A Personalized and Diversified Model for Decentralized Scientific Search and Recommendation, Numev'2013

Multi-Site Diversified Search and Recommendation, Numev'2014


R. Uricaru, C. Michotey, H. Chiapello, E. Rivals,
YOC, a new strategy for pairwise alignment of collinear genomes

R. Blanc-Mathieu, B. Verhelst, E. Derelle, S. Rombauts, G. Piganeau, F-Y. Bouget, I. Carré, A. Chateau, AC Eyre-Walker, N. Grimsley, H. Moreau, B. Piegu, E. Rivals, Y. van de Peer, W. Schackwitz,
An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina read de novo assemblies, BMC Genomics 15:1103 doi:10.1186/1471-2164-15-1103 2014.

E. Drezen, G. Rizk, R. Chikhi, C. Deltel, C. Lemaitre, P. Peterlongo, D. Lavenier,
GATB: Genome Assembly & Analysis Tool Box, Bioinformatics, 2014

L. Noé, D. E. K. Martin,
A coverage criterion for spaced seeds and its applications to support vector machine string kernels and k-mer distances, Journal of Computational Biology, Vol. 21, p. 947-963, 2014.

M. C. Frith, L. Noé,
Improved search heuristics find 20 000 new alignments between human and mouse genomes, Nucleic Acids Research, Vol. 42, p. e59, 2014.

C. Vroland, M. Salson, H. Touzet,
Lossless seeds for searching short patterns with high error rates, International Workshop On Combinatorial Algorithms (IWOCA) to appear in LNCS (2014)

Joly, A., Goëau, H., Glotin, H., Spampinato, C., Bonnet, P., Vellinga, W. P., ... & Müller, H. (2014).
Lifeclef 2014: multimedia life species identification challenges. In Information Access Evaluation. Multilinguality, Multimodality, and Interaction (pp. 229-249). Springer International Publishing.

Joly, A., Müller, H., Goëau, H., Glotin, H., Spampinato, C., Rauber, A., ... & Fisher, B.
LifeCLEF: Multimedia Life Species Identification. In International Workshop on Environmental Multimedia Retrieval, 2014..

Joly, A., Goëau, H., Bonnet, P., Spampinato, C., Glotin, H., Rauber, A., ... & Müller, H. (2014, November).
Are Species Identification Tools Biodiversity-friendly?. In Proceedings of the 3rd ACM International Workshop on Multimedia Analysis for Ecological Data (pp. 31-36). ACM.

Goëau, H., Joly, A., Bonnet, P., Selmi, S., Molino, J. F., Barthélémy, D., & Boujemaa, N. (2014).
Lifeclef plant identification task 2014. In CLEF2014 Working Notes. Working Notes for CLEF 2014 Conference, Sheffield, UK, September 15-18, 2014 (pp. 598-615).

Goëau, H., Glotin, H., Vellinga, W. P., & Rauber, A. (2014).
LifeCLEF bird identification task 2014. CLEF working notes, 2014.

Spampinato, C., Palazzo, S., Boom, B., & Fisher, R. B. (2014).
Overview of the LifeCLEF 2014 Fish Task. CLEF working notes, 2014.

Pierre Bonnet, Alexis Joly, Hervé Goëau, Christel Vignau, Jean-François Molino, Daniel Barthélémy, Nozha Boujemaa (2014).
Plant identification: Man vs. Machine - On beyond LifeCLEF 2014 plant identification challenge. Submitted to Multimedia Tools and Applications.

M Servajean, E Pacitti, M Liroz-Gistau, S Amer-Yahia and A El Abbadi.
"Exploiting Diversification in Gossip-Based Recommendation" in Data Management in Cloud, Grid and P2P Systems (Globe), 12 pages, to appear, in München, Deutschland, 2014.

M Servajean, R Akbarinia, E Pacitti and S Amer-Yahia.
"Profile Diversity for Query Processing using User Recommendations" Information Systems, Elsevier, 44-63, 2015.

M Servajean, E Pacitti, M Liroz Gistau, S Amer-Yahia and A El Abaddi.
"Exploiting Diversification in Distributed Recommendation" in Journée Bases de Données Avancées (BDA), 15 pages, in Grenoble, France, 2014.

M Servajean, E Pacitti, M Liroz-Gistau, A Joly and J Champ.
"PlantRT: Multi-Site Diversified Search and Recommendation for Citizen Sciences" in Journée Bases de Données Avancées (BDA), 5 pages, in Grenoble, France, 2014.

L. Salmela, E. Rivals,
LoRDEC: accurate and efficient long read error correction Bioinformatics, doi:10.1093/bioinformatics/btu538 August 26, 2014.

B. Cazaux, T. Lecroq, E. Rivals,
From Indexing Data Structures to de Bruijn Graphs, Proc. of the 25th Annual Symposium on Combinatorial Pattern Matching (CPM), Lecture Notes in Computer Science (LNCS) Vol. 8486, p. 89–99, 2014.

B. Cazaux, E. Rivals,
Approximation of greedy algorithms for Max-ATSP, Maximal Compression, Maximal Cycle Cover, and Shortest Cyclic Cover of Strings in press Prague Stringology Conference, Stringology: 148-161 2014.

B. Cazaux, E. Rivals,
Reverse Engineering of Compact Suffix Trees and Links: a Novel Algorithm vol. 28, String- Masters 2012 & 2013 Special Issue, p. 9-22 J. Discrete Algorithms, 2014.

J. Buard, E. Rivals, D. Dunoyer de Segonzac, C. Garres, P. Caminade, B. de Massy, P. Boursot,
Diversity of Prdm9 ZnF array in wild mice unravels new facets of the evolutionary turnover of this coding minisatellite, PLOS One DOI: 10.1371/journal.pone.0085021, 2014.

N. Philippe, E. Bou Samara, A. Boureux, F. Ruffl ́ , Q. Bai, A. Mancheron, J. Devos, E. Rivals, T. Commes,
Combining DGE and RNA-Sequencing data to identify new polyA+ non-coding transcripts in the human genome, Nucleic Acids Research, doi 10.1093/nar/gkt1300, 2013.

N. Valimaki, E. Rivals,
Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data, 9th International Symposium on Bioinformatics Research and Applications (ISBRA), Lecture Notes in Bioinformatics (LNBI), Springer Verlag, Z. Cai et al. (Eds.), LNBI 7875, p. 237–248, 2013.

I. Alles,
Times Series Clustering in the field of Agronomy, 2013. Encadré par F. Masseglia et F. Tardieu.

M. Giraud, M. Salson, M. Duez, JS Varré, C. Villenet, S. Quief, A. Caillault, N. Grardel, C. Roumier, C. Preudhomme, M. Figeac.
Suivi de la leucémie résiduelle par séquençage haut-débit. In JOBIM, Toulouse, France, July 2013

N. Philippe, M. Salson, T. Commes, E. Rivals,
CRAC : an integrated approach to the analysis of RNA-seq reads, Genome Biology, 14 :R30, 2013.

E. Rivals,
Building the Assembly De Bruijn Graph from an Implicit Suffix Tree, Workshop on the Storage, Search and Annotation of Multiple Similar Genomes, conférence invitée, Univ. Bielefeld, Bielefeld, Allemagne, 9-10 décembre, 2013.

M. Servajean, E. Pacitti, S. Amr-Yahia, P. Neveu.
Profile diversity in search and recommendation, 4th Int. Workshop on Social Recommender Systems, WWW (Companion Book) 973-980, 2013.

M. Servajean, E. Pacitti, S. Amer-Yahia, P. Neveu.
Profile Diversity for Phenotyping Data Search and Recommendation. Journées de Bases de Données Avancées (BDA) 2013.

M. Servajean, E. Pacitti, M. Liroz, S. Amr-Yahia, A. El Abbadi.
Exploiting Diversification in Gossip based Recommendations (submitted paper), 2013.


CONFERENCES sans actes :

  • E. Kopylova, L. Noé, P. Pericard, M. Salson, H. Touzet,
    SortMeRNA 2: ribosomal RNA classification for taxonomic assignation, Workshop on Recent Computational Advances in Metagenomics, ECCB (2014) and Bioinformatics for Environmental Genomics (BGE) (2014)