Sebastian Böcker

Summary

Affiliation: Friedrich Schiller University
Country: Germany

Publications

  1. ncbi request reprint New kids on the block: novel informatics methods for natural product discovery
    Franziska Hufsky
    Lehrstuhl für Bioinformatik, Friedrich Schiller Universitat Jena, Ernst Abbe Platz 2, 07743 Jena, Germany
    Nat Prod Rep 31:807-17. 2014
  2. pmc Fast alignment of fragmentation trees
    Franziska Hufsky
    Chair for Bioinformatics, Friedrich Schiller University, Jena, Germany
    Bioinformatics 28:i265-73. 2012
  3. 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
  4. 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
  5. doi request reprint Determination of ¹⁵N-incorporation into plant proteins and their absolute quantitation: a new tool to study nitrogen flux dynamics and protein pool sizes elicited by plant-herbivore interactions
    Lynn Ullmann-Zeunert
    Max Planck Institute for Chemical Ecology, Jena, Germany
    J Proteome Res 11:4947-60. 2012
  6. doi request reprint Identifying the unknowns by aligning fragmentation trees
    Florian Rasche
    Chair for Bioinformatics, Friedrich Schiller University, Jena, Germany
    Anal Chem 84:3417-26. 2012
  7. 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
  8. 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
  9. 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
  10. 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

Collaborators

Detail Information

Publications24

  1. ncbi request reprint New kids on the block: novel informatics methods for natural product discovery
    Franziska Hufsky
    Lehrstuhl für Bioinformatik, Friedrich Schiller Universitat Jena, Ernst Abbe Platz 2, 07743 Jena, Germany
    Nat Prod Rep 31:807-17. 2014
    ..Furthermore, when a potential drug lead has been determined, these tools may help to identify it and elucidate its structure...
  2. pmc Fast alignment of fragmentation trees
    Franziska Hufsky
    Chair for Bioinformatics, Friedrich Schiller University, Jena, Germany
    Bioinformatics 28:i265-73. 2012
    ..Fragmentation pattern similarities are strongly correlated with the chemical similarity of the molecules, and allow us to cluster compounds based solely on their fragmentation patterns...
  3. 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...
  4. 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...
  5. doi request reprint Determination of ¹⁵N-incorporation into plant proteins and their absolute quantitation: a new tool to study nitrogen flux dynamics and protein pool sizes elicited by plant-herbivore interactions
    Lynn Ullmann-Zeunert
    Max Planck Institute for Chemical Ecology, Jena, Germany
    J Proteome Res 11:4947-60. 2012
    ....
  6. doi request reprint Identifying the unknowns by aligning fragmentation trees
    Florian Rasche
    Chair for Bioinformatics, Friedrich Schiller University, Jena, Germany
    Anal Chem 84:3417-26. 2012
    ..We apply this tool to metabolites from Icelandic poppy. Our method allows fully automated computational identification of small molecules that cannot be found in any database...
  7. 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...
  8. 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...
  9. 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
    ....
  10. 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...
  11. 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...
  12. 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...
  13. doi request reprint Computing fragmentation trees from tandem mass spectrometry data
    Florian Rasche
    Chair for Bioinformatics, Friedrich Schiller University Jena, Jena, Germany
    Anal Chem 83:1243-51. 2011
    ..This is an important step toward the automated identification of unknowns from the CID spectra of compounds that are not in any database...
  14. doi request reprint Analysis of different synthetic homopolymers by the use of a new calculation software for tandem mass spectra
    Anja Baumgaertel
    Laboratory of Organic and Macromolecular Chemistry IOMC and Jena Center for Soft Mater JCSM, Friedrich Schiller University Jena, Humboldtstr 10, 07743 Jena, Germany
    Rapid Commun Mass Spectrom 25:1765-78. 2011
    ..This contribution describes a fast and automated software tool for the rapid analysis of homopolymers...
  15. pmc Polynomial supertree methods revisited
    Malte Brinkmeyer
    Department of Computer Science, Friedrich Schiller University, 07743 Jena, Germany
    Adv Bioinformatics 2011:524182. 2011
    ..Based on our results, we make some general suggestions for supertree methods yet to come...
  16. 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...
  17. 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...
  18. pmc Metabolite identification through multiple kernel learning on fragmentation trees
    Huibin Shen
    Department of Information and Computer Science, Aalto University, Espoo, Finland, Helsinki Institute for Information Technology, Espoo, Finland and Chair for Bioinformatics, Friedrich Schiller University Jena, Jena, GermanyDepartment of Information and Computer Science, Aalto University, Espoo, Finland, Helsinki Institute for Information Technology, Espoo, Finland and Chair for Bioinformatics, Friedrich Schiller University Jena, Jena, Germany
    Bioinformatics 30:i157-i164. 2014
    ..Machine learning methods have been used to map mass spectra to molecular fingerprints; predicted fingerprints, in turn, can be used to score candidate molecular structures...
  19. doi request reprint Mass spectrometry imaging of surface lipids on intact Drosophila melanogaster flies
    Filip Kaftan
    Institute of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic, v v i, Flemingovo nam 2, CZ 166 10, Prague 6, Czech Republic Department of Analytical Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030 8, CZ 128 43, Prague 2, Czech Republic Max Planck Institute for Chemical Ecology, Hans Knöll Straße 8, D 07745, Jena, Germany
    J Mass Spectrom 49:223-32. 2014
    ..2 and 0.3 Da. We use in-house developed software for mass recalibration, to eliminate the mass deviation effects and help with the detection of low-intensity mass signals...
  20. doi request reprint Towards de novo identification of metabolites by analyzing tandem mass spectra
    Sebastian Böcker
    Chair for Bioinformatics, Friedrich Schiller University Jena, Jena, Germany
    Bioinformatics 24:i49-i55. 2008
    ..De novo identification of metabolite mass spectra requires new concepts and methods since, unlike proteins, metabolites possess a non-linear molecular structure...
  21. 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...
  22. pmc Unbiased transcriptional comparisons of generalist and specialist herbivores feeding on progressively defenseless Nicotiana attenuata plants
    Geetha Govind
    Max Planck Institute for Chemical Ecology, Jena, Germany
    PLoS ONE 5:e8735. 2010
    ..Unbiased transcriptional analyses of how neonate larvae cope with these induced plant defenses are lacking...
  23. 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
    ....
  24. 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
    ..Decomp has an easy-to-use graphical interface, which caters for both types of users: those interested in solving MCP instances and those submitting MS data...