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Bibliography

Major publications by the team in recent years
  • 1R. Andonov, N. Malod-Dognin, N. Yanev.

    Maximum Contact Map Overlap Revisited, in: Journal of Computational Biology, January 2011, vol. 18, no 1, pp. 1-15. [ DOI : 10.1089/cmb.2009.0196 ]

    http://hal.inria.fr/inria-00536624/en
  • 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, no 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
  • 5N. Maillet, C. Lemaitre, R. Chikhi, D. Lavenier, P. Peterlongo.

    Compareads: comparing huge metagenomic experiments, in: RECOMB Comparative Genomics 2012, Niterói, Brazil, October 2012.

    https://hal.inria.fr/hal-00720951
  • 6N. Malod-Dognin, R. Andonov, N. Yanev.

    Maximum Cliques in Protein Structure Comparison, in: SEA 2010 9th International Symposium on Experimental Algorithms, Naples, Italy, P. Festa (editor), Springer, May 2010, vol. 6049, pp. 106-117. [ DOI : 10.1007/978-3-642-13193-6_10 ]

    https://hal.inria.fr/inria-00536700
  • 7V. H. Nguyen, D. Lavenier.

    PLAST: parallel local alignment search tool for database comparison, in: Bmc Bioinformatics, October 2009, vol. 10, 24 p.

    http://hal.inria.fr/inria-00425301
  • 8G. 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 ]

    https://hal.inria.fr/hal-01081089
  • 9G. Rizk, D. Lavenier.

    GASSST: Global Alignment Short Sequence Search Tool, in: Bioinformatics, August 2010, vol. 26, no 20, pp. 2534-2540.

    http://hal.archives-ouvertes.fr/hal-00531499
  • 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

Doctoral Dissertations and Habilitation Theses

Articles in International Peer-Reviewed Journals

  • 14D. Eoche-Bosy, M. Gautier, M. Esquibet, F. Legeai, A. Bretaudeau, O. Bouchez, S. Fournet, E. Grenier, J. Montarry.

    Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida, in: Molecular Ecology, July 2017, vol. 26, no 18, pp. 4700–4711. [ DOI : 10.1111/mec.14240 ]

    https://hal.inria.fr/hal-01605681
  • 15A. Gouin, A. Bretaudeau, K. Nam, S. Gimenez, J.-M. Aury, B. Duvic, F. Hilliou, N. Durand, N. Montagné, I. Darboux, S. Kuwar, T. Chertemps, D. Siaussat, A. Bretschneider, Y. Moné, S.-J. Ahn, S. Hänniger, A.-S. Gosselin Grenet, D. Neunemann, F. Maumus, I. Luyten, K. Labadie, W. Xu, F. Koutroumpa, J.-M. Escoubas, A. Llopis, M. Maïbèche-Coisne, F. Salasc, A. Tomar, A. R. Anderson, S. A. Khan, P. DUMAS, M. ORSUCCI, J. Guy, C. Belser, A. Alberti, B. Noel, A. Couloux, J. Mercier, S. Nidelet, E. Dubois, N.-Y. Liu, I. Boulogne, O. Mirabeau, G. Le Goff, K. Gordon, J. Oakeshott, F. L. Consoli, A.-N. Volkoff, H. W. Fescemyer, J. H. Marden, D. S. Luthe, S. Herrero, D. G. Heckel, P. Wincker, G. J. Kergoat, J. Amselem, H. Quesneville, A. T. Groot, E. Jacquin-Joly, N. Nègre, C. Lemaitre, F. Legeai, E. D’Alençon, P. Fournier.

    Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges, in: Scientific Reports, December 2017, vol. 7, no 1, pp. 1-12. [ DOI : 10.1038/s41598-017-10461-4 ]

    https://hal.inria.fr/hal-01633879
  • 16L. Lima, B. Sinaimeri, G. Sacomoto, H. Lopez-Maestre, C. Marchet, V. Miele, M.-F. Sagot, V. Lacroix.

    Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads, in: Algorithms for Molecular Biology, December 2017, vol. 12, no 1, 2 p. [ DOI : 10.1186/s13015-017-0091-2 ]

    https://hal.inria.fr/hal-01474524
  • 17T. C. Mathers, Y. Chen, G. Kaithakottil, F. Legeai, S. T. Mugford, P. Baa-Puyoulet, A. Bretaudeau, B. Clavijo, S. Colella, O. Collin, T. Dalmay, T. Derrien, H. Feng, T. Gabaldon, A. Jordan, I. Julca, G. J. Kettles, K. Kowitwanich, D. Lavenier, P. Lenzi, S. Lopez-Gomollon, D. Loska, D. Mapleson, F. Maumus, S. Moxon, D. R. G. Price, A. Sugio, M. v. Munster, M. Uzest, D. Waite, G. Jander, D. Tagu, A. C. C. Wilson, C. van Oosterhout, D. Swarbreck, S. A. Hogenhout.

    Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species, in: Genome Biology, 2017, vol. 18, no 1, 27 p. [ DOI : 10.1186/s13059-016-1145-3 ]

    https://hal-univ-rennes1.archives-ouvertes.fr/hal-01500475
  • 18G. Richard, F. Legeai, N. Prunier-Leterme, A. Bretaudeau, D. Tagu, J. Jaquiéry, G. Le Trionnaire.

    Dosage compensation and sex-specific epigenetic landscape of the X chromosome in the pea aphid, in: Epigenetics & Chromatin, June 2017, vol. 10, no 1, 30 p. [ DOI : 10.1186/s13072-017-0137-1 ]

    https://hal.inria.fr/hal-01555242
  • 19A. Rochefort, S. Boukthir, S. Moullec, A. Meygret, Y. Adnani, D. Lavenier, A. Faili, S. Kayal.

    Full Sequencing and Genomic Analysis of Three emm75 Group A Streptococcus Strains Recovered in the Course of an Epidemiological Shift in French Brittany, in: Genome Announcements, 2017, vol. 5, no 39, e00957 p. [ DOI : 10.1128/genomeA.00957-17 ]

    https://hal-univ-rennes1.archives-ouvertes.fr/hal-01617890
  • 20A. Sczyrba, P. Hofmann, P. Belmann, D. Koslicki, S. Janssen, J. Dröge, I. Gregor, S. Majda, J. Fiedler, E. Dahms, A. Bremges, A. Fritz, R. Garrido-Oter, T. S. Jørgensen, N. Shapiro, P. D. Blood, A. Gurevich, Y. Bai, D. Turaev, M. Z. DeMaere, R. Chikhi, N. Nagarajan, C. Quince, L. H. Hansen, S. J. Sørensen, B. K. H. Chia, B. Denis, J. L. Froula, Z. Wang, R. Egan, D. Don Kang, J. J. Cook, C. Deltel, M. Beckstette, C. Lemaitre, P. Peterlongo, G. Rizk, D. Lavenier, Y.-W. Wu, S. W. Singer, C. Jain, M. Strous, H. Klingenberg, P. Meinicke, M. D. Barton, T. Lingner, H.-H. Lin, Y.-C. Liao, G. G. Z. Silva, D. A. Cuevas, R. A. Edwards, S. Saha, V. C. Piro, B. Y. Renard, M. Pop, H.-P. Klenk, M. Göker, N. C. Kyrpides, T. Woyke, J. A. Vorholt, P. Schulze-Lefert, E. M. Rubin, A. E. Darling, T. Rattei, A. C. McHardy.

    Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software, in: Nature Methods, October 2017, vol. 14, no 11, pp. 1063 - 1071. [ DOI : 10.1038/nmeth.4458 ]

    https://hal.archives-ouvertes.fr/hal-01633525
  • 21S. C. Varma, P. Kolin, M. Balakrishnan, D. Lavenier.

    Hardware acceleration of de novo genome assembly, in: International Journal of Embedded Systems, February 2017, vol. 9, no 1, pp. 74-89. [ DOI : 10.1504/IJES.2017.10002593 ]

    https://hal.inria.fr/hal-01481800
  • 22J. A. Wenger, B. J. Cassone, F. Legeai, J. S. Johnston, R. Bansal, A. D. Yates, B. S. Coates, V. A. C. Pavinato, A. Michel.

