Two Strikes Against the Phage Recombination Problem.

Anne Bergeron Manuel Lafond Anne Bergeron Krister M. Swenson Two Strikes Against the Phage Recombination Problem. 68-83 2023 RECOMB-CG https://doi.org/10.1007/978-3-031-36911-7_5 conf/recombcg/2023 db/conf/recombcg/recombcg2023.html#LafondBS23 Anne Bergeron Marie-Jean Meurs Romy Valiquette-Labonté Krister M. Swenson On the Comparison of Bacteriophage Populations. 3-20 2022 RECOMB-CG https://doi.org/10.1007/978-3-031-06220-9_1 conf/recombcg/2022 db/conf/recombcg/recombcg2022.html#BergeronMVS22

Sèverine Bérard Annie Chateau Nicolas Pompidor Paul Guertin Anne Bergeron Krister M. Swenson Aligning the unalignable: bacteriophage whole genome alignments. 30 2016 17 BMC Bioinform. https://doi.org/10.1186/s12859-015-0869-5 https://www.wikidata.org/entity/Q27319503 db/journals/bmcbi/bmcbi17.html#BerardCPGBS16

Philippe Lavoie-Mongrain Mahdi Belcaid Aïda Ouangraoua Anne Bergeron Guylaine Poisson Reconstructing the history of a WD40 beta-propeller tandem repeat using a phylogenetically informed algorithm. e6 2015 1 PeerJ Comput. Sci. https://doi.org/10.7717/peerj-cs.6 https://www.wikidata.org/entity/Q110949909 db/journals/peerj-cs/peerj-cs1.html#Lavoie-Mongrain15

Krister M. Swenson Paul Guertin Hugo Deschênes Anne Bergeron Reconstructing the modular recombination history of Staphylococcus aureus phages. S17 2013 14 BMC Bioinform. S-15 https://doi.org/10.1186/1471-2105-14-S15-S17 https://www.wikidata.org/entity/Q35101704 db/journals/bmcbi/bmcbi14S.html#SwensonGDB13

Anne Bergeron Jens Stoye The Genesis of the DCJ Formula. 63-81 2013 Models and Algorithms for Genome Evolution https://doi.org/10.1007/978-1-4471-5298-9_5 books/daglib/0032286 db/books/daglib/0032286.html#BergeronS13 Aïda Ouangraoua Krister M. Swenson Anne Bergeron On the Comparison of Sets of Alternative Transcripts. 201-212 2012 ISBRA https://doi.org/10.1007/978-3-642-30191-9_19 conf/isbra/2012 db/conf/isbra/isbra2012.html#OuangraouaSB12

Mahdi Belcaid Anne Bergeron Guylaine Poisson The evolution of the tape measure protein: units, duplications and losses. S10 2011 12 BMC Bioinform. S-9 https://doi.org/10.1186/1471-2105-12-S9-S10 https://www.wikidata.org/entity/Q34094333 db/journals/bmcbi/bmcbi12S.html#BelcaidBP11

Aïda Ouangraoua Anne Bergeron Krister M. Swenson Theory and Practice of Ultra-Perfection. 1219-1230 2011 18 J. Comput. Biol. 9 https://doi.org/10.1089/cmb.2011.0086 https://www.wikidata.org/entity/Q51533886 db/journals/jcb/jcb18.html#OuangraouaBS11

Aïda Ouangraoua Anne Bergeron Combinatorial Structure of Genome Rearrangements Scenarios. 1129-1144 2010 17 J. Comput. Biol. 9 https://doi.org/10.1089/cmb.2010.0126 https://www.wikidata.org/entity/Q51655072 db/journals/jcb/jcb17.html#OuangraouaB10

Anne Bergeron Paul Medvedev Jens Stoye Rearrangement Models and Single-Cut Operations. 1213-1225 2010 17 J. Comput. Biol. 9 https://doi.org/10.1089/cmb.2010.0091 https://www.wikidata.org/entity/Q51655053 db/journals/jcb/jcb17.html#BergeronMS10

Mahdi Belcaid Anne Bergeron Guylaine Poisson Mosaic Graphs and Comparative Genomics in Phage Communities. 1315-1326 2010 17 J. Comput. Biol. 9 https://doi.org/10.1089/cmb.2010.0108 https://www.wikidata.org/entity/Q35067223 db/journals/jcb/jcb17.html#BelcaidBP10

Aïda Ouangraoua Anne Bergeron Krister M. Swenson Ultra-Perfect Sorting Scenarios. 50-61 2010 RECOMB-CG https://doi.org/10.1007/978-3-642-16181-0_5 conf/recomb/2010cg db/conf/recomb/recomb-cg2010.html#OuangraouaBS10 Anne Bergeron Julia Mixtacki Jens Stoye A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance. 2010 Structure Discovery in Biology: Motifs, Networks & Phylogenies http://drops.dagstuhl.de/opus/volltexte/2010/2689/ conf/dagstuhl/2010P10231 db/conf/dagstuhl/P10231.html#BergeronMS10

