| 2020 | SPIRE | Smaller Fully-Functional Bidirectional BWT Indexes. | Djamal Belazzougui, Fabio Cunial |
| 2019 | CPM | Fully-Functional Bidirectional Burrows-Wheeler Indexes and Infinite-Order De Bruijn Graphs. | Djamal Belazzougui, Fabio Cunial |
| 2017 | CiE | Flexible Indexing of Repetitive Collections. | Djamal Belazzougui, Fabio Cunial, Travis Gagie, Nicola Prezza, Mathieu Raffinot |
| 2017 | CPM | Representing the Suffix Tree with the CDAWG. | Djamal Belazzougui, Fabio Cunial |
| 2017 | SPIRE | Fast Label Extraction in the CDAWG. | Djamal Belazzougui, Fabio Cunial |
| 2015 | CPM | A Framework for Space-Efficient String Kernels. | Djamal Belazzougui, Fabio Cunial |
| 2015 | CPM | Composite Repetition-Aware Data Structures. | Djamal Belazzougui, Fabio Cunial, Travis Gagie, Nicola Prezza, Mathieu Raffinot |
| 2015 | SPIRE | Space-Efficient Detection of Unusual Words. | Djamal Belazzougui, Fabio Cunial |
| 2014 | SPIRE | Indexed Matching Statistics and Shortest Unique Substrings. | Djamal Belazzougui, Fabio Cunial |
| 2013 | ESA | Versatile Succinct Representations of the Bidirectional Burrows-Wheeler Transform. | Djamal Belazzougui, Fabio Cunial, Juha Krkkinen, Veli Mkinen |
| 2011 | DCC | Sequence Similarity by Gapped LZW. | Alberto Apostolico, Fabio Cunial |
| 2009 | DCC | Probing the Randomness of Proteins by Their Subsequence Composition. | Alberto Apostolico, Fabio Cunial |
| 2008 | DCC | Table Compression by Record Intersections. | Alberto Apostolico, Fabio Cunial, Vineith Kaul |