A complete list of publications prior to 2012 is available at here

2024

• AGO, a Framework for the Reconstruction of Ancestral Syntenies and Gene Orders.
  E. Cribbie, D. Doerr, C. Chauve. Comparative Genomics, Methods in Molecular Biology, 2802:247–265, 2024.
• A vector representation for phylogenetic trees.
  C. Chauve, C. Colijn, L. Zhang. Revised version to appear in Philosophical Transactions of the Royal Society B, 2024.
  Preprint: arXiv:2405.07110, 2024.
• PlasEval: a framework for comparing and evaluating plasmid detection tools.
  A. Mane, H. Sanderson, A.P. White, R. Zaheer, R.G. Beiko, C. Chauve. biorXiv 2024.04.30.591963, 2024.
• TKSM: Highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator.
  F. Karaoglanoglu, B. Orabi, R. Flannigan, C. Chauve, F. Hach. Bioinformatics 40:btae051, 2024.
  Preprint: biorXiv 544410v1, 2023.

2023

• plASgraph2: Using Graph Neural Networks to Detect Plasmid Contigs from an Assembly Graph.
  J. Sielemann, K. Sielemann, B. Brejova, T. Vinar, C. Chauve. Frontiers Microbiology 14:1267695, 2023.
  Preprint: biorXiv 493339v1, 2022.
• TKSM: Highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator.
  F. Karaoglanoglu, B. Orabi, R. Flannigan, C. Chauve, F. Hach. biorXiv 544410v1, 2023.
• PlasBin-flow: A flow-based MILP algorithm for plasmid contigs binning
  A. Mane, M. Faizrahnemoon, T. Vinar, B. Brejova, C. Chauve. Bioinformatics 39:i288–i296.
  Presented at ISMB/ECCB 2023, 2023.

2022

• Freddie: Annotation-independent Detection and Discovery of Transcriptomic Alternative Splicing Isoforms Using Long-read Sequencing.
  B. Orabi, N. Xie, C. Chauve, X. Dong, F. Hach. Nucleic Acids Research 51(2):e11, 2022.
  Preprint: biorXiv 489097v1, 2021.
• plASgraph - using graph neural networks to detect plasmid contigs from an assembly graph.
  J. Sielemann, K. Sielemann, B. Brejova, T. Vinar, C. Chauve. biorXiv 493339v1, 2022.
• A Mixed Integer Linear Programming Algorithm for Plasmid Binning.
  A. Mane, M. Faizrahnemoon, C. Chauve, LNCS/LNBI 13234:279-292, 2022.
  Presented at RECOMB Comparative Genomics 2022.
• scTagger: Fast and accurate matching of cellular barcodes across short- and long-reads of single-cell RNA-seq experiments.
  G. Ebrahimi, B. Orabi, M. Robinson, C. Chauve, R. Flannigan, F. Hach, iScience, 25(7):104530, 2022.
  Preprint: biorXiv 489097v1, 2022.
  Presented at RECOMB-Seq 2022.
• Genion, an accurate tool to detect gene fusion from long transcriptomics reads.
  F. Karaoglanoglu, C. Chauve, F. Hach, BMC Genomics, 23:129, 2022.
• Automated identification of maximal differential cell populations in flow cytometry data.
  A. Yue, C. Chauve, R. Brinkman, M. Libbrecht, Cytometry A, 101(2):177-184, 2022.

2021

• Small Parsimony for natural genomes in the DCJ-Indel model.
  C. Chauve, D. Doerr, Journal of Bioinformatics and Computational Biology 19(6):2140009, proceedings of RECOMB – Comparative Genomics 2021, 2021.
  Preprint: arXiv:2108.04297, 2021.
• Gating flow cytometry samples using few-shot image segmentation.
  A. Yue, M. Libbrecht, C. Chauve, R. Brinkman, poster MLCB 2021, 2021.
• Refined upper bounds on the size of the condensed neighbourhood of sequences.
  C. Chauve, M. Mishna, F. Paquet-Nadeau, proceedings of The Prague Stringology Conference 2021 p. 30-40, 2021.
• Freddie: Annotation-independent Detection and Discovery of Transcriptomic Alternative Splicing Isoforms.
  B. Orabi, B. McConeghy, C. Chauve, F. Hach, biorXiv 427493v1, 2021.
  Short abstract to appear in the proceedings of RECOMB 2021.
  Presented at RECOMB 2021 and JOBIM 2021.

2020

• Geographic heterogeneity impacts drug resistance predictions in Mycobacterium tuberculosis.
  G. Liang Gan, M. Nguyen, E. Willie, B. Lee, C. Chauve, M. Libbrecht, L. Chindelevitch, biorXiv 301226v1, 2020.
• A graph-theoretic barcode ordering model for linked-reads.
  Y. Dufresne, C. Sun, P. Marijon, D. Lavenier, C. Chauve, R. Chikhi, WABI 2020, LIPIcs 172:11:1--11:17. 2020.
• Breakpoint distance and PQ-trees.
  H. Jiang, H. Liu, C. Chauve, B. Zhu, Information and Computation 275, 104584, 2020.
  Long version of Breakpoint Distance and PQ-Trees, CPM 2010.
• The Distance and Median Problems in the Single-Cut-or-Join model with Single-Gene Duplications.
  A.Mane, M. Lafond, P. Feijao, C. Chauve, Algorithms for Molecular Biology 15:8, 2020.
  Full version of LNCS/LNBI 11183:28-48 and LNCS/LNBI 10562:14-30, 2017-2018.
• Ancestral genome organization as a diagnosis tool for phylogenomics.
  E. Tannier, A. Bazin, A. Davin, L. Guéguen, S. Bérard, C. Chauve, in Phylogenetics in the Genomic Era, chapter 2.5, 2020.
• PathOGiST: a novel method for clustering pathogen isolates by combining multiple genotyping signals
  M. Katebi, P. Feijao, J. Booth, M. Mansouri, S. La, A. Sweeten, S.R. Miraskarshahi, M. Nguyen, J. Wong, W. Hsiao, C. Chauve, L. Chindelevitch, AlCoB 2020, LNCS/LNBI 12099:108-124, 2020.
• Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models
  C. Chauve, Y. Ponty, M. Wallner, Journal of Mathematical Biology, 80:1353-1388, 2020.
  Preprint: arXiv:1905.04971, 2019.
• HASLR: Fast Hybrid Assembly of Long Reads
  E. Haghshenas, H. Asghari, J. Stoye, C. Chauve, F. Hach, iScience 23, 101389, 2020.
  Preprint: biorXiv 921817, 2020.
  Presented at DSB 2020 and RECOMB-Seq 2020.
• Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies
  R.M.Waterhouse et al., BMC Biology, 18:1, 2020.
  Preprint: biorXiv 434670v3, 2019.

2019

• Identifying differential cell populations in flow cytometry data accounting for marker frequency
  A. Yue, C. Chauve, R. Brinkman, M. Libbrecht, biorXiv 837765, 2019.
  Presented at MLCB 2019.
• Deconvoluting the Diversity of Within-host Pathogen Strains in a Multi-Locus Sequence Typing Framework
  G.L. Gan, E. Willie, C. Chauve, L. Chindelevitch, BMC Bioinformatics 20:637, proceedings of RECOMBCG 2019, 2019.
• The SCJ Small Parsimony Problem for Weighted Gene Adjacencies
  N. Luhmann, M. Lafond, A. Thévenin, A. Ouangraoua, R. Wittler, C. Chauve, IEEE/ACM TCBB 16(4):1364-1373, 2019.
  Preliminary version (2016) in the proceedings of ISBRA 2016.
• Exponentially few RNA structures are designable.
  H-T. Yao, M. Regnier, C. Chauve, Y. Ponty, ACM-BCB 2019, BCB'19:289-298, 2019.
  Preprint: biorXiv 652313.
• HyAsP, a greedy tool for plasmids identification
  R. Mueller, C. Chauve, Bioinformatics, 35(21):4436-4439, 2019.
• Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models
  C. Chauve, Y. Ponty, M. Wallner, arXiv:1905.04971, 2019.
  To appear, with revisions, in Journal of Mathematical Biology.
• Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies
  R.M.Waterhouse et al., biorXiv 434670v3, 2019.
  To appear in BMC Biology
• Alignment-free Clustering of UMI Tagged DNA Molecules.
  B. Orabi, E. Erhan, B. McConeghy, S.V. Volik, S. Le Bihan, R. Bell, C. C. Collins, C. Chauve, F. Hach, Bioinformatics, 35(11):1829-1836, 2019.

2018

• Counting, Generating, Analyzing and Sampling Tree Alignments.
  C. Chauve, J. Courtiel, Y. Ponty, Int. J. Foundations Comput. Sci. 29(5):741–767, 2018.
• Gene Tree Construction and Correction Using SuperTree and Reconciliation
  M. Lafond, C. Chauve, A. Ouangraoua, N. El-Mabrouk, APBC 2017, IEEE/ACM TCBB 15(5):1560-1570, 2018.
• The The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform
  T.C. Matthews et al., biorXiv 381830, 2018.
• The rooted median with single gene duplications.
  A. C. Mane, M. Lafond, P. Feijao, C. Chauve, RECOMB-CG 2018, LNCS/LNBI 11183:28-48, 2018.
• Detecting introgression in Anopheles mosquito genomes using a reconciliation-based approach.
  C. Chauve, J. Feng, L. Wang, RECOMB-CG 2018, LNCS/LNBI 11183:163-178, 2018.
• PRINCE: Accurate Approximation of the Copy Number of Tandem Repeats
  M. Mansouri, J. Booth, M. Vityaz, C. Chauve, L. Chindelevitch, WABI 2018, LIPIcs 113:20:1--20:13, 2018.
• Beaver Fever: Whole-Genome Characterization of Waterborne Outbreak and Sporadic Isolates To Study the Zoonotic Transmission of Giardiasis.
  C. K.-M. Tsui, R. Miller, M. Uyaguari-Diaz, P. Tang, C. Chauve, W. Hsiao, J. Isaac-Renton, N. Prystajecky, mSphere 3(2):e00090-18, 2018.
• Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework.
  N. Luhmann, C. Chauve, J. Stoye, R. Wittler, IEEE/ACM TCBB, 15(6):2094-2100, 2018.
• flowLearn: Fast and precise identification and quality checking of cell populations in flow cytometry.
  M. Lux, R. Brinkman, C. Chauve, A. Laing, A. Lorenc, L. Abeler-Dorner, B. Hammer, Bioinformatics 13:2245-2253, 2018.
• Comparative Methods for Reconstructing Ancient Genome Organization.
  Y. Anselmetti, N. Luhmann, S. Bérard, E. Tannier, C. Chauve, Methods in Molecular Biology 1704:343-362, 2018.
• Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.
  Y. Anselmetti, W. Duchemin, E. Tannier, C. Chauve, S. Bérard, APBC 2018, BMC Genomics 19(Suppl 2):96, 2018.
• MentaLiST - A fast MLST caller for large MLST schemes.
  P. Feijao, H. Yao, D. Fornika, J. Gardy, W. Hsiao, C. Chauve, L. Chindelevitch, Microbial Genomics 2018:4.