Anne Bergeron Julia Mixtacki Jens Stoye A new linear time algorithm to compute the genomic distance via the double cut and join distance. 5300-5316 2009 410 Theor. Comput. Sci. 51 https://doi.org/10.1016/j.tcs.2009.09.008 db/journals/tcs/tcs410.html#BergeronMS09

Aïda Ouangraoua Anne Bergeron Parking Functions, Labeled Trees and DCJ Sorting Scenarios. 24-35 2009 RECOMB-CG https://doi.org/10.1007/978-3-642-04744-2_3 conf/recomb/2009cg db/conf/recomb/recomb-cg2009.html#OuangraouaB09 Guylaine Poisson Mahdi Belcaid Anne Bergeron Comparative Genomics and Extensive Recombinations in Phage Communities. 205-216 2009 RECOMB-CG https://doi.org/10.1007/978-3-642-04744-2_17 conf/recomb/2009cg db/conf/recomb/recomb-cg2009.html#PoissonBB09

Aïda Ouangraoua Anne Bergeron Parking functions, labeled trees and DCJ sorting scenarios http://arxiv.org/abs/0903.2499 2009 CoRR abs/0903.2499 db/journals/corr/corr0903.html#abs-0903-2499

Anne Bergeron Cédric Chauve Fabien de Montgolfier Mathieu Raffinot Computing Common Intervals of K Permutations, with Applications to Modular Decomposition of Graphs. 1022-1039 2008 22 SIAM J. Discret. Math. 3 https://doi.org/10.1137/060651331 db/journals/siamdm/siamdm22.html#BergeronCMR08

Anne Bergeron Julia Mixtacki Jens Stoye HP Distance Via Double Cut and Join Distance. 56-68 2008 CPM https://doi.org/10.1007/978-3-540-69068-9_8 conf/cpm/2008 db/conf/cpm/cpm2008.html#BergeronMS08 Anne Bergeron Julia Mixtacki Jens Stoye On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios. 226-240 2008 RECOMB-CG https://doi.org/10.1007/978-3-540-87989-3_17 conf/recomb/2008cg db/conf/recomb/recomb-cg2008.html#BergeronMS08 Vincent Lacroix Michael Sammeth Roderic Guigó Anne Bergeron Exact Transcriptome Reconstruction from Short Sequence Reads. 50-63 2008 WABI https://doi.org/10.1007/978-3-540-87361-7_5 conf/wabi/2008 db/conf/wabi/wabi2008.html#LacroixSGB08

Eric Tannier Anne Bergeron Marie-France Sagot Advances on sorting by reversals. 881-888 2007 155 Discret. Appl. Math. 6-7 https://doi.org/10.1016/j.dam.2005.02.033 db/journals/dam/dam155.html#TannierBS07

Guylaine Poisson Cédric Chauve Xin Chen Anne Bergeron FragAnchor: A Large-Scale Predictor of Glycosylphosphatidylinositol Anchors in Eukaryote Protein Sequences by Qualitative Scoring. 121-130 2007 5 Genom. Proteom. Bioinform. 2 https://doi.org/10.1016/S1672-0229(07)60022-9 https://www.wikidata.org/entity/Q37318346 db/journals/gpb/gpb5.html#PoissonCCB07

Sèverine Bérard Anne Bergeron Cédric Chauve Christophe Paul Perfect Sorting by Reversals Is Not Always Difficult. 4-16 2007 4 IEEE ACM Trans. Comput. Biol. Bioinform. 1 https://doi.org/10.1109/TCBB.2007.1011 https://doi.ieeecomputersociety.org/10.1109/TCBB.2007.1011 https://dl.acm.org/doi/10.1109/TCBB.2007.1011 https://www.wikidata.org/entity/Q51627771 db/journals/tcbb/tcbb4.html#BerardBCP07

Mahdi Belcaid Anne Bergeron Annie Chateau Cédric Chauve Yannick Gingras Guylaine Poisson M. Vendette Exploring Genome Rearrangements using Virtual Hybridization. 205-214 2007 conf/apbc/2007 APBC http://www.comp.nus.edu.sg/~wongls/psZ/apbc2007/apbc217a.pdf db/conf/apbc/apbc2007.html#BelcaidBCCGPV07 Anne Bergeron Julia Mixtacki Jens Stoye The inversion distance problem. 2007 Mathematics of Evolution and Phylogeny books/ox/07/G2007 db/books/collections/G2007.html#BergeronMS07

Anne Bergeron Julia Mixtacki Jens Stoye On Sorting by Translocations. 567-578 2006 13 J. Comput. Biol. 2 https://doi.org/10.1089/cmb.2006.13.567 https://www.wikidata.org/entity/Q51944558 db/journals/jcb/jcb13.html#BergeronMS06

