| 2012 | CPM | Computing the Burrows-Wheeler Transform of a String and Its Reverse. | Enno Ohlebusch, Timo Beller, Mohamed Ibrahim Abouelhoda |
| 2009 | CLUSTER | WinBioinfTools: Bioinformatics tools for Windows cluster. | Hisham Mohamed, Mohamed Ibrahim Abouelhoda |
| 2008 | APBC | Alignment of Minisatellite Maps: A Minimum Spanning Tree-based Approach. | Mohamed Ibrahim Abouelhoda, Robert Giegerich, Behshad Behzadi, Jean-Marc Steyaert |
| 2007 | SPIRE | A Chaining Algorithm for Mapping cDNA Sequences to Multiple Genomic Sequences. | Mohamed Ibrahim Abouelhoda |
| 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 | 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 |