Team, Visitors, External Collaborators
Overall Objectives
Research Program
Highlights of the Year
New Software and Platforms
New Results
Partnerships and Cooperations
Dissemination
Bibliography
XML PDF e-pub
PDF e-Pub


Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

[1]
T. Rocher.
Compressing and indexing labeled sequences, Université de Lille, February 2018.
https://tel.archives-ouvertes.fr/tel-01758361
[2]
C. Saad.
Characterization of non-random sequencing errors, application to mosaicism and heterogeneous tumors, Université de Lille Nord de France, September 2018.
https://tel.archives-ouvertes.fr/tel-01936291

Articles in International Peer-Reviewed Journals

[3]
V. 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
[4]
T. 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
[5]
M. 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
[6]
T. 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
[7]
C. 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

[8]
R. 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
[9]
A. 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
[10]
P. 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

[11]
R. 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

[12]
R. Chikhi, A. Schönhuth.
Dualities in Tree Representations, November 2018, https://arxiv.org/abs/1804.04263 - CPM 2018, extended version.
https://hal.archives-ouvertes.fr/hal-01935566