Anne Bergeron Jens Stoye On the Similarity of Sets of Permutations and Its Applications to Genome Comparison. 1340-1354 2006 13 J. Comput. Biol. 7 https://doi.org/10.1089/cmb.2006.13.1340 https://www.wikidata.org/entity/Q51931170 db/journals/jcb/jcb13.html#BergeronS06

Anne Bergeron Julia Mixtacki Jens Stoye A Unifying View of Genome Rearrangements. 163-173 2006 conf/wabi/2006 WABI https://doi.org/10.1007/11851561_16 db/conf/wabi/wabi2006.html#BergeronMS06

Anne Bergeron A very elementary presentation of the Hannenhalli-Pevzner theory. 134-145 2005 146 Discret. Appl. Math. 2 https://doi.org/10.1016/j.dam.2004.04.010 db/journals/dam/dam146.html#Bergeron05

Anne Bergeron Cédric Chauve Fabien de Montgolfier Mathieu Raffinot Computing Common Intervals of <i>K</i> Permutations, with Applications to Modular Decomposition of Graphs. 779-790 2005 conf/esa/2005 ESA https://doi.org/10.1007/11561071_69 db/conf/esa/esa2005.html#BergeronCMR05 Anne Bergeron Julia Mixtacki Jens Stoye On Sorting by Translocations. 615-629 2005 conf/recomb/2005 RECOMB https://doi.org/10.1007/11415770_47 db/conf/recomb/recomb2005.html#BergeronMS05 Sèverine Bérard Anne Bergeron Cédric Chauve Christophe Paul Perfect Sorting by Reversals Is Not Always Difficult. 228-238 2005 conf/wabi/2005 WABI https://doi.org/10.1007/11557067_19 db/conf/wabi/wabi2005.html#BerardBCP05

Anne Bergeron Sylvie Hamel From cascade decompositions to bit-vector algorithms. 3-16 2004 313 Theor. Comput. Sci. 1 https://doi.org/10.1016/j.tcs.2003.10.010 https://www.wikidata.org/entity/Q60704267 db/journals/tcs/tcs313.html#BergeronH04

Marie-Pierre Béal Anne Bergeron Sylvie Corteel Mathieu Raffinot An algorithmic view of gene teams. 395-418 2004 320 Theor. Comput. Sci. 2-3 https://doi.org/10.1016/j.tcs.2004.02.036 db/journals/tcs/tcs320.html#BealBCR04

Anne Bergeron Julia Mixtacki Jens Stoye Reversal Distance without Hurdles and Fortresses. 388-399 https://doi.org/10.1007/978-3-540-27801-6_29 2004 conf/cpm/2004 CPM db/conf/cpm/cpm2004.html#BergeronMS04 Sèverine Bérard Anne Bergeron Cédric Chauve Conservation of Combinatorial Structures in Evolution Scenarios. 1-14 https://doi.org/10.1007/978-3-540-32290-0_1 2004 conf/recomb/2004rcg Comparative Genomics db/conf/recomb/rcg2004.html#BerardBC04 Anne Bergeron Mathieu Blanchette Annie Chateau Cédric Chauve Reconstructing Ancestral Gene Orders Using Conserved Intervals. 14-25 https://doi.org/10.1007/978-3-540-30219-3_2 2004 conf/wabi/2004 WABI db/conf/wabi/wabi2004.html#BergeronBCC04

Nicolas Luc Jean-Loup Risler Anne Bergeron Mathieu Raffinot Gene teams: a new formalization of gene clusters for comparative genomics. 59-67 2003 27 Comput. Biol. Chem. 1 https://doi.org/10.1016/S1476-9271(02)00097-X https://www.wikidata.org/entity/Q52014604 db/journals/candc/candc27.html#LucRBR03

Anne Bergeron Jens Stoye On the Similarity of Sets of Permutations and Its Applications to Genome Comparison. 68-79 https://doi.org/10.1007/3-540-45071-8_9 2003 conf/cocoon/2003 COCOON db/conf/cocoon/cocoon2003.html#BergeronS03

Anne Bergeron Sylvie Hamel Vector Algorithms for Approximate String Matching. 53-66 2002 13 Int. J. Found. Comput. Sci. 1 https://doi.org/10.1142/S0129054102000947 https://www.wikidata.org/entity/Q60704269 db/journals/ijfcs/ijfcs13.html#BergeronH02

