Bibliography

Major publications by the team in recent years

• 1R. Andonov, S. Balev, N. Yanev.
  Protein Threading: From Mathematical Models to Parallel Implementations, in: INFORMS Journal on Computing, 2004, vol. 16, n^o 4, pp. 393-405. [ DOI : 10.1287/ijoc.1040.0092 ]
  http://joc.journal.informs.org/content/16/4/393.abstract
• 2R. Andonov, N. Malod-Dognin, N. Yanev.
  Maximum Contact Map Overlap Revisited, in: Journal of Computational Biology, January 2011, vol. 18, n^o 1, pp. 1-15. [ DOI : 10.1089/cmb.2009.0196 ]
  http://hal.inria.fr/inria-00536624/en
• 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, n^o 1, 22 p. [ DOI : 10.1186/1748-7188-8-22 ]
  http://hal.inria.fr/hal-00868805
• 4F. Legeai, G. Rizk, T. Walsh, O. Edwards, K. Gordon, D. Lavenier, N. Leterme, A. Mereau, J. Nicolas, D. Tagu, S. Jaubert-Possamai.
  Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum, in: BMC Genomics, 2010, vol. 11, n^o 1, 281 p. [ DOI : 10.1186/1471-2164-11-281 ]
  http://www.hal.inserm.fr/inserm-00482283
• 5A. Mucherino, C. Lavor, L. Liberti, N. Maculan.
  The Discretizable Molecular Distance Geometry Problem, in: Computational Optimization and Applications, 2012, vol. 52, pp. 115-146.
  http://hal.inria.fr/hal-00756940
• 6V. 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
• 7P. Peterlongo, R. Chikhi.
  Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer, in: BMC Bioinformatics, March 2012, vol. 13, n^o 48. [ DOI : 10.1186/1471-2105-13-48 ]
  http://hal.inria.fr/hal-00675974
• 8G. Rizk, D. Lavenier.
  GASSST: Global Alignment Short Sequence Search Tool, in: Bioinformatics, August 2010, vol. 26, n^o 20, pp. 2534-2540.
  http://hal.archives-ouvertes.fr/hal-00531499
• 9G. A. T. Sacomoto, J. Kielbassa, R. Chikhi, R. Uricaru, P. Antoniou, M.-F. Sagot, P. Peterlongo, V. Lacroix.
  KisSplice: de-novo calling alternative splicing events from RNA-seq data, in: BMC Bioinformatics, March 2012.
  http://hal.inria.fr/hal-00681995

Publications of the year

Articles in International Peer-Reviewed Journals

• 10V. Costa, A. Mucherino, C. Lavor, A. Cassioli, L. M. Carvalho, N. Maculan.
  Discretization Orders for Protein Side Chains, in: Journal of Global Optimization, January 2014, vol. 60, n^o 2, pp. 333–349.
  https://hal.inria.fr/hal-01093052
• 11E. 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
• 12H. Falentin, D. Naquin, V. Loux, F. Barloy-Hubler, P. Loubière, S. Nouaille, D. Lavenier, P. Le Bourgeois, P. François, J. Schrenzel, D. Hernandez, S. Even, Y. Le Loir.
  Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis LD61, in: Genome Announcements, 2014, vol. 2, n^o 1, 1 p. [ DOI : 10.1128/genomeA.01176-13 ]
  https://hal.archives-ouvertes.fr/hal-01019560
• 13D. Gonçalves, A. Mucherino.
  Discretization Orders and Efficient Computation of Cartesian Coordinates for Distance Geometry, in: Optimization Letters, February 2014, vol. 8, n^o 7, pp. 2111–2125.
  https://hal.inria.fr/hal-01093049
• 14A. Gouin, F. Legeai, P. Nouhaud, A. Whibley, J.-C. Simon, C. Lemaitre.
  Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads, in: Heredity, October 2014, 8 p. [ DOI : 10.1038/hdy.2014.85 ]
  https://hal.inria.fr/hal-01081094
• 15J. Jaquiéry, S. Stoeckel, C. Larose, P. Nouhaud, C. Rispe, L. Mieuzet, J. Bonhomme, F. Mahéo, F. Legeai, J.-P. Gauthier, N. Prunier-Leterme, D. Tagu, J.-C. Simon.
  Genetic Control of Contagious Asexuality in the Pea Aphid, in: PLoS Genetics, 2014, vol. 10, n^o 12, e1004838. [ DOI : 10.1371/journal.pgen.1004838 ]
  https://hal-univ-rennes1.archives-ouvertes.fr/hal-01093572
• 16F. Legeai, S. Gimenez, B. Duvic, J.-M. Escoubas, A.-S. Gosselin Grenet, F. Blanc, F. Cousserans, I. Séninet, A. Bretaudeau, D. Mutuel, P.-A. Girard, C. Monsempes, G. Magdelenat, F. Hilliou, R. Feyereisen, M. Ogliastro, A.-N. Volkoff, E. Jacquin-Joly, E. D'Alençon, N. Nègre, P. Fournier.
  Establishment and analysis of a reference transcriptome for Spodoptera frugiperda, in: BMC Genomics, 2014, vol. 15, n^o 1, 704 p. [ DOI : 10.1186/1471-2164-15-704 ]
  https://hal.inria.fr/hal-01058982
• 17L. Liberti, C. Lavor, N. Maculan, A. Mucherino.
  Euclidean Distance Geometry and Applications, in: SIAM Review, February 2014, vol. 56, n^o 1, pp. 3–69.
  https://hal.inria.fr/hal-01093056
• 18L. Liberti, B. Masson, J. Lee, C. Lavor, A. Mucherino.
  On the Number of Realizations of Certain Henneberg Graphs arising in Protein Conformation, in: Discrete Applied Mathematics, March 2014, vol. 165, pp. 213–232.
  https://hal.inria.fr/hal-01093060
• 19G. Rizk, A. Gouin, R. Chikhi, C. Lemaitre.
  MindTheGap: integrated detection and assembly of short and long insertions, in: Bioinformatics, December 2014, vol. 30, n^o 24, pp. 3451 - 3457. [ DOI : 10.1093/bioinformatics/btu545 ]
  https://hal.inria.fr/hal-01081089
• 20R. 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