2017

• A tractable variant of the Single Cut or Join distance with duplicated genes.
  P. Feijao, A. Mane, C. Chauve, RECOMB-CG 2017. LNCS/LNBI 10562:14-30, 2017.
• MentaLiST - A fast MLST caller for large MLST schemes.
  P. Feijao, H. Yao, D. Fornika, J. Gardy, W. Hsiao, C. Chauve, L. Chindelevitch, biorXiv 172858, 2017.
• LRCstats, a tool for evaluating long reads correction methods.
  S. La, E. Haghshenas, C. Chauve, Bioinformatics 33(22):3652-3654, 2017.
• ReMixT: clone-specific genomic structure estimation in cancer .
  A. W. McPherson, A. Roth, G. Ha, C. Chauve, A. Steif, C. P. E. de Souza, P. Eirew, A. Bouchard-Côté, S. Aparicio, S. C. Sahinalp and S. P. Shah, Genome Biology 18:140, 2017.
• Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes.
  N. Luhmann, D. Doerr, C. Chauve, Microbial Genomics 2017:3, 2017.
• The gene family-free median of three.
  D. Doerr, M. Balaban, P. Feijao, C. Chauve, Algorithms for Molecular Biology 12:14, 2017.
  Preliminary version (2016) in the proceedings of WABI 2016.
• Constructing a Consensus Phylogeny from a Leaf-Removal Distance
  C. Chauve, M. Jones, M. Lafond, C. Scornavacca, M. Weller, SPIRE 2017. LNCS 10508:129-143. 2017.
  C. Chauve, M. Jones, M. Lafond, C. Scornavacca, M. Weller, arXiv:1705.05295. 2017.
• DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies.
  W. Duchemin, Y. Anselmetti, M. Patterson, Y. Ponty, S. Bérard, C. Chauve, C. Scornavacca, V. Daubin, E. Tannier, Genome Biology and Evolution 9(5):1312-1319, 2017.
• MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers.
  C. Chauve, A. Rafiey, A. Davin, C. Scornavacca, P. Veber, B. Boussau, G. Szollosi, V. Daubin, E. Tannier, biorXiv 127548.
  Peer-reviewed and recommended by Peer Community In Evolutionary Biology (Giraud & Gabaldón 2017. doi: 10.24072/pci.evolbiol.100037).
• The Bralibase dent: A tale of benchmark design and interpretation.
  B. Loews, C. Chauve, Y. Ponty, R. Giegerich, Briefings in Bioinformatics 18(2):306-311, 2017.
• An Exact Enumeration of Distance-Hereditary Graphs
  C. Chauve, E. Fusy, J. Lumbroso, proceedings of ANALCO 2017, pp. 31-45.
• Algorithms and complexity results for genome mapping problems.
  A. Rajaraman, J.P.P. Zanetti, J. Manuch, C. Chauve, IEEE/ACM TCBB 14(2):418-430. 2017.

2016

• CoLoRMap: Correcting Long Reads by Mapping short reads
  E. Haghshenas, F. Hach, S.C. Sahinalp, C. Chauve, Bioinformatics 32(17):i545-i551, 2016.
• Improved assemblies and comparison of two ancient Yersinia pestis genomes
  N. Luhmann, D. Doerr, C. Chauve, bioRxiv:073445. 2016.
• The Gene Family-Free Median of Three
  D. Doerr, P. Feijao, M. Balaban, C. Chauve, WABI 2016, LNCS/LNBI 9838:102-120, 2016.
  D. Doerr, P. Feijao, M. Balaban, C. Chauve, arXiv:1606.05910v1 [cs.DS], 2016.
• The SCJ small parsimony problem for weighted gene adjacencies.
  N. Luhmann, A. Thévenin, A. Ouangraoua, R. Wittler, C. Chauve, ISBRA 2016, LNCS/LNBI 9683:200-210, 2016.
  N. Luhmann, A. Thévenin, A. Ouangraoua, R. Wittler, C. Chauve, arXiv:1603.08819 [cs.DS], 2016.
• Counting, generating and sampling tree alignments.
  J. Courtiel, C. Chauve, Y. Ponty, AlCoB 2016, LNCS/LNBI 9702:53-64, 2016.
  J. Courtiel, C. Chauve, Y. Ponty, HAL 01154030v2, 2016.
• ecceTERA: Comprehensive gene tree-species tree reconciliation using parsimony.
  E. Jacox, C. Chauve, G. Szollosi, Y. Ponty, C. Scornavacca, Bioinformatics 32(17):2056-2058, 2016.

