• Enno Ohlebusch, Timo Beller, Mohamed Ibrahim Abouelhoda
  Computing the Burrows-Wheeler Transform of a String and its Reverse in Parallel.
  Journal of Discrete Algorithms, 25:21-33, 2014.

• Simon Gog, Enno Ohlebusch
  Compressed suffix trees: Efficient computation and storage of LCP-values.
  Journal of Experimental Algorithmics, 18(1), 2013.

• Timo Beller, Simon Gog, Enno Ohlebusch, Thomas Schnattinger
  Computing the longest common prefix array based on the Burrows-Wheeler transform.
  Journal of Discrete Algorithms, 18:22-31, 2013.

• Thomas Schnattinger, Enno Ohlebusch, Simon Gog
  Bidirectional search in a string with wavelet trees and bidirectional matching statistics.
  Information and Computation, 213:13-22, 2012.

• Michael Arnold, Enno Ohlebusch
  Linear Time Algorithms for Generalizations of the Longest Common Substring Problem
  Algorithmica, 60(4):806--818, 2011.
  
  
• Enno Ohlebusch, Simon Gog
  Efficient Algorithms for the All Pairs Suffix-Prefix Problem and the All Pairs Substring-Prefix Problem
  Information Processing Letters 110(3):123-128, 2010.
  
  
• Martin Bader, Mohamed I. Abouelhoda, Enno Ohlebusch
  A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions
  BMC Bioinformatics, 9:516, 2008.
  
  
• Mohamed I. Abouelhoda, Stefan Kurtz, Enno Ohlebusch
  CoCoNUT: an efficient system for the comparison and analysis of genomes
  BMC Bioinformatics, 9:476, 2008.
  
  
• Adrian Kügel, Enno Ohlebusch
  A Space Efficient Solution to the Frequent String Mining Problem for Many Databases
  Data Mining and Knowledge Discovery Journal, 17(1):24-38, 2008.  /fileadmin/website_uni_ulm/iui.inst.190/Mitarbeiter/ohlebusch/PAPERS/BI08.pdf[Preprint]
  
  
• Simon Gog, Martin Bader, Enno Ohlebusch
  GENESIS: Genome Evolution Scenarios
  Bioinformatics, 24(5):711-712, 2008. [Preprint]
  
  
• Enno Ohlebusch, Stefan Kurtz
  Space Efficient Computation of Rare Maximal Exact Matches between Multiple Sequences
  Journal of Computational Biology, 15(4):357-377, 2008. [Preprint]
  
  
• Martin Bader, Enno Ohlebusch
  Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions
  Journal of Computational Biology, 14(5):615-636, 2007. [Preprint]
  
  
• Enno Ohlebusch, Mohamed Ibrahim Abouelhoda, Kathrin Hockel
  A Linear Time Algorithm for the Inversion Median Problem in Circular Bacterial Genomes
  Journal of Discrete Algorithms, 5:637-646, 2007. [Preprint]
  
  
• Mohamed Ibrahim Abouelhoda, Enno Ohlebusch
  Chaining Algorithms for Multiple Genome Comparison
  Journal of Discrete Algorithms, 3:321-341, 2005. [Preprint]
  
  
• Michael Beckstette, Jens Mailänder, Richard J. Marhöfer, Alexander Sczyrba, Enno Ohlebusch, Robert Giegerich, Paul M. Selzer
  <link enno papers jda04.pdf download>Genlight: Interactive high-throughput sequence analysis and comparative genomics
  Journal of Integrative Bioinformatics, Article 8, 2004
  
  
• Mohamed Ibrahim Abouelhoda, Stefan Kurtz, Enno Ohlebusch
  Replacing Suffix Trees with Enhanced Suffix Arrays
  Journal of Discrete Algorithms, 2(1):53-86, 2004.
  
  
• Patrick Chain, Stefan Kurtz, Enno Ohlebusch, Tom Slezak
  An Applications-Focused Review of Comparative Genomics Tools: Capabilities, Limitations and Future Challenges
  Briefings in Bioinformatics, 4(2):105-123, 2003.
  
  
• Michael Höhl, Stefan Kurtz, Enno Ohlebusch
  Efficient Multiple Genome Alignment
  Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, in: Bioinformatics, 18(Supplement 1):312-320, 2002.
  
  
• Stefan Kurtz, Jomuna Choudhuri, Enno Ohlebusch, Chris Schleiermacher, Jens Stoye, Robert Giegerich
  REPuter: The Manifold Applications of Repeat Analysis on a Genomic Scale
  Nucleic Acids Research, 29(22):4633-4642, 2001.
  
  
• Enno Ohlebusch
  Hierarchical Termination Revisited
  Information Processing Letters, 84(4):207-214, 2002.
  
  
• Jürgen Giesl, Thomas Arts, Enno Ohlebusch
  Modular Termination Proofs for Rewriting Using Dependency Pairs
  Journal of Symbolic Computation, 34:21-58, 2002.
  
  
• Alfons Geser, Aart Middeldorp, Enno Ohlebusch, Hans Zantema
  Relative Undecidability in Term Rewriting, Part 2: The Confluence Hierarchy
  Information and Computation, 178(1):132-148, 2002.
  
  
• Alfons Geser, Aart Middeldorp, Enno Ohlebusch, Hans Zantema
  Relative Undecidability in Term Rewriting, Part 1: The Termination Hierarchy
  Information and Computation, 178(1):101-131, 2002.
  
  
• Enno Ohlebusch
  Termination of Logic Programs: Transformational Approaches Revisited
  Applicable Algebra in Engineering, Communication and Computing, 12:73-116, 2001. The publication is available on LINK at http://link.springer.de © Springer-Verlag.
  
  
• Enno Ohlebusch
  Implementing Conditional Term Rewriting by Graph Rewriting
  Theoretical Computer Science, 262:311-331, 2001.
  
  
• Enno Ohlebusch
  A Uniform Framework for Term and Graph Rewriting Applied to Combined Systems
  Information Processing Letters, 73:53-59, 2000.
  
  
• Bernd Bütow, Robert Giegerich, Enno Ohlebusch, Stephan Thesing
  Semantic Matching for Left-Linear Convergent Rewrite Systems
  The Journal of Functional and Logic Programming, Volume 1999, Article 10, The MIT Press.
  
  
• Enno Ohlebusch
  Modularity of Termination for Disjoint Term Graph Rewrite Systems: A Simple Proof.
  Bulletin of the European Association for Theoretical Computer Science, 66:171-177, 1998.
  
  
• Enno Ohlebusch, Esko Ukkonen
  On the Equivalence Problem for E-Pattern Languages
  Theoretical Computer Science, 186:231-248, 1997.
  
  
• Enno Ohlebusch
   Modular Properties of Composable Term Rewriting Systems
  Journal of Symbolic Computation, 20:1-41, 1995.
  
  
• Enno Ohlebusch
  Termination is not Modular for Confluent Variable-Preserving Term Rewriting Systems
  Information Processing Letters, 53:223-228, 1995.
  
  
• Enno Ohlebusch
  On the Modularity of Termination of Term Rewriting Systems
  Theoretical Computer Science, 136:333-360, 1994.
  
  
• Enno Ohlebusch
  A Simple Proof of Sufficient Conditions for the Termination of the Disjoint Union of Term Rewriting Systems
  Bulletin of the European Association for Theoretical Computer Science, 49:178-183, 1993.
  
  
• Robert Giegerich, Enno Ohlebusch
  An Implicit Representation of Infinite Sequences of Terms
  Bulletin of the European Association for Theoretical Computer Science, 43:173-182, 1991.