Anne Bergeron Steffen Heber Jens Stoye Common intervals and sorting by reversals: a marriage of necessity. 54-63 2002 conf/eccb/2002 ECCB db/conf/eccb/eccb2002.html#BergeronHS02 https://doi.org/10.1093/bioinformatics/18.suppl_2.s54 Anne Bergeron Sylvie Corteel Mathieu Raffinot The Algorithmic of Gene Teams. 464-476 2002 conf/wabi/2002 WABI https://doi.org/10.1007/3-540-45784-4_36 https://www.wikidata.org/entity/Q56686759 db/conf/wabi/wabi2002.html#BergeronCR02 Anne Bergeron A Very Elementary Presentation of the Hannenhalli-Pevzner Theory. 106-117 2001 conf/cpm/2001 CPM https://doi.org/10.1007/3-540-48194-X_9 db/conf/cpm/cpm2001.html#Bergeron01 Anne Bergeron François Strasbourg Experiments in Computing Sequences of Reversals. 164-174 2001 conf/wabi/2001 WABI https://doi.org/10.1007/3-540-44696-6_13 db/conf/wabi/wabi2001.html#BergeronS01 Anne Bergeron Sylvie Hamel Cascade Decompositions are Bit-Vector Algorithms. 13-26 2001 conf/wia/2001 CIAA https://doi.org/10.1007/3-540-36390-4_2 https://www.wikidata.org/entity/Q60704270 db/conf/wia/ciaa2001.html#BergeronH01 Anne Bergeron Sylvie Hamel Fast Implementations of Automata Computations. 47-56 2000 conf/wia/2000 CIAA https://doi.org/10.1007/3-540-44674-5_3 https://www.wikidata.org/entity/Q60704271 db/conf/wia/ciaa2000.html#BergeronH00 Anne Bergeron Jean-Christophe Manzoni An Automated Analysis of Ping-Pong Interactions in E-mail Services. 134-147 1999 conf/tacas/1999 TACAS https://doi.org/10.1007/3-540-49059-0_10 db/conf/tacas/tacas99.html#BergeronM99 Anne Bergeron Riccardo Catalano Analysis of Reactive Systems with n Timers. 27-38 1999 conf/wia/1999 WIA https://doi.org/10.1007/3-540-45526-4_3 db/conf/wia/wia1999.html#BergeronC99

Anne Bergeron Paul Geanta Dominique Bergeron The Death factors: a combinatorial analysis. 147-158 1998 1 Silico Biol. 3 http://content.iospress.com/articles/in-silico-biology/isb00013 http://www.bioinfo.de/isb/abstracts/01/0013.html db/journals/isb/isb1.html#BergeronGB98

Marie-Chantal Beaulieu Anne Bergeron Automata and Computational Probabilities. 164-177 1998 conf/wia/1998 Workshop on Implementing Automata https://doi.org/10.1007/3-540-48057-9_14 db/conf/wia/wia1998.html#BeaulieuB98

Anne Bergeron On the Rational Behaviors of Concurrent Timers. 229-237 1997 189 Theor. Comput. Sci. 1-2 db/journals/tcs/tcs189.html#Bergeron97 https://doi.org/10.1016/S0304-3975(97)00074-1

Anne Bergeron Sharing Out Control in Distributed Processes. 163-186 1995 139 Theor. Comput. Sci. 1&2 db/journals/tcs/tcs139.html#Bergeron95 https://doi.org/10.1016/0304-3975(94)00132-3

Anne Bergeron Symbolic Timing Devices. 504-517 1995 conf/amast/1995 AMAST db/conf/amast/amast95.html#Bergeron95 https://doi.org/10.1007/3-540-60043-4_74

Anne Bergeron A Unified Approach to Control Problems in Discrete Event Processes. 555-573 1993 27 RAIRO Theor. Informatics Appl. 6 db/journals/ita/ita27.html#Bergeron93 https://doi.org/10.1051/ita/1993270605551

Anne Bergeron Assisted Mathematics: The Case of Discrete Probabilities. 40-49 1992 conf/its/1992 Intelligent Tutoring Systems db/conf/its/its1992.html#Bergeron92 https://doi.org/10.1007/3-540-55606-0_7 Marie-Pierre Béal Marie-Chantal Beaulieu Mahdi Belcaid Sèverine Bérard Dominique Bergeron Mathieu Blanchette Riccardo Catalano Annie Chateau Cédric Chauve Xin Chen Sylvie Corteel Hugo Deschênes Paul Geanta Yannick Gingras Paul Guertin Roderic Guigó Sylvie Hamel Steffen Heber Vincent Lacroix Manuel Lafond Philippe Lavoie-Mongrain Nicolas Luc Jean-Christophe Manzoni Paul Medvedev Marie-Jean Meurs Julia Mixtacki Fabien de Montgolfier Aïda Ouangraoua Christophe Paul Guylaine Poisson Nicolas Pompidor Mathieu Raffinot Jean-Loup Risler Marie-France Sagot Michael Sammeth Jens Stoye François Strasbourg Krister M. Swenson Eric Tannier Romy Valiquette-Labonté M. Vendette