| 2026 | CPM | The TAG Array of a Multiple Sequence Alignment. | Jannik Olbrich, Enno Ohlebusch |
| 2024 | SPIRE | Faster Computation of Chinese Frequent Strings and Their Net Frequencies. | Enno Ohlebusch, Thomas Bchler, Jannik Olbrich |
| 2022 | SPIRE | On the Optimisation of the GSACA Suffix Array Construction Algorithm. | Jannik Olbrich, Enno Ohlebusch, Thomas Bchler |
| 2020 | DCC | Edge Minimization in de Bruijn Graphs. | Uwe Baier, Thomas Bchler, Enno Ohlebusch, Pascal Weber |
| 2019 | SPIRE | On the Computation of Longest Previous Non-overlapping Factors. | Enno Ohlebusch, Pascal Weber |
| 2018 | SPIRE | Trickier XBWT Tricks. | Enno Ohlebusch, Stefan Stau, Uwe Baier |
| 2015 | CPM | Efficient Construction of a Compressed de Bruijn Graph for Pan-Genome Analysis. | Timo Beller, Enno Ohlebusch |
| 2015 | SPIRE | Parallel Construction of Succinct Representations of Suffix Tree Topologies. | Uwe Baier, Timo Beller, Enno Ohlebusch |
| 2014 | SPIRE | Alphabet-Independent Algorithms for Finding Context-Sensitive Repeats in Linear Time. | Enno Ohlebusch, Timo Beller |
| 2013 | SPIRE | Space-Efficient Construction of the Burrows-Wheeler Transform. | Timo Beller, Maike Zwerger, Simon Gog, Enno Ohlebusch |
| 2012 | CPM | Computing the Burrows-Wheeler Transform of a String and Its Reverse. | Enno Ohlebusch, Timo Beller, Mohamed Ibrahim Abouelhoda |
| 2012 | SPIRE | Space-Efficient Computation of Maximal and Supermaximal Repeats in Genome Sequences. | Timo Beller, Katharina Berger, Enno Ohlebusch |
| 2011 | ALENEX | Fast and Lightweight LCP-Array Construction Algorithms. | Simon Gog, Enno Ohlebusch |
| 2011 | CPM | Lempel-Ziv Factorization Revisited. | Enno Ohlebusch, Simon Gog |
| 2011 | SPIRE | Computing the Longest Common Prefix Array Based on the Burrows-Wheeler Transform. | Timo Beller, Simon Gog, Enno Ohlebusch, Thomas Schnattinger |
| 2010 | CPM | Bidirectional Search in a String with Wavelet Trees. | Thomas Schnattinger, Enno Ohlebusch, Simon Gog |
| 2010 | SPIRE | CST++. | Enno Ohlebusch, Johannes Fischer, Simon Gog |
| 2010 | SPIRE | Computing Matching Statistics and Maximal Exact Matches on Compressed Full-Text Indexes. | Enno Ohlebusch, Simon Gog, Adrian Kgel |
| 2009 | SPIRE | A Compressed Enhanced Suffix Array Supporting Fast String Matching. | Enno Ohlebusch, Simon Gog |
| 2006 | RECOMB | Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions. | Martin Bader, Enno Ohlebusch |
| 2005 | CPM | The Median Problem for the Reversal Distance in Circular Bacterial Genomes. | Enno Ohlebusch, Mohamed Ibrahim Abouelhoda, Kathrin Hockel, Jan Stallkamp |
| 2003 | CPM | Multiple Genome Alignment: Chaining Algorithms Revisited. | Mohamed Ibrahim Abouelhoda, Enno Ohlebusch |
| 2003 | WABI | A Local Chaining Algorithm and Its Applications in Comparative Genomics. | Mohamed Ibrahim Abouelhoda, Enno Ohlebusch |
| 2002 | ISMB | Efficient multiple genome alignment. | Michael Hhl, Stefan Kurtz, Enno Ohlebusch |
| 2002 | SPIRE | Optimal Exact Strring Matching Based on Suffix Arrays. | Mohamed Ibrahim Abouelhoda, Enno Ohlebusch, Stefan Kurtz |
| 2002 | WABI | The Enhanced Suffix Array and Its Applications to Genome Analysis. | Mohamed Ibrahim Abouelhoda, Stefan Kurtz, Enno Ohlebusch |
| 2000 | ISMB | Computation and Visualization of Degenerate Repeats in Complete Genomes. | Stefan Kurtz, Enno Ohlebusch, Chris Schleiermacher, Jens Stoye, Robert Giegerich |
| 1999 | FLOPS | On Quasi-Reductive and Quasi-Simplifying Deterministic Conditional Rewrite Systems. | Enno Ohlebusch |
| 1999 | LPAR | Transforming Conditional Rewrite Systems with Extra Variables into Unconditional Systems. | Enno Ohlebusch |
| 1997 | CPM | A Filter Method for the Weighted Local Similarity Search Problem. | Enno Ohlebusch |
| 1996 | CSL | Relative Undecidability in Term Rewriting. | Alfons Geser, Aart Middeldorp, Enno Ohlebusch, Hans Zantema |
| 1996 | MFCS | On the Equivalence Problem for E-Pattern Languages. | Enno Ohlebusch, Esko Ukkonen |