EN FR
EN FR


previous Previous | up Home


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
  • 2R. 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
  • 3E. 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
  • 4N. 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
  • 5N. 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
  • 6A. 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
  • 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
  • 8P. Peterlongo, R. Chikhi.

    Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer, in: BMC Bioinformatics, March 2012, vol. 13, no 48. [ DOI : 10.1186/1471-2105-13-48 ]

    http://hal.inria.fr/hal-00675974
  • 9G. 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
  • 10G. 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
  • 11G. 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

Doctoral Dissertations and Habilitation Theses

  • 12M. Le Boudic-Jamin.

    Global and Local Similarities and Divergences of Protein Structures , Universite Rennes 1, December 2015.

    https://hal.inria.fr/tel-01250540
  • 13F. Moreews.

    Design and share data analysis workflows. Application to bioinformatics intensivetreatments, université de rennes 1, December 2015.

    https://hal.inria.fr/tel-01233191

Articles in International Peer-Reviewed Journals

  • 14N. Abbas, S. Derrien, S. Rajopadhye, P. Quinton, A. Cornu, D. Lavenier.

    Combining execution pipelines to improve parallel implementation of HMMER on FPGA, in: Microprocessors and Microsystems, October 2015, vol. 39, pp. 457-470. [ DOI : 10.1016/j.micpro.2015.06.006 ]

    https://hal.inria.fr/hal-01235328
  • 15R. Andonov, H. Djidjev, G. Klau, M. Boudic-Jamin, I. Wohlers.

    Automatic Classification of Protein Structure Using the Maximum Contact Map Overlap Metric, in: Algorithms and Combinatorics, December 2015, vol. 8, no 4. [ DOI : 10.3390/a8040850 ]

    https://hal.inria.fr/hal-01248543
  • 16G. Benoit, C. Lemaitre, D. Lavenier, E. Drezen, T. Dayris, R. Uricaru, G. Rizk.

    Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph, in: BMC Bioinformatics, September 2015, vol. 16, no 1. [ DOI : 10.1186/s12859-015-0709-7 ]

    https://hal.inria.fr/hal-01214682
  • 17A. Cassioli, B. Bardiaux, G. Bouvier, A. Mucherino, R. Alves, L. Liberti, M. Nilges, C. Lavor, T. E. Malliavin.

    An algorithm to enumerate all possible protein conformations verifying a set of distance constraints, in: BMC Bioinformatics, January 2015, vol. 16, no 1, 23 p.

    https://hal.inria.fr/hal-01199667
  • 18G. Chapuis, M. Le Boudic-Jamin, R. Andonov, H. Djidjev, D. Lavenier.

    Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection, in: Scientific Programming, April 2015, vol. 2015. [ DOI : 10.1155/2015/279715 ]

    https://hal.inria.fr/hal-01235331
  • 19P. DUMAS, F. Legeai, C. Lemaitre, E. Scaon, M. ORSUCCI, K. Labadie, S. Gimenez, A. L. Clamens, H. Henri, F. Vavre, J.-M. Aury, P. Fournier, G. Kergoat, E. D'Alençon.

    Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species?, in: Genetica, 2015, vol. 143, no 3, pp. 305-316. [ DOI : 10.1007/s10709-015-9829-2 ]

    https://hal.archives-ouvertes.fr/hal-01208780
  • 20H. Djidjev, G. Chapuis, R. Andonov, S. Thulasidasan, D. Lavenier.

    All-Pairs Shortest Path Algorithms for Planar Graph for GPU-Accelerated Clusters, in: Journal of Parallel and Distributed Computing, November 2015, vol. 85, pp. 91-103. [ DOI : 10.1016/j.jpdc.2015.06.008 ]

    https://hal.inria.fr/hal-01235348
  • 21N. Glaser, A. Gallot, F. Legeai, M. Harry, L. Kaiser, B. Le Ru, P.-A. Calatayud, E. Jacquin-Joly.

    Differential expression of the chemosensory transcriptome in two populations of the stemborer Sesamia nonagrioides, in: Insect Biochemistry and Molecular Biology, September 2015, vol. 65, pp. 28-34.

    https://hal.inria.fr/hal-01240447
  • 22A. 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, May 2015, vol. 114, pp. 494-501. [ DOI : 10.1038/hdy.2014.85 ]

    https://hal.inria.fr/hal-01081094
  • 23F. Legeai, T. Derrien.

    Identification of long non-coding RNAs in insects genomes, in: Current Opinion in Insect Science, February 2015, vol. 7, pp. 37 - 44. [ DOI : 10.1016/j.cois.2015.01.003 ]

    https://hal.inria.fr/hal-01240461
  • 24V. Loux, M. Mariadassou, S. Almeida, H. Chiapello, A. Hammani, J. Buratti, A. Gendrault, V. Barbe, J.-M. Aury, S.-M. Deutsch, S. Parayre, M.-N. Madec, V. Chuat, G. Jan, P. Peterlongo, V. Azevedo, Y. Le Loir, H. Falentin.

    Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii, in: BMC Genomics, December 2015, vol. 16, no 1, 35 p. [ DOI : 10.1186/s12864-015-1467-7 ]

    https://hal.inria.fr/hal-01142363
  • 25F. Moreews, O. Sallou, H. Ménager, Y. Le Bras, C. MONJEAUD, C. Blanchet, O. Collin.

    BioShaDock: a community driven bioinformatics shared Docker-based tools registry, in: F1000Research, December 2015. [ DOI : 10.12688/f1000research.7536.1 ]

    https://hal.inria.fr/hal-01243520

International Conferences with Proceedings

  • 26E. Joly, E. Poivet, A. Gallot, F. Legeai, N. Montagné.

    The chemosensory transcriptome of the cotton leafworm Spodoptera littoralis, in: 24. Annual Meeting of the European-Chemoreception-Research-Organization (ECRO), NA, France, Chemical Senses, Oxford University Press, 2015, vol. 40, no 3.

    https://hal.archives-ouvertes.fr/hal-01208791
  • 27A. Mucherino.

    A Pseudo de Bruijn Graph Representation for Discretization Orders for Distance Geometry, in: Proceedings of IWBBIO15, Granada, Spain, F. Ortuno, I. Rojas (editors), Lectures Notes in Computer Science, May 2015, vol. 9043, pp. 514–523.

    https://hal.inria.fr/hal-01196707
  • 28N. Prajapati, W. Ranasinghe, V. K. Tandrapati, R. Andonov, H. Djidjev, S. Rajopadhye.

    Energy Modeling and Optimization for Tiled Nested-Loop Codes , in: Parallel and Distributed Processing Symposium Workshop (IPDPSW), Hyderabad , India, Parallel and Distributed Processing Symposium Workshop (IPDPSW), 2015 IEEE International, May 2015, pp. 888 - 895. [ DOI : 10.1109/IPDPSW.2015.94 ]

    https://hal.inria.fr/hal-01250602

National Conferences with Proceedings

  • 29M. Le Boudic-Jamin, R. Andonov.

    De novo detection of structure repeats in Proteins, in: Journées Ouvertes de Biologie, Informatique et Mathématiques JOBIM, Clermont-Ferrand, France, Société Française de BioInformatique (SFBI), July 2015.

    https://hal.inria.fr/hal-01250541

Conferences without Proceedings

  • 30C. Bettembourg, O. Dameron, A. Bretaudeau, F. Legeai.

    AskOmics : Intégration et interrogation de réseaux de régulation génomique et post-génomique, in: IN OVIVE (INtégration de sources/masses de données hétérogènes et Ontologies, dans le domaine des sciences du VIVant et de l’Environnement), Rennes, France, June 2015, 7 p.

    https://hal.inria.fr/hal-01184903
  • 31F. Moreews, O. Sallou, Y. Le Bras, G. Marie, C. MONJEAUD, T. A. Darde, O. Collin, C. Blanchet.

    A curated Domain centric shared Docker registry linked to the Galaxy toolshed, in: Galaxy Community Conference 2015, Norwich, United Kingdom, July 2015.

    https://hal.inria.fr/hal-01160514
  • 32A. Mucherino.

    Discretization Orders and Distance Geometry, in: 16ème conférence ROADEF :, Marseille, France, Proceedings of ROADEF2015, February 2015.

    https://hal.inria.fr/hal-01196717
  • 33A. Mucherino.

    Optimal Discretization Orders for Distance Geometry: a Theoretical Standpoint, in: LSSC2015 - Proceedings of Large Scale Scientific Computations, Sozopol, Bulgaria, Lecture Notes in Computer Science, June 2015.

    https://hal.inria.fr/hal-01196701
  • 34I. Petrov, S. Brillet, E. Drezen, S. Quiniou, L. Antin, P. Durand, D. Lavenier.

    KLAST: fast and sensitive software to compare large genomic databanks on cloud, in: World Congress in Computer Science, Computer Engineering, and Applied Computing, Las Vegas, United States, July 2015.

    https://hal.inria.fr/hal-01235339

Scientific Books (or Scientific Book chapters)

  • 35Distance Geometry and Applications, December 2015, vol. 197.

    https://hal.inria.fr/hal-01202376
  • 36D. S. Gonçalves, J. Nicolas, A. Mucherino, C. Lavor.

    Finding Optimal Discretization Orders for Molecular Distance Geometry by Answer Set Programming, in: Studies in Computational Intelligence, S. Fidanova (editor), Recent Advances in Computational Optimization, Springer, July 2015, vol. 610, pp. 1-15.

    https://hal.inria.fr/hal-01196714
  • 37J. Nicolas, P. Peterlongo, S. Tempel.

    Finding and Characterizing Repeats in Plant Genomes, in: Plant Bioinformatics: Methods and Protocols, D. Edