News

I'm no longer at the university, but I still give support for my programs. If you have any questions about my software or my publications, you can contact me using the following email address:

Areas of Interest

• Bioinformatics
• Cryptography
• Raytracing
• and many more...

Teaching

• Übungen zur VorlesungFormale Grundlagen der Informatik (WS2010/11)
• Übungen zur Vorlesung Praktische Informatik (SS 2010)
• Projekt Sequenzanalyse (SS 2010)
• Übungen zur Vorlesung Highlights der Theoretischen Informatik (WS 2009/10)
• Praktikum Datenkompression (WS 2009/10)
• Übungen zur Vorlesung Logik (SS 2009)
• Praktikum Datenkompression (SS 2009)
• Hauptseminar Datenkompression (WS 2008/09)
• Übungen zur Vorlesung Algorithmen und Datenstrukturen (WS 2008/09)
• Hauptseminar Bioinformatik (SS 2008)
• Übungen zur Vorlesung Highlights der Theoretischen Informatik (SS 2008)
• Übungen zur Vorlesung Theoretische Informatik I (WS 2007/08)
• Hauptseminar Bioinformatik (SS 2007)
• Proseminar Evolutionäre Algorithmen (WS 2006/07)
• Übungen zur Vorlesung Algorithmen der Bioinformatik (WS 2006/07)
• Übungen zur Vorlesung Theoretische Informatik (SS 2006)

Software

• GENESIS: Genome Evolution Scenarios
• phylo v1.0.6: A program for phylogenetic reconstruction based on weighted reversals and transpositions
  Including the programs revDist (pairwise reversal distance solver, exact), minswrt (pairwise weighted reversal and transposition distance, 1.5 approximation), weightedbb (pairwise weighted reversal and transposition solver, exact branch and bound algorithm), and median (exact median solver for reversal distance, transposition distance, and weighted reversal and transposition distance).
• dcjdDist: A program for phylogenetic reconstruction based on Reversals, Block Interchanges, Tandem Duplications, and Deletions. This is just a preliminary beta version. It has the full functionality but could be rather slow.

Publications

• Martin Bader
  Genome Rearrangement Algorithms
  PhD Thesis, Ulm University, 2011   pdf
• Martin Bader
  The Transposition Median Problem is NP-complete
  Theoretical Computer Science 2011, 412, pages 1099-1110
  © Elsevier   Preprint
• Martin Bader
  Genome rearrangements with duplications
  BMC Bioinformatics 2010, 11 (Suppl 1), page S27
  BMC Bioinformatics   pdf   Slides
• Martin Bader
  On Reversal and Transposition Medians
  Proceedings of World Academy of Science, Engineering and Technology 2009, 54, pages 667-675   Preprint   Slides
• Martin Bader
  On Reversal and Transposition Medians
  Technical Report UIB-2009-04, Ulm University, Faculty of Electrical Engineering and Computer Science   pdf
• Martin Bader
  Sorting by Reversals, Block Interchanges, Tandem Duplications, and Deletions
  BMC Bioinformatics 2009, 10 (Suppl 1), page S9
  BMC Bioinformatics   pdf   Slides
• Martin Bader, Mohamed I. Abouelhoda, Enno Ohlebusch
  A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions
  BMC Bioinformatics 2008, 9, page 516
  BMC Bioinformatics   pdf
• Simon Gog, Martin Bader
  Fast algorithms for transforming back and forth between a signed permutation and its equivalent simple permutation
  Journal of Computational Biology 2008, 15(8), pages 1-13
  © Mary Ann Liebert, Inc.   Preprint
• Simon Gog, Martin Bader, Enno Ohlebusch
  GENESIS: genome evolution scenarios
  Bioinformatics. 2008, 24(5), pages 711-712
  © Oxford Journals   Preprint
• Simon Gog, Martin Bader
  How to achieve an equivalent simple permutation in linear time
  Proceedings of the 5th Annual RECOMB Satellite Workshop on Comparative Genomics, pages 58-68, LNCS 4751, 2007.
  © Springer-Verlag   Preprint
• Martin Bader, Enno Ohlebusch
  Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions
  Journal of Computational Biology. 2007, 14(5), pages 615-636
  © Mary Ann Liebert, Inc.   Preprint
• Martin Bader, Enno Ohlebusch
  Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions
  Proceedings of the 10th Annual International Conference on Research in Computational Molecular Biology, pages 564-578, LNCS 3909, 2006.
  © Springer-Verlag   Preprint
• Martin Bader
  Sorting by weighted transpositions and reversals
  Diploma thesis, Universität Ulm (December 2005) pdf