Selected Publications. A complete list, including preliminary versions and posters is available here

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 9838:102-12, 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.
• The Bralibase dent: A tale of benchmark design and interpretation.
  B. Loews, C. Chauve, Y. Ponty, R. Giegerich, Briefings in Bioinformatics (advance access), 2016.
• Algorithms and complexity results for genome mapping problems.
  A. Rajaraman, J.P.P. Zanetti, J. Manuch, C. Chauve, IEEE/ACM TCBB (in press). 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.