Major publications by the team in recent years
  • 1G. Benoit, C. Lemaitre, D. Lavenier, E. Drezen, T. Dayris, R. Uricaru, G. Rizk.

    Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph, in: BMC Bioinformatics, September 2015, vol. 16, no 1. [ DOI : 10.1186/s12859-015-0709-7 ]

  • 2G. Benoit, P. Peterlongo, M. Mariadassou, E. Drezen, S. Schbath, D. Lavenier, C. Lemaitre.

    Multiple comparative metagenomics using multiset k -mer counting, in: PeerJ Computer Science, November 2016, vol. 2. [ DOI : 10.7717/peerj-cs.94 ]

  • 3R. Chikhi, G. Rizk.

    Space-efficient and exact de Bruijn graph representation based on a Bloom filter, in: Algorithms for Molecular Biology, 2013, vol. 8, no 1, 22 p. [ DOI : 10.1186/1748-7188-8-22 ]

  • 4E. Drezen, G. Rizk, R. Chikhi, C. Deltel, C. Lemaitre, P. Peterlongo, D. Lavenier.

    GATB: Genome Assembly & Analysis Tool Box, in: Bioinformatics, 2014, vol. 30, pp. 2959-2961. [ DOI : 10.1093/bioinformatics/btu406 ]

  • 5S. François, R. Andonov, D. Lavenier, H. Djidjev.

    Global optimization approach for circular and chloroplast genome assembly, in: BICoB 2018 - 10th International Conference on Bioinformatics and Computational Biology, Las Vegas, United States, March 2018, pp. 1-11. [ DOI : 10.1101/231324 ]

  • 6C. Guyomar, F. Legeai, E. Jousselin, C. C. Mougel, C. Lemaitre, J.-C. Simon.

    Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches, in: Microbiome, December 2018, vol. 6, no 1. [ DOI : 10.1186/s40168-018-0562-9 ]

  • 7A. Limasset, G. Rizk, R. Chikhi, P. Peterlongo.

    Fast and scalable minimal perfect hashing for massive key sets, in: 16th International Symposium on Experimental Algorithms, London, United Kingdom, June 2017, vol. 11, pp. 1-11.

  • 8C. Marchet.

    From reads to transcripts: de novo methods for the analysis of transcriptome second and third generation sequencing, Université de Rennes 1, September 2018.

  • 9G. Rizk, A. Gouin, R. Chikhi, C. Lemaitre.

    MindTheGap: integrated detection and assembly of short and long insertions, in: Bioinformatics, December 2014, vol. 30, no 24, pp. 3451-3457. [ DOI : 10.1093/bioinformatics/btu545 ]

  • 10R. Uricaru, G. Rizk, V. Lacroix, E. Quillery, O. Plantard, R. Chikhi, C. Lemaitre, P. Peterlongo.

    Reference-free detection of isolated SNPs, in: Nucleic Acids Research, November 2014, pp. 1-12. [ DOI : 10.1093/nar/gku1187 ]

Publications of the year

Articles in International Peer-Reviewed Journals

  • 11R. Andonov, H. Djidjev, S. François, D. Lavenier.

    Complete Assembly of Circular and Chloroplast Genomes Based on Global Optimization, in: Journal of Bioinformatics and Computational Biology, 2019, pp. 1-28, forthcoming. [ DOI : 10.1142/S0219720019500148 ]

  • 12G. Benoit, M. Mariadassou, S. Robin, S. Schbath, P. Peterlongo, C. Lemaitre.

    SimkaMin: fast and resource frugal de novo comparative metagenomics, in: Bioinformatics, September 2019, pp. 1-2. [ DOI : 10.1093/bioinformatics/btz685 ]

  • 13H. Boulain, F. Legeai, J. Jaquiéry, E. Guy, S. Morliere, J.-C. Simon, A. Sugio.

    Differential Expression of Candidate Salivary Effector Genes in Pea Aphid Biotypes With Distinct Host Plant Specificity, in: Frontiers in Plant Science, October 2019, vol. 10, pp. 1-12. [ DOI : 10.3389/fpls.2019.01301 ]

  • 14J. Ferreira De Carvalho, J. Lucas, G. Deniot, C. Falentin, O. Filangi, M. Gilet, F. Legeai, M. Lode, J. Morice, G. Trotoux, J.-M. Aury, V. Barbe, J. Keller, R. Snowdon, Z. He, F. Denoeud, P. Wincker, I. Bancroft, A.-M. Chèvre, M. Rousseau-Gueutin.

    Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica, in: Plant Journal, February 2019, vol. 98, no 3, pp. 434-447. [ DOI : 10.1111/tpj.14228 ]

  • 15L. Guillot, L. Delage, A. Viari, Y. Vandenbrouck, E. Com, A. A. Ritter, R. Lavigne, D. Marie, P. Peterlongo, P. Potin, C. Pineau.

    Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes, in: BMC Genomics, January 2019, vol. 20, no 1, 56 p. [ DOI : 10.1186/s12864-019-5431-9 ]

  • 16A. Limasset, J.-F. Flot, P. Peterlongo.

    Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs, in: Bioinformatics, February 2019. [ DOI : 10.1093/bioinformatics/btz102 ]

  • 17C. Marchet, P. Morisse, L. Lecompte, A. Lefebvre, T. Lecroq, P. Peterlongo, A. Limasset.

    ELECTOR: evaluator for long reads correction methods, in: NAR Genomics and Bioinformatics, March 2020, vol. 2, no 1. [ DOI : 10.1093/nargab/lqz015 ]

  • 18S. Robin, M. Ravallec, M. Frayssinet, J. Whitfield, V. Jouan, F. Legeai, A.-N. Volkoff.

    Evidence for an ichnovirus machinery in parasitoids of coleopteran larvae, in: Virus Research, 2019, vol. 263, pp. 189-206. [ DOI : 10.1016/j.virusres.2019.02.001 ]

  • 19M. Wery, O. Dameron, J. Nicolas, E. Rémy, A. Siegel.

    Formalizing and enriching phenotype signatures using Boolean networks, in: Journal of Theoretical Biology, 2019, vol. 467, pp. 66-79. [ DOI : 10.1016/j.jtbi.2019.01.015 ]


International Conferences with Proceedings

  • 20J. N. Alanko, H. Bannai, B. Cazaux, P. Peterlongo, J. Stoye.

    Finding all maximal perfect haplotype blocks in linear time, in: WABI 2019 - Workshop on Algorithms in Bioinformatics, Niagara Falls, United States, ACM, September 2019, pp. 1-9.

  • 21L. Bourneuf, J. Nicolas.

    Concept Lattices as a Search Space for Graph Compression, in: ICFCA 2019 - 15th International Conference on Formal Concept Analysis, Francfort, Germany, D. C. L. B. Sertkaya (editor), ICFCA: International Conference on Formal Concept Analysis, Springer, May 2019, vol. 15th International Conference, no 15, pp. 274-289. [ DOI : 10.1007/978-3-030-21462-3_18 ]


National Conferences with Proceedings

  • 22C. Guyomar, W. Delage, F. Legeai, C. Mougel, J.-C. Simon, C. Lemaitre.

    Reference-guided genome assembly in metagenomic samples, in: JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Nantes, France, July 2019, pp. 1-8.

  • 23L. Lecompte, P. Peterlongo, D. Lavenier, C. Lemaitre.

    Genotyping Structural Variations using Long Read data, in: JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Nantes, France, July 2019, pp. 1-8.


Conferences without Proceedings

  • 24L. Lecompte, P. Peterlongo, D. Lavenier, C. Lemaitre.

    Genotyping Structural Variations using Long Read Data, in: HiTSeq 2019 - Conference on High Throughput Sequencing, Basel, Switzerland, July 2019, pp. 1-3.

  • 25C. Marchet, M. Kerbiriou, A. Limasset.

    Indexing De Bruijn graphs with minimizers, in: Recomb seq, Whashinton, United States, April 2019. [ DOI : 10.1101/546309 ]

  • 26P. Morisse, C. Marchet, A. Limasset, T. Lecroq, A. Lefebvre.

    CONSENT: Scalable self-correction of long reads with multiple sequence alignment, in: Recomb Seq, Washinton, France, May 2019.

  • 27H. S. Pham, G. Virlet, D. Lavenier, A. Termier.

    Statistically Significant Discriminative Patterns Searching, in: DaWaK 2019 - 21st International Conference on Big Data Analytics and Knowledge Discovery, Linz, Austria, Springer, August 2019, pp. 105-115. [ DOI : 10.1007/978-3-030-27520-4_8 ]


Other Publications

  • 28A. Badual.

    Stockage d'information sur ADN, Université Rennes 1, June 2019.

  • 29L. Conde-Canencia, B. Hamoum, D. Lavenier, E. Roux.

    Error Correction Schemes for DNA Storage with Nanopore Sequencing, July 2019, JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Poster.

  • 30K. Da Silva, N. Pons, M. Berland, F. Plaza Oñate, M. Almeida, P. Peterlongo.

    From genomics to metagenomics: benchmark of variation graphs, July 2019, JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Poster.

  • 31V. Epain.

    De novo long reads assembly using integer linear programing, Université de Rennes 1 [UR1], September 2019.

  • 32J. Gauthier, C. Mouden, T. Suchan, N. Alvarez, N. Arrigo, C. Riou, C. Lemaitre, P. Peterlongo.

    DiscoSnp-RAD: de novo detection of small variants for population genomics, October 2019, working paper or preprint.

  • 33R. Laso-Jadart, K. Sugier, E. Petit, K. Labadie, P. Peterlongo, C. Ambroise, P. Wincker, J.-L. Jamet, M.-A. Madoui.

    Linking Allele-Specific Expression And Natural Selection In Wild Populations, September 2019, working paper or preprint. [ DOI : 10.1101/599076 ]

  • 34D. Lavenier, E. Roux, L. Conde-Canencia, B. Hamoum.

    Advanced Coding Schemes for DNA-Based Data Storage Using Nanopore Sequencing Technologies, November 2019, Journées CominLabs 2019, Poster.

  • 35L. Lecompte, P. Peterlongo, D. Lavenier, C. Lemaitre.

    SVJedi : Structural variation genotyping using long reads, July 2019, HiTSeq 2019 - Conference on High Throughput Sequencing, Poster.

  • 36T. Lemane.

    Search engine for genomic sequencing data, Université Rennes1, July 2019.

  • 37K. Thuillier.

    Linear programming for metabolic network completion, Inria Rennes - Bretagne Atlantique and University of Rennes 1, France, December 2019.

References in notes