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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

  • 11P. Peterlongo.

    Lire les lectures : analyse de données de séquençage, Université rennes1, January 2016, Habilitation à diriger des recherches.

    https://hal.inria.fr/tel-01278275

Articles in International Peer-Reviewed Journals

  • 12G. 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
  • 13G. Boutet, S. Alves Carvalho, M. Falque, P. Peterlongo, E. Lhuillier, O. Bouchez, C. Lavaud, M.-L. Pilet-Nayel, N. Rivière, A. Baranger.

    SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population, in: BMC Genomics, December 2016, vol. 17, no 1, 121 p. [ DOI : 10.1186/s12864-016-2447-2 ]

    https://hal.inria.fr/hal-01275696
  • 14R. Chikhi, A. Limasset, P. Medvedev.

    Compacting de Bruijn graphs from sequencing data quickly and in low memory, in: Bioinformatics, November 2016, vol. 32, no 12, i201 - i208. [ DOI : 10.1093/bioinformatics/btw279 ]

    https://hal.archives-ouvertes.fr/hal-01395704
  • 15I. Eyres, J. Jaquiéry, A. Sugio, L. Duvaux, K. Gharbi, J.-J. Zhou, F. Legeai, M. Nelson, J.-C. Simon, C. M. Smadja, R. Butlin, J. Ferrari.

    Differential gene expression according to race and host plant in the pea aphid, in: Molecular Ecology, 2016, vol. 25, no 17, pp. 4197-4215. [ DOI : 10.1111/mec.13771 ]

    https://hal-univ-rennes1.archives-ouvertes.fr/hal-01371828
  • 16Y. Le Bras, O. Collin, C. MONJEAUD, V. Lacroix, E. Rivals, C. Lemaitre, V. Miele, G. Sacomoto, C. Marchet, B. Cazaux, A. Zine El Aabidine, L. Salmela, S. Alves-Carvalho, A. Andrieux, R. Uricaru, P. Peterlongo.

    Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads, in: GigaScience, February 2016, vol. 5, no 1. [ DOI : 10.1186/s13742-015-0105-2 ]

    https://hal.inria.fr/hal-01280238
  • 17A. Limasset, B. Cazaux, E. Rivals, P. Peterlongo.

    Read mapping on de Bruijn graphs, in: BMC Bioinformatics, December 2016, vol. 17, no 1. [ DOI : 10.1186/s12859-016-1103-9 ]

    https://hal.inria.fr/hal-01349636
  • 18H. Lopez-Maestre, L. Brinza, C. Marchet, J. Kielbassa, S. Bastien, M. Boutigny, D. Monnin, A. El Filali, C. M. Carareto, C. Vieira, F. Picard, N. Kremer, F. Vavre, M.-F. Sagot, V. Lacroix.

    SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence, in: Nucleic Acids Research, 2016. [ DOI : 10.1093/nar/gkw655 ]

    https://hal.inria.fr/hal-01352586
  • 19T. Marschall, M. Marz, T. Abeel, L. Dijkstra, B. E. Dutilh, A. Ghaffaari, P. Kersey, W. P. Kloosterman, V. Makinen, A. M. Novak, B. Paten, D. Porubsky, E. Rivals, C. Alkan, J. A. Baaijens, P. I. W. D. Bakker, V. Boeva, R. J. P. Bonnal, F. Chiaromonte, R. Chikhi, F. D. Ciccarelli, R. Cijvat, E. Datema, C. M. V. Duijn, E. E. Eichler, C. Ernst, E. Eskin, E. Garrison, M. El-Kebir, G. W. Klau, J. O. Korbel, E.-W. Lameijer, B. Langmead, M. Martin, P. Medvedev, J. C. Mu, P. Neerincx, K. Ouwens, P. Peterlongo, N. Pisanti, S. Rahmann, B. Raphael, K. Reinert, D. d. Ridder, J. d. Ridder, M. Schlesner, O. Schulz-Trieglaff, A. D. Sanders, S. Sheikhizadeh, C. Shneider, S. Smit, D. Valenzuela, J. Wang, L. Wessels, Y. Zhang, V. Guryev, F. Vandin, K. Ye, A. Schönhuth.

    Computational pan-genomics: status, promises and challenges, in: Briefings in Bioinformatics, October 2016. [ DOI : 10.1093/bib/bbw089 ]

    https://hal.inria.fr/hal-01390478
  • 20A. Meygret, V. Pascal, S. Moullec, J. Nacazume, Y. Adnani, D. Lavenier, S. Kayal, A. Faili.

    Genome sequence of the uncommon Streptococcus pyogenes M/emm66 strain STAB13021, isolated from clonal clustered cases in French Brittany, in: Genome Announcements, July 2016, vol. 4, no 4, 16 p, e00689. [ DOI : 10.1128/genomeA.00689-16 ]

    https://hal.inria.fr/hal-01385659
  • 21C. Rispe, F. Legeai, D. Papura, A. Bretaudeau, S. Hudaverdian, G. Le Trionnaire, D. Tagu, J. Jaquiéry, F. Delmotte.

