| 2010 | RECOMB | Ultra-Perfect Sorting Scenarios. | Ada Ouangraoua, Anne Bergeron, Krister M. Swenson |
| 2009 | RECOMB | Parking Functions, Labeled Trees and DCJ Sorting Scenarios. | Ada Ouangraoua, Anne Bergeron |
| 2009 | RECOMB | Comparative Genomics and Extensive Recombinations in Phage Communities. | Guylaine Poisson, Mahdi Belcaid, Anne Bergeron |
| 2008 | CPM | HP Distance Via Double Cut and Join Distance. | Anne Bergeron, Julia Mixtacki, Jens Stoye |
| 2008 | RECOMB | On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios. | Anne Bergeron, Julia Mixtacki, Jens Stoye |
| 2008 | WABI | Exact Transcriptome Reconstruction from Short Sequence Reads. | Vincent Lacroix, Michael Sammeth, Roderic Guig, Anne Bergeron |
| 2007 | APBC | Exploring Genome Rearrangements using Virtual Hybridization. | Mahdi Belcaid, Anne Bergeron, Annie Chateau, Cdric Chauve, Yannick Gingras, Guylaine Poisson, M. Vendette |
| 2006 | WABI | A Unifying View of Genome Rearrangements. | Anne Bergeron, Julia Mixtacki, Jens Stoye |
| 2005 | ESA | Computing Common Intervals of | Anne Bergeron, Cdric Chauve, Fabien de Montgolfier, Mathieu Raffinot |
| 2005 | RECOMB | On Sorting by Translocations. | Anne Bergeron, Julia Mixtacki, Jens Stoye |
| 2005 | WABI | Perfect Sorting by Reversals Is Not Always Difficult. | Sverine Brard, Anne Bergeron, Cdric Chauve, Christophe Paul |
| 2004 | CPM | Reversal Distance without Hurdles and Fortresses. | Anne Bergeron, Julia Mixtacki, Jens Stoye |
| 2004 | RECOMB | Conservation of Combinatorial Structures in Evolution Scenarios. | Sverine Brard, Anne Bergeron, Cdric Chauve |
| 2004 | WABI | Reconstructing Ancestral Gene Orders Using Conserved Intervals. | Anne Bergeron, Mathieu Blanchette, Annie Chateau, Cdric Chauve |
| 2003 | COCOON | On the Similarity of Sets of Permutations and Its Applications to Genome Comparison. | Anne Bergeron, Jens Stoye |
| 2002 | ECCB | Common intervals and sorting by reversals: a marriage of necessity. | Anne Bergeron, Steffen Heber, Jens Stoye |
| 2002 | WABI | The Algorithmic of Gene Teams. | Anne Bergeron, Sylvie Corteel, Mathieu Raffinot |
| 2001 | CPM | A Very Elementary Presentation of the Hannenhalli-Pevzner Theory. | Anne Bergeron |
| 2001 | WABI | Experiments in Computing Sequences of Reversals. | Anne Bergeron, Franois Strasbourg |
| 1999 | TACAS | An Automated Analysis of Ping-Pong Interactions in E-mail Services. | Anne Bergeron, Jean-Christophe Manzoni |
| 1992 | ITS | Assisted Mathematics: The Case of Discrete Probabilities. | Anne Bergeron |