    Whole genome sequence of the soybean aphid, Aphis glycines, in: Insect Biochemistry and Molecular Biology, January 2017, vol. 18, no 1, 27 p. [ DOI : 10.1016/j.ibmb.2017.01.005 ]

    https://hal.inria.fr/hal-01555244
  • 23V. Wucher, F. Legeai, B. Hedan, G. Rizk, L. Lagoutte, T. Leeb, V. Jagannathan, E. Cadieu, A. David, H. Lohi, S. Cirera, M. Fredholm, N. Botherel, P. A. J. Leegwater, C. Le Beguec, H. Fieten, J. Johnson, J. Alföldi, C. André, K. Lindblad-Toh, C. Hitte, T. Derrien.

    FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome, in: Nucleic Acids Research, 2017, vol. 45, no 8, 12 p. [ DOI : 10.1093/nar/gkw1306 ]

    https://hal-univ-rennes1.archives-ouvertes.fr/hal-01532061

Invited Conferences

  • 24V. Wucher, F. Legeai, L. Bourneuf, T. Derrien, A. Gallot, S. Hudaverdian, S. Jaubert-Possamai, N. Leterme-Prunier, J. Nicolas, H. Seitz, A. Siegel, S. TANGUY, G. Le Trionnaire, D. Tagu.

    Integrative genomics and gene networks for studying phenotypic plasticity in the pea aphid, in: 10th Arthropod Genomics Symposium, Notre Dame, United States, June 2017.

    https://hal.inria.fr/hal-01566438

International Conferences with Proceedings

  • 25S. Francois, 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.

    https://hal.inria.fr/hal-01666830
  • 26S. François, R. Andonov, D. Lavenier, H. Djidjev.

    Global Optimization for Scaffolding and Completing Genome Assemblies, in: International Network Optimization Conference, Lisboa, Portugal, European Network Optimization Group (ENOG), February 2017, 15 p.

    https://hal.inria.fr/hal-01499859
  • 27A. 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://arxiv.org/abs/1702.03154.

    https://hal.inria.fr/hal-01566246

Conferences without Proceedings

  • 28X. Garnier, A. Bretaudeau, O. Filangi, F. Legeai, A. Siegel, O. Dameron.

    AskOmics, a web tool to integrate and query biological data using semantic web technologies, in: JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Lille, France, July 2017, 1 p.

    https://hal.inria.fr/hal-01577425
  • 29X. Garnier, O. Dameron, O. Filangi, F. Legeai, A. Bretaudeau.

    Integration of Linked Data into Galaxy using Askomics , in: Galaxy Community Conference, Montpellier, France, June 2017.

    https://hal.inria.fr/hal-01576870
  • 30C. Guyomar, F. Legeai, C. Mougel, C. Lemaitre, J.-C. Simon.

    Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches, in: International Conference on Holobionts, Paris, France, April 2017.

    https://hal.archives-ouvertes.fr/hal-01638839
  • 31A. Meng, E. Corre, P. Peterlongo, C. Marchet, A. Alberti, C. d. Silva, P. Wincker, I. Probert, N. Suzuki, S. Le Crom, L. Bittner, F. Not.

    A transcriptomic approach to study marine plankton holobionts, in: International Conference on Holobionts, Paris, France, April 2017.

    https://hal.inria.fr/hal-01575069
  • 32H.-S. Pham, J.-H. Ferrasse, O. Boutin, N. Alpy, M. Saez.

    Analyse thermodynamique du cycle de conversion utilisant le CO2 Supercritique pour une application en réacteur modulaire, in: SFGP 2017, Nancy, France, July 2017.

    https://hal.archives-ouvertes.fr/hal-01679087

Scientific Books (or Scientific Book chapters)

  • 33G. BENOIT, C. Lemaitre, G. Rizk, E. Drezen, D. Lavenier.

    De Novo NGS Data Compression, in: Algorithms for Next-Generation Sequencing Data, M. Elloumi (editor), Springer, 2017, pp. 91-115. [ DOI : 10.1007/978-3-319-59826-0_4 ]

    https://hal.archives-ouvertes.fr/hal-01633718

Internal Reports

  • 34L. Bouri, D. Lavenier.