    De novo transcriptome assembly of the grapevine phylloxera allows identification of genes differentially expressed between leaf- and root-feeding forms, in: BMC Genomics, December 2016, vol. 17, no 1, 219 p. [ DOI : 10.1186/s12864-016-2530-8 ]

    https://hal.inria.fr/hal-01286528

International Conferences with Proceedings

  • 22S. Fidanova, O. Roeva, A. Mucherino, K. Kapanova.

    InterCriteria Analysis of Ant Algorithm with Environment Change for GPS Surveying Problem, in: 17th International Conference on Artificial Intelligence: Methodology , Systems, Applications (AIMSA16), Varna, Bulgaria, C. Dichev, G. Agre (editors), Lecture Notes in Artificial Intelligence, Springer, September 2016, vol. 9883, pp. 271–278. [ DOI : 10.1007/978-3-319-44748-3_26 ]

    https://hal.inria.fr/hal-01402412
  • 23W. Gramacho, A. Mucherino, J.-H. Lin, C. Lavor.

    A New Approach to the Discretization of Multidimensional Scaling, in: IEEE Conference Proceedings of FedCSIS16, Gandz, Poland, September 2016.

    https://hal.inria.fr/hal-01402390
  • 24C. Marchet, A. Limasset, L. Bittner, P. Peterlongo.

    A resource-frugal probabilistic dictionary and applications in (meta)genomics, in: Prageu Stringology Conference, Prague, Czech Republic, August 2016.

    https://hal.inria.fr/hal-01386744

Conferences without Proceedings

  • 25S. François, R. Andonov, H. Djidjev, D. Lavenier.

    Global Optimization Methods for Genome Scaffolding, in: 12th International Workshop on Constraint-Based Methods for Bioinformatics, Toulouse, France, September 2016.

    https://hal.inria.fr/hal-01385665
  • 26D. Lavenier, J.-F. Roy, D. Furodet.

    DNA Mapping using Processor-in-Memory Architecture, in: Workshop on Accelerator-Enabled Algorithms and Applications in Bioinformatics, Shenzhen, China, December 2016.

    https://hal.archives-ouvertes.fr/hal-01399997
  • 27F. Legeai, C. Bettembourg, A. Bretaudeau, Y. Chaussin, O. Dameron, D. Tagu.

    BIPAA/Askomics, a new and easy approach for querying genomics and epigenomics elements in interaction, in: XXVth International Congress of Entomology 2016, Orlando, Florida, United States, September 2016.

    https://hal.inria.fr/hal-01391080
  • 28H.-S. Pham, D. Lavenier, A. Termier.

    Identifying Genetic Variant Combinations using Skypatterns, in: 7th International Workshop on Biological Knowledge Discovery and Data Mining (Workshop BIOKDD '16 ), Porto, Portugal, DEXA, September 2016. [ DOI : 10.1109/DEXA.2016.13 ]

    https://hal.inria.fr/hal-01385614

Scientific Books (or Scientific Book chapters)

  • 29J. A. Brisson, J. Jaquiéry, F. Legeai, G. L. Trionnaire, D. Tagu.

    Genomics of Phenotypic plastity in Aphids, in: Management of Insect Pests to Agriculture, H. Czosnek, M. Ghanim (editors), Springer International Publishing, 2016, pp. 65-96. [ DOI : 10.1007/978-3-319-24049-7_3 ]

    https://hal-univ-rennes1.archives-ouvertes.fr/hal-01314988
  • 30G. Chapuis, H. Djidjev, D. Lavenier, R. Andonov.

    GPU-accelerated shortest paths computations for planar graphs, in: Advances in GPU Research and Practice, H. Azad (editor), Elsevier, September 2016, 774 p.

    https://hal.inria.fr/hal-01385634
  • 31A. Mucherino, S. Fidanova, M. Ganzha.

    Introducing the Environment in Ant Colony Optimization, in: Studies in Computational Intelligence, Recent Advances in Computational Optimization, Springer, July 2016, vol. 655, pp. 147–158.

    https://hal.inria.fr/hal-01402423

Internal Reports

Other Publications

  • 35G. Benoit, P. Peterlongo, M. Mariadassou, E. Drezen, S. Schbath, D. Lavenier, C. Lemaitre.

    Multiple Comparative Metagenomics using Multiset k-mer Counting, April 2016, working paper or preprint.

    https://hal.inria.fr/hal-01300485
  • 36A. Evrard, C. Bettembourg, M. M. Jubault, O. Dameron, O. Filangi, A. Bretaudeau, F. F. Legeai.

    Integration and query of biological datasets with Semantic Web technologies: AskOmics, June 2016, Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM 2016), Poster.

    https://hal.inria.fr/hal-01391087
  • 37A. Limasset, C. Marchet, P. Peterlongo, L. Bittner.

    Minimal perfect hash functions in large scale bioinformatics Problem, June 2016, JOBIM 2016, Poster.

    https://hal.archives-ouvertes.fr/hal-01341718
  • 38C. Marchet, A. Limasset, L. Bittner, P. Peterlongo.

    A resource-frugal probabilistic dictionary and applications in (meta)genomics, May 2016, working paper or preprint.

    https://hal.inria.fr/hal-01322440
  • 39F. Moreews, D. Lavenier.

    Seamless Coarse Grained Parallelism Integration in Intensive Bioinformatics Workflows, May 2016, working paper or preprint. [ DOI : 10.1145/2488551.2488588 ]

    https://hal.inria.fr/hal-00908842


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