International Conferences with Proceedings

• 21E. Drezen, D. Lavenier.
  Quality metrics for benchmarking sequences comparison tools, in: BSB - 9th Brazilian Symposium on Bioinformatics, Belo Honrizonte, Brazil, S. Campos (editor), Advances in Bioinformatics and Computational Biology Lecture Notes in Computer Science, Springer, October 2014, vol. 8826, pp. 144-153.
  https://hal.archives-ouvertes.fr/hal-01088595
• 22D. Gonçalves, A. Mucherino, C. Lavor.
  An Adaptive Branching Scheme for the Branch & Prune Algorithm applied to Distance Geometry, in: Federated Conference on Computer Science and Information Systems (FedCSIS14), Workshop on Computational Optimization (WCO14), Warsaw, Poland, September 2014, pp. 463-469.
  https://hal.inria.fr/hal-01093063
• 23F. Legeai, T. Derrien, V. Wucher, D. Audrey, G. Le Trionnaire, D. Tagu.
  Long non-­‐coding RNA in the pea aphid; identification and comparative expression in sexual and asexual embryos, in: Arthropod Genomics Symposium, Urbana, United States, June 2014.
  https://hal.inria.fr/hal-01091304
• 24C. Lemaitre, L. Ciortuz, P. Peterlongo.
  Mapping-free and assembly-free discovery of inversion breakpoints from raw NGS reads, in: Algorithms for Computational Biology, Tarragona, Spain, A.-H. Dediu, C. Martín-Vide, B. Truthe (editors), July 2014, vol. 8542, pp. 119-130. [ DOI : 10.1007/978-3-319-07953-0_10 ]
  https://hal.inria.fr/hal-01063157
• 25N. Maillet, G. Collet, T. Vannier, D. Lavenier, P. Peterlongo.
  COMMET: comparing and combining multiple metagenomic datasets, in: IEEE BIBM 2014, Belfast, United Kingdom, November 2014.
  https://hal.inria.fr/hal-01080050
• 26I. Wohlers, M. Le Boudic-Jamin, H. Djidjev, G. W. Klau, R. Andonov.
  Exact Protein Structure Classification Using the Maximum Contact Map Overlap Metric, in: AlCoB - 1st International Conference on Algorithms for Computational Biology, Tarragona, Spain, July 2014, pp. 262 - 273. [ DOI : 10.1007/978-3-319-07953-0_21 ]
  https://hal.inria.fr/hal-01093803

