| 2025 | COCOON | Counting Overlapping Pairs of Words. | Eric Rivals, Pengfei Wang |
| 2025 | SOFSEM | Incremental Computation of the Set of Period Sets. | Eric Rivals |
| 2023 | ICALP | Convergence of the Number of Period Sets in Strings. | Eric Rivals, Michelle Sweering, Pengfei Wang |
| 2021 | CPM | A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs. | Sangsoo Park, Sung Gwan Park, Bastien Cazaux, Kunsoo Park, Eric Rivals |
| 2020 | SPIRE | Efficient Construction of Hierarchical Overlap Graphs. | Sung Gwan Park, Bastien Cazaux, Kunsoo Park, Eric Rivals |
| 2019 | CPM | Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length Encoding. | Bastien Cazaux, Eric Rivals |
| 2018 | CPM | Superstrings with multiplicities. | Bastien Cazaux, Eric Rivals |
| 2017 | DCC | Full Compressed Affix Tree Representations. | Rodrigo Cnovas, Eric Rivals |
| 2017 | RECOMB | Rearrangement Scenarios Guided by Chromatin Structure. | Sylvain Pulicani, Pijus Simonaitis, Eric Rivals, Krister M. Swenson |
| 2016 | AAIM | Superstring Graph: A New Approach for Genome Assembly. | Bastien Cazaux, Gustavo Sacomoto, Eric Rivals |
| 2016 | DCC | Shortest DNA Cyclic Cover in Compressed Space. | Bastien Cazaux, Rodrigo Cnovas, Eric Rivals |
| 2015 | LATA | Construction of a de Bruijn Graph for Assembly from a Truncated Suffix Tree. | Bastien Cazaux, Thierry Lecroq, Eric Rivals |
| 2014 | CPM | From Indexing Data Structures to de Bruijn Graphs. | Bastien Cazaux, Thierry Lecroq, Eric Rivals |
| 2010 | RECOMB | Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps. | Raluca Uricaru, Alban Mancheron, Eric Rivals |
| 2009 | WABI | mpscan: Fast Localisation of Multiple Reads in Genomes. | Eric Rivals, Leena Salmela, Petteri Kiiskinen, Petri Kalsi, Jorma Tarhio |
| 2006 | CPM | Tiling an Interval of the Discrete Line. | Olivier Bodini, Eric Rivals |
| 2005 | CPM | Hardness of Optimal Spaced Seed Design. | Franois Nicolas, Eric Rivals |
| 2003 | CPM | Complexities of the Centre and Median String Problems. | Franois Nicolas, Eric Rivals |
| 2002 | RECOMB | Comparison of minisatellites. | Sverine Brard, Eric Rivals |
| 2001 | ICALP | Combinatorics of Periods in Strings. | Eric Rivals, Sven Rahmann |
| 2000 | CPM | Exact and Efficient Computation of the Expected Number of Missing and Common Words in Random Texts. | Sven Rahmann, Eric Rivals |
| 1999 | PSB | Location of Repetitive Regions in Sequences By Optimizing A Compression Method. | Olivier Delgrange, Max Dauchet, Eric Rivals |
| 1999 | RECOMB | Untitled record | Stefan Burkhardt, Andreas Crauser, Paolo Ferragina, Hans-Peter Lenhof, Eric Rivals, Martin Vingron |
| 1996 | DCC | A Guaranteed Compression Scheme for Repetitive DNA Sequences. | Eric Rivals, Jean-Paul Delahaye, Max Dauchet, Olivier Delgrange |