| 2023 | SPIRE | Approximation and Fixed Parameter Algorithms for the Approximate Cover Problem. | Guillaume Blin, Alexandru Popa, Mathieu Raffinot, Raluca Uricaru |
| 2020 | Algosensors | VectorTSP: A Traveling Salesperson Problem with Racetrack-Like Acceleration Constraints. | Arnaud Casteigts, Mathieu Raffinot, Jason Schoeters |
| 2017 | CiE | Flexible Indexing of Repetitive Collections. | Djamal Belazzougui, Fabio Cunial, Travis Gagie, Nicola Prezza, Mathieu Raffinot |
| 2017 | TAMC | On the Shortest Common Superstring of NGS Reads. | Tristan Braquelaire, Marie Gasparoux, Mathieu Raffinot, Raluca Uricaru |
| 2015 | CPM | Composite Repetition-Aware Data Structures. | Djamal Belazzougui, Fabio Cunial, Travis Gagie, Nicola Prezza, Mathieu Raffinot |
| 2013 | CIAC | Average Optimal String Matching in Packed Strings. | Djamal Belazzougui, Mathieu Raffinot |
| 2013 | ISAAC | Single and Multiple Consecutive Permutation Motif Search. | Djamal Belazzougui, Adeline Pierrot, Mathieu Raffinot, Stphane Vialette |
| 2012 | CPM | Faster and Simpler Minimal Conflicting Set Identification - (Extended Abstract). | Ada Ouangraoua, Mathieu Raffinot |
| 2011 | CiE | Consecutive Ones Property Testing: Cut or Swap. | Mathieu Raffinot |
| 2011 | SPIRE | Approximate Regular Expression Matching with Multi-strings. | Djamal Belazzougui, Mathieu Raffinot |
| 2008 | SPIRE | Faster Text Fingerprinting. | Roman Kolpakov, Mathieu Raffinot |
| 2006 | CPM | New Algorithms for Text Fingerprinting. | Roman Kolpakov, Mathieu Raffinot |
| 2005 | ESA | Computing Common Intervals of | Anne Bergeron, Cdric Chauve, Fabien de Montgolfier, Mathieu Raffinot |
| 2004 | CPM | Maximal Common Connected Sets of Interval Graphs. | Michel Habib, Christophe Paul, Mathieu Raffinot |
| 2002 | RECOMB | Approximate matching of secondary structures. | Nadia El-Mabrouk, Mathieu Raffinot |
| 2002 | WABI | The Algorithmic of Gene Teams. | Anne Bergeron, Sylvie Corteel, Mathieu Raffinot |
| 2001 | CPM | Efficient Experimental String Matching by Weak Factor Recognition. | Cyril Allauzen, Maxime Crochemore, Mathieu Raffinot |
| 2001 | RECOMB | Fast and simple character classes and bounded gaps pattern matching, with application to protein searching. | Gonzalo Navarro, Mathieu Raffinot |
| 2000 | CPM | Simple Optimal String Matching Algorithm. | Cyril Allauzen, Mathieu Raffinot |
| 1999 | CPM | A General Practical Approach to Pattern Matching over Ziv-Lempel Compressed Text. | Gonzalo Navarro, Mathieu Raffinot |
| 1999 | SOFSEM | Factor Oracle: A New Structure for Pattern Matching. | Cyril Allauzen, Maxime Crochemore, Mathieu Raffinot |
| 1998 | CPM | A Bit-Parallel Approach to Suffix Automata: Fast Extended String Matching. | Gonzalo Navarro, Mathieu Raffinot |