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  • The Inria's Research Teams produce an annual Activity Report presenting their activities and their results of the year. These reports include the team members, the scientific program, the software developed by the team and the new results of the year. The report also describes the grants, contracts and the activities of dissemination and teaching. Finally, the report gives the list of publications of the year.

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Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

Articles in International Peer-Reviewed Journals

  • 3V. G. Crawford, A. Kuhnle, C. Boucher, R. Chikhi, T. Gagie.

    Practical dynamic de Bruijn graphs, in: Bioinformatics, June 2018. [ DOI : 10.1093/bioinformatics/bty500 ]

    https://hal.archives-ouvertes.fr/hal-01935559
  • 4T. 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. De 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. De Ridder, J. De 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, 2018, vol. 19, no 1, pp. 118-135. [ DOI : 10.1093/bib/bbw089 ]

    https://hal.inria.fr/hal-01390478
  • 5M. Pupin, A. Flissi, P. Jacques, V. Leclère.

    Bioinformatics tools for the discovery of new lipopeptides with biocontrol applications, in: European Journal of Plant Pathology, July 2018. [ DOI : 10.1007/s10658-018-1544-2 ]

    https://hal.archives-ouvertes.fr/hal-01937890
  • 6T. Rocher, M. Giraud, M. Salson.

    Indexing labeled sequences, in: PeerJ Computer Science, 2018, vol. 4, pp. 1-14. [ DOI : 10.7717/peerj-cs.148 ]

    https://hal.archives-ouvertes.fr/hal-01743104
  • 7C. Saad, L. Noé, H. Richard, J. Leclerc, M.-P. Buisine, H. Touzet, M. Figeac.

    DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data, in: BMC Bioinformatics, December 2018, vol. 19, no 1. [ DOI : 10.1186/s12859-018-2215-1 ]

    https://hal.inria.fr/hal-01881466

Conferences without Proceedings

  • 8R. Chikhi, V. Jovičić, S. Kratsch, P. Medvedev, M. Milanic, S. Raskhodnikova, N. Varma.

    Bipartite Graphs of Small Readability, in: COCOON 2018 - The 24th International Computing and Combinatorics Conference, Qingdao, China, July 2018, https://arxiv.org/abs/1805.04765.

    https://hal.archives-ouvertes.fr/hal-01935562
  • 9A. Kuosmanen, T. Paavilainen, T. Gagie, R. Chikhi, A. I. Tomescu, V. Makinen.

    Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-Linear Chaining Extended, in: RECOMB 2018 - 22nd Annual International Conference on Research in Computational Molecular Biology, Paris, France, April 2018, https://arxiv.org/abs/1705.08754.

    https://hal.archives-ouvertes.fr/hal-01935568
  • 10P. Marquet, M. Pupin, Y. Secq.

    L codent, L créent: créations numériques artistiques pour démystifier l'informatique... au féminin! (descriptif d’atelier), in: Didapro 7 – DidaSTIC. De 0 à 1 ou l’heure de l’informatique à l’école, Lausanne, Switzerland, February 2018, pp. 1-2.

    https://hal.archives-ouvertes.fr/hal-01753402

Scientific Popularization

  • 11R. David, L. Mabile, M. Yahia, A. Cambon-Thomsen, A.-S. Archambeau, L. Bezuidenhout, S. Bekaert, G. Bertier, E. Bravo, J. Carpenter, A. Cohen-Nabeiro, A. Delavaud, M. De Rosa, L. Dollé, F. Grattarola, F. Murphy, S. Pamerlon, A. Specht, A.-M. Tassé, M. Thomsen, M. Zilioli.

    Operationalizing and evaluating the FAIRness concept for a good quality of data sharing in Research: the RDA-SHARC-IG (SHAring Rewards and Credit Interest Group), November 2018, assemblée MaDICS 2018, Poster. [ DOI : 10.5281/zenodo.1745374 ]

    https://hal.archives-ouvertes.fr/hal-01929834

Other Publications