatics 12:106. 2011
    ..Given k input strings and a distance threshold d, we search for a string within Hamming distance at most d to each input string. This problem is NP complete...
  11. pmc SIRIUS: decomposing isotope patterns for metabolite identification
    Sebastian Böcker
    Lehrstuhl für Bioinformatik, Friedrich Schiller Universitat Jena, Jena, Germany
    Bioinformatics 25:218-24. 2009
    ..Determination of the sum formula is a crucial step in the identification of an unknown metabolite, as it reduces its possible structures to a hopefully manageable set...
  12. doi request reprint DECOMP--from interpreting Mass Spectrometry peaks to solving the Money Changing Problem
    Sebastian Böcker
    Lehrstuhl Bioinformatik, Friedrich Schiller Universitat Jena, Ernst Abbe Platz 2, 07743 Jena, Germany
    Bioinformatics 24:591-3. 2008
    ..AVAILABILITY: Decomp is freely accessible at http://bibiserv.techfak.uni-bielefeld.de/decomp/...
  13. doi request reprint Computation of median gene clusters
    Sebastian Böcker
    Institut fur Informatik, Friedrich Schiller Universitat Jena, Jena, Germany
    J Comput Biol 16:1085-99. 2009
    ....