    Evaluation of long read error correction software, Inria Rennes - Bretagne Atlantique ; GenScale, February 2017, no RR-9028.

    https://hal.inria.fr/hal-01463694
  • 35L. Bouri, D. Lavenier, J.-F. J.-F. Gibrat, V. F. Dominguez Del Angel.

    Evaluation of genome assembly software based on long reads, France Genomique, March 2017. [ DOI : 10.5281/zenodo.345098 ]

    https://hal.inria.fr/hal-01481801

Other Publications

  • 36G. BENOIT, P. Peterlongo, M. Mariadassou, E. Drezen, S. Schbath, D. Lavenier, C. Lemaitre.

    Simka: large scale de novo comparative metagenomics, July 2017, 234 p, JOBIM 2017 - Journées Ouvertes Biologie Informatique Mathématiques, Poster - Acte onlineReference paper: Benoit et al. (2016) Multiple comparative metagenomics using multiset k-mer counting. PeerJComputer Science. https://doi.org/10.7717/peerj-cs.94.

    https://hal.archives-ouvertes.fr/hal-01595071
  • 37C. Benoit-Pilven, C. Marchet, E. Chautard, L. Lima, M.-P. Lambert, G. Sacomoto, A. Rey, C. Bourgeois, D. Auboeuf, V. Lacroix.

    Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data, November 2017, working paper or preprint. [ DOI : 10.1101/074807 ]

    https://hal.archives-ouvertes.fr/hal-01643169
  • 38C. Diot, F. Herault, J. Navarro, L. Le Calvez, E. Baeza, C. Klopp, O. Bouchez, D. Esquerre, P. Peterlongo.

    Genome specific expression in the liver of mule and hinny duck hybrids, June 2017, 1 p, 10. European Symposium on Poultry Genetics (ESPG), Poster.

    https://hal.archives-ouvertes.fr/hal-01594559
  • 39J. 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, November 2017, working paper or preprint.

    https://hal.inria.fr/hal-01634232
  • 40C. Guyomar, F. Legeai, C. Mougel, C. Lemaitre, J.-C. Simon.

    Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches, July 2017, JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Poster.

    https://hal.archives-ouvertes.fr/hal-01638884
  • 41A. Limasset, J.-F. Flot, P. Peterlongo.

    Toward perfect reads, November 2017, https://arxiv.org/abs/1711.03336 - RECOMB 2018 Submission.

    https://hal.inria.fr/hal-01644163
  • 42C. Marchet, L. Lecompte, C. Da Silva, C. Cruaud, J.-M. Aury, J. Nicolas, P. Peterlongo.

    De novo Clustering of Gene Expressed Variants in Transcriptomic Long Reads Data Sets, November 2017, working paper or preprint. [ DOI : 10.1101/170035 ]

    https://hal.archives-ouvertes.fr/hal-01643156
  • 43C. Marchet, L. Lecompte, A. Limasset, L. Bittner, P. Peterlongo.

    A resource-frugal probabilistic dictionary and applications in bioinformatics, November 2017, https://arxiv.org/abs/1703.00667 - Submitted to Journal of Discrete Algorithms. arXiv admin note: substantial text overlap with arXiv:1605.08319.

    https://hal.archives-ouvertes.fr/hal-01643162
  • 44A. Meng, C. Marchet, E. Corre, P. Peterlongo, A. Alberti, C. Da Silva, P. Wincker, E. Pelletier, I. Probert, J. Decelle, S. Le Crom, F. Not, L. Bittner.

    A de novo approach to disentangle partner identity and function in holobiont systems, November 2017, working paper or preprint. [ DOI : 10.1101/221424 ]

    https://hal.archives-ouvertes.fr/hal-01643153
References in notes
  • 45J. T. Simpson, K. Wong, S. D. Jackman, J. E. Schein, S. J. M. Jones, I. Birol.

    ABySS: a parallel assembler for short read sequence data, in: Genome Res, Jun 2009, vol. 19, no 6, pp. 1117–1123.


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