2015

• Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach.
  C. Chauve, Y. Ponty, J.P.P. Zanetti, BMC Bioinformatics 2015, 16(Suppl 19):S6, 2015.
  Preprint: bioRxiv:026310, 2015.
  Preliminary version (2014) in the proceedings of BSB 2014.
• Ancestral gene synteny reconstruction improves extant species scaffolding.
  Y. Anselmetti, V. Berry, C. Chauve, A. Chateau, E. Tannier, S. Berard, biorXiv:023085, 2015.
  Y. Anselmetti, V. Berry, C. Chauve, A. Chateau, E. Tannier, S. Berard, RECOMB-CG 2015, BMC Genomics 16(Suppl 10):S11, 2015.
• Chaining fragments in sequences: to sweep or not.
  J. Allali, L. Bourgeade, C. Chauve, arXiv:1506.07458, 2015.
  J. Allali, L. Bourgeade, C. Chauve, SPIRE 2015, LNCS 9309:116-123, 2015.
• Assessing the robustness of parsimonious predictions for gene neighborhoods from reconciled phylogenies.
  A. Rajaraman, C. Chauve, Y. Ponty, ISBRA 2015, LNCS/LNBI 9096:260-271, 2015.
  Preprint: arXiv:1503.05292, 2015.
• Chaining Sequence/Structure Seeds for Computing RNA Similarity.
  L. Bourgeade, C. Chauve, J. Allali., J. Comput. Biol. 22(3):205-217, 2015.
  Preliminary version (2014) in the proceedings of CMSR 2014.
• Joint inference of genome structure and content in heterogeneous tumor samples.
  A. McPherson, A. Roth, C. Chauve, S.C. Sahinalp, RECOMB 2015, LNCS/LNBI 9069:256-258, 2015.
  A. McPherson, A. Roth, G. Ha, S.P. Shah, C. Chauve, S.C. Sahinalp, arXiv:1504.03080 [q-bio.GN], 2015.

2014

• Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes .
  D. E. Neafsey, R. M. Waterhouse, et al Science 347:1258522, 2015.
• Polytomy Refinement for the Correction of Dubious Duplications in Gene Trees.
  M. Lafond, C. Chauve, R. Dondi, N. El-Mabrouk ECCB 2014, Bioinformatics 30:i519-i526, 2014.
• Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach.
  C. Chauve, Y. Ponty, J.P.P. Zanetti BSB 2014, LNCS/LNBI 8826:49-56, 2014.
• Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework.
  N. Luhmann, C. Chauve, J. Stoye, R. Wittler BSB 2014, LNCS/LNBI 8826:135-143, 2014.
• Chaining Sequence/Structure Seeds for Computing RNA Similarity.
  L. Bourgeade, C. Chauve, J. Allali. CMSR 2014, pp. 1-12. 2014.

2013

• Models and Algorithms for Genome Evolution.
  C. Chauve, N. El-Mabrouk, E Tannier (eds). Computational Biology. 2013.
• Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later.
  C. Chauve, N. El-Mabrouk, L. Guéguen, M. Semeria, E Tannier. Models and Algorithms for Genome Evolution, Computational Biology, 19:47-62. 2013.
• The Potential of Family-Free Genome Comparison.
  M. Braga, C. Chauve, D. Doerr, K. Jahn, J. Stoye, A. Thévenin, R. Wittler. Models and Algorithms for Genome Evolution, Computational Biology, 19:287-307. 2013.
• FPSAC: Fast Phylogenetic Scaffolding of Ancient Contigs.
  A. Rajaraman, E. Tannier, C. Chauve. Bioinformatics, 29:2987-2994. 2013.
• The genome of the medieval Black Death agent (extended abstract).
  A. Rajaraman, E. Tannier, C. Chauve. arXiv:1307.7642 [q-bio.GN]. 2013.
  Presented as a talk at JOBIM 2013.
• Hypergraph covering problems motivated by genome assembly questions.
  C. Chauve, M. Patterson, A. Rajaraman. arXiV:1306.4353v2 [cs.DS] and IWOCA 2013, LNCS 8288:428-432. 2013.

