Bibliography

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, n^o 1. [ DOI : 10.1186/s12859-015-0709-7 ]
  
  https://hal.inria.fr/hal-01214682
• 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 ]
  
  https://hal.inria.fr/hal-01397150
• 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, n^o 1, 22 p. [ DOI : 10.1186/1748-7188-8-22 ]
  
  http://hal.inria.fr/hal-00868805
• 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 ]
  
  https://hal.archives-ouvertes.fr/hal-01088571
• 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 ]
  
  https://hal.inria.fr/hal-01666830
• 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, n^o 1. [ DOI : 10.1186/s40168-018-0562-9 ]
  
  https://hal.archives-ouvertes.fr/hal-01926402
• 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.
  
  https://hal.inria.fr/hal-01566246
• 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.
  
  https://tel.archives-ouvertes.fr/tel-01939193
• 9G. Rizk, A. Gouin, R. Chikhi, C. Lemaitre.
  
  MindTheGap: integrated detection and assembly of short and long insertions, in: Bioinformatics, December 2014, vol. 30, n^o 24, pp. 3451-3457. [ DOI : 10.1093/bioinformatics/btu545 ]
  
  https://hal.inria.fr/hal-01081089
• 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 ]
  
  https://hal.inria.fr/hal-01083715

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 ]
  
  https://hal.archives-ouvertes.fr/hal-02151798
• 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 ]
  
  https://hal.inria.fr/hal-02308101
• 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 ]
  
  https://hal.inria.fr/hal-02378266
• 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, n^o 3, pp. 434-447. [ DOI : 10.1111/tpj.14228 ]
  
  https://hal-univ-rennes1.archives-ouvertes.fr/hal-02019346
• 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, n^o 1, 56 p. [ DOI : 10.1186/s12864-019-5431-9 ]
  
  https://hal.inria.fr/hal-01987197
• 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 ]
  
  https://hal.inria.fr/hal-02407243
• 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, n^o 1. [ DOI : 10.1093/nargab/lqz015 ]
  
  https://hal.inria.fr/hal-02371117
• 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 ]
  
  https://hal.archives-ouvertes.fr/hal-02059774
• 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 ]
  
  https://hal.inria.fr/hal-02018724

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.
  
  https://hal.inria.fr/hal-02187246
• 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, n^o 15, pp. 274-289. [ DOI : 10.1007/978-3-030-21462-3_18 ]
  
  https://hal.inria.fr/hal-02399578

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.
  
  https://hal.inria.fr/hal-02308257
• 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.
  
  https://hal.inria.fr/hal-02288091

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.
  
  https://hal.inria.fr/hal-02289484
• 25C. Marchet, M. Kerbiriou, A. Limasset.
  
  Indexing De Bruijn graphs with minimizers, in: Recomb seq, Whashinton, United States, April 2019. [ DOI : 10.1101/546309 ]
  
  https://hal.archives-ouvertes.fr/hal-02435086
• 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.
  
  https://hal.archives-ouvertes.fr/hal-02435116
• 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 ]
  
  https://hal.archives-ouvertes.fr/hal-02190793

Other Publications

• 28A. Badual.
  
  Stockage d'information sur ADN, Université Rennes 1, June 2019.
  
  https://hal.inria.fr/hal-02401641
• 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.
  
  https://hal.archives-ouvertes.fr/hal-02400744
• 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.
  
  https://hal.inria.fr/hal-02284559
• 31V. Epain.
  
  De novo long reads assembly using integer linear programing, Université de Rennes 1 [UR1], September 2019.
  
  https://hal.inria.fr/hal-02413832
• 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.
  
  https://hal.inria.fr/hal-01634232
• 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 ]
  
  https://hal.inria.fr/hal-02275928
• 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.
  
  https://hal.archives-ouvertes.fr/hal-02400656
• 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.
  
  https://hal.inria.fr/hal-02290884
• 36T. Lemane.
  
  Search engine for genomic sequencing data, Université Rennes1, July 2019.
  
  https://hal.inria.fr/hal-02410102
• 37K. Thuillier.
  
  Linear programming for metabolic network completion, Inria Rennes - Bretagne Atlantique and University of Rennes 1, France, December 2019.
  
  https://hal.inria.fr/hal-02408003

References in notes

• 38R. S. Harris, P. Medvedev.
  
  Improved representation of sequence bloom trees, in: Bioinformatics, 08 2019, btz662.
  
  https://doi.org/10.1093/bioinformatics/btz662