Conferences without Proceedings

• 27G. Chapuis, H. Djidjev, R. Andonov, S. Thulasidasan, D. Lavenier.
  Efficient Multi-GPU Algorithm for All-Pairs Shortest Paths, in: IPDPS 2014, Phoenix, United States, Manish Parashar, May 2014.
  https://hal.inria.fr/hal-00905738
• 28F. Moreews, Y. Le Bras, O. Dameron, C. Monjeaud, O. Collin.
  Integrating GALAXY workflows in a metadata management environment, in: Galaxy Community Conference, Baltimore, United States, July 2014.
  https://hal.inria.fr/hal-01093058

Scientific Books (or Scientific Book chapters)

• 29J. Seo, J.-K. Kim, J. Ryu, C. Lavor, A. Mucherino, D.-S. Kim.
  BetaMDGP: Protein Structure Determination Algorithm Based on the Beta-complex, in: Transactions on Computational Science XXII, M. Gavrilova, C. Tan (editors), Springer, February 2014, vol. Lecture Notes in Computer Science, n^o 8360, pp. 130–155.
  https://hal.inria.fr/hal-01093066

Internal Reports

• 30I. Wohlers, M. Le Boudic-Jamin, H. Djidjev, G. W. Klau, R. Andonov.
  Exact Protein Structure Classification Using the Maximum Contact Map Overlap Metric, Inria Rennes - Bretagne Atlantique and University of Rennes 1, France ; Genome Informatics, University of Duisburg-Essen, Germany ; Life Sciences, CWI, Science Park 123, 1098 XG Amsterdam, The Netherlands ; Los Alamos National Laboratory, Los Alamos, NM, USA, 2014, pp. 262 - 273. [ DOI : 10.1007/978-3-319-07953-0_21 ]
  https://hal.inria.fr/hal-01093776

Other Publications

• 31S. Alves Carvalho, R. Uricaru, J. Duarte, C. Lemaitre, N. Rivière, G. Boutet, A. Baranger, P. Peterlongo.
  Reference-free high-throughput SNP detection in pea: an example of discoSnp usage for a non-model complex genome, September 2014, ECCB 2014.
  https://hal.inria.fr/hal-01091184
• 32G. Benoit, D. Lavenier, C. Lemaitre, G. Rizk.
  Bloocoo, a memory efficient read corrector, September 2014, European Conference on Computational Biology (ECCB).
  https://hal.inria.fr/hal-01092960
• 33G. Chapuis, M. Le Boudic-Jamin, R. Andonov, H. Djidjev, D. Lavenier.
  Parallel seed-based approach to multiple protein structure similarities detection *, December 2014.
  https://hal.inria.fr/hal-01093809
• 34E. Drezen, P. Durand, D. Lavenier.
  KLAST: a new high-­performance sequence similarity search tool, April 2014, Bio-IT World Conference.
  https://hal.archives-ouvertes.fr/hal-01088629
• 35E. Drezen, G. Rizk, R. Chikhi, C. Deltel, C. Lemaitre, P. Peterlongo, D. Lavenier.
  GATB: a software toolbox for genome assembly and analysis, April 2014, Bio-IT World Conference.
  https://hal.archives-ouvertes.fr/hal-01088641
• 36E. Drezen, G. Rizk, R. Chikhi, C. Deltel, C. Lemaitre, P. Peterlongo, D. Lavenier.
  GATB: Toolbox for developing efficient NGS software, October 2014, BSB - 9th Brazilian Symposium on Bioinformatics.
  https://hal.archives-ouvertes.fr/hal-01088828
• 37D. Gonçalves, A. Mucherino.
  Challenges for Extending Discretizable Molecular Distance Geometry to Interval Data, October 2014, Proceedings of Many Faces of Distances (MFD14).
  https://hal.inria.fr/hal-01093071
• 38D. Gonçalves, J. Nicolas, A. Mucherino.
  Searching for Optimal Orders for Discretized Distance Geometry, October 2014, Proceedings of Many Faces of Distances (MDF14).
  https://hal.inria.fr/hal-01093072
• 39A. Gouin, A. Bretaudeau, C. Lemaitre, F. Legeai.
  Identification and correction of genome mis-assemblies due to heterozygosity, September 2014, European Conference on Computational Biology (ECCB).
  https://hal.inria.fr/hal-01092959
• 40G. Rizk, A. Gouin, R. Chikhi, C. Lemaitre.
  MindTheGap: integrated detection and assembly of short and long insertions, September 2014, European Conference on Computational Biology (ECCB).
  https://hal.inria.fr/hal-01087832