2012

• Linearization of ancestral multichromosomal genomes.
  J. Manuch, M. Patterson, R. Wittler, C. Chauve, E. Tannier. RECOMB-CG 2012, BMC Bioinformatics 13(Suppl. 19):S11.
• ANGES: reconstructing ANcestral GEnomeS maps.
  B.R. Jones, A. Rajaraman, E. Tannier, C. Chauve. Bioinformatics, 28:2388-2390.
• A tight bound on the length of odd cycles in the incompatibility graph of a non-C1P matrix.
  M. Malekesmaeili, C. Chauve, T. Stephen. IPL 12:799-803.
• An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework.
  J.P. Doyon, S. Hamel, C. Chauve. IEEE/ACM TCBB 9:26-39.
• Hardness Results for the Gapped Consecutive-Ones Property.
  J. Manuch, M. Patterson, C. Chauve. Discrete Applied Math, 160(18):2760-2768.
• Efficient chaining of seeds in ordered trees.
  J. Allali, C. Chauve, P. Ferraro, A.-L. Gaillard. J. Discrete Algorithms 14:107-118.
• BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms.
  J. Allali et al. Advances in Bioinformatics 2012:893048.

2011

• À la recherche des génomes perdus : Modèles, Méthodologies et Algorithmes pour la Comparaison de Génomes.
  C. Chauve. Habilitation à diriger des recherches, LaBRI, University Bordeaux I.
• Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes.
  R. Witler, C. Chauve. RECOMB-CG 2011, BMC Bioinformatics 12:S21.
• Mapping ancestral genomes with massive gene loss: a matrix sandwich problem.
  H. Gavranovic, C. Chauve, J. Salse, E. Tannier. ISMB/ECCB 2011, Bioinformatics 27:i257-i265.
• Reconstructing the architecture of the ancestral amniote genome.
  A. Ouangraoua, E. Tannier, C. Chauve. Bioinformatics 27:2664-2671.
• A 2-Approximation for the Minimum Duplication Speciation Problem.
  A. Ouangraoua, K. Swenson, C. Chauve. J. Comp. Biol. 18:1041-1053.
• Branch-and-Bound Approach for Parsimonious Inference of a Species Tree From a Set of Gene Family Trees.
  J.P. Doyon, C. Chauve. Software Tools and Algorithms for Biological Systems, chap. 29.
  
• Average-case analysis of perfect sorting by reversals.
  M. Bouvel, C. Chauve, M. Mishna, D. Rossin. Discrete Math. Algorithms Applications 3:369-392.
• Tractability results for the Double-Cut-and-Join circular median problem.
  A. Mahmoody-Ghaidary, C. Chauve, L. Stacho. arXiv:cs.DM/11115872v1.
• Tractability results for the Consecutive-Ones Property with multiplicity.
  C. Chauve, J. Manuch, M. Patterson, R. Wittler. CPM 2011, LNCS 6661:90-103.
• A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes.
  A. Ouangraoua, V. Guignon, S. Hamel, C. Chauve. Theoret. Comput. Sci. 412:753-764.

2010

• Yeast ancestral genome reconstructions: the possibilities of computational methods II.
  C. Chauve, H. Gavranovic, A. Ouangraoua, E. Tannier. J. Comput. Biol. 17:1097-1112.
• Minimal Conflicting Sets for the Consecutive Ones Property in ancestral genome reconstruction.
  C. Chauve, U.-U. Haus, T. Stephen, V.P. You. J. Comput. Biol. 17:1167-1181.
• Breakpoint distance and PQ-trees.
  H. Jiang, C. Chauve, B. Zhu. CPM 2010, LNCS 6219:112-124.

2009

• Prediction of contiguous ancestral regions in the amniote ancestral genome.
  A. Ouangraoua, F. Boyer, A. McPherson, E. Tannier, C. Chauve. ISBRA 2009, LNCS/LNBI 5542:173-185.
• Space of Gene/Species Trees Reconciliations and Parsimonious Models.
  J.P. Dpyon, S. Hamel, C. Chauve. J. Comput. Biol. 16:1399-1418.
• Computation of perfect DCJ rearrangement scenarios with linear and circular chromosomes.
  S. Bérard, A. Chateau, C. Chauve, C. Paul, E. Tannier. J. Comput. Biol. 16:1287-1309.
• New perspectives on gene family evolution: losses in reconciliation and a link with supertrees.
  C. Chauve, N. El-Mabrouk. RECOMB 2009, LNCS/LNBI 5541:46-58.

2008

• A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.
  C. Chauve, E. Tannier. PLoS Comput. Biol. 4:e1000234.
• Gene family evolution by duplication, speciation and loss.
  C. Chauve, J.P. Doyon, N. El-Mabrouk. J. Comput. Biol. 15:1043-1062.
• A more efficient algorithm for perfect sorting by reversals.
  S. Bérard, C. Chauve, C. Paul. Inform. Proc. Letters 106:90-95.
• Formal models of gene clusters.
  A. Bergeron, C. Chauve, Y. Gingras. Bioinformatics Algorithms: Techniques and Applications, pp. 177-202.
• Computing common intervals of K permutations with application to graph decomposition.
  A. Bergeron, C. Chauve, F. de Montgolfier, M. Raffinot. SIAM J. Discrete Math. 22:1022-1039.

2007

• Perfect sorting by reversals is not always difficult.
  S. Bérard, A. Bergeron, C. Chauve, C. Paul. IEEE/ACM TCBB 4:4-16.
• Comparing genomes with duplicates: a computational complexity point of view .
  G. Blin, C. Chauve, G. Fertin, R. Rizzi, S. Vialette. IEEE/ACM TCBB 4:523-534.
• Exploring genome rearrangements using virtual hybridization.
  M. Belacid, A. Bergeron, C. Chauve, G. Poisson, M. Vendette. APBC 2007, Adv. Bioinfo. Comput. Biol. 5:205-214.
• FragAnchor a large-scale all Eukaryota predictor of glycosylphosphatidylinositol-anchor in protein sequences by qualitative scoring.
  G. Poisson, X. Chen, C. Chauve, A. Bergeron. Genomics, Proteomics & Bioinformatics 5:121-130.

2006

• Inferring positional homologs using common intervals of sequences.
  G. Blin, A. Chateau, C. Chauve, Y. Gingras. RCG 2006, LNCS/LNBI 4205:24-38.
• On common intervals with errors.
  C. Chauve, Y. Diekman, S. Heber, J. Mixtacki, S. Rahmann, J. Stoye. Report 2006-02, Technische Fakultat der Universitat Bielefeld.

2005

• An edit distance between RNA stem-loops.
  V. Guignon, C. Chauve, S. Hamel. SPIRE 2005, LNCS 3772:334-345.
• Genes order and phylogenetic reconstruction: application to gamma-Proteobacteria.
  G. Blin, C. Chauve, G. Fertin. RCG 2005, LNCS/LNBI 3678:11-20.

2004

• Reconstructing ancestral gene orders using conserved intervals.
  A. Bergeron, M. Blanchette, A. Chateau, C. Chauve. WABI 2004, LNCS/LNBI 3240:14-25.
• Conserved structures in evolution scenarios.
  S. Bérard, A. Bergeron, C. Chauve. RCG 2004, LNCS/LNBI 3388:1-15.
• The breakpoints distance for signed sequences.
  G. Blin, C. Chauve, G. Fertin. CompBioNets 2004, Texts in Algorithms 3:3-16.
• On maximal instances for the original syntenic distance.
  C. Chauve, G. Fertin. Theoret. Comput. Sci. 326:29-43.

2002

• On the properties of sequences of reversals that sort a signed permutation.
  A. Bergeron, C. Chauve, T. Hartman, K. St-Onge. JOBIM 2002, pp. 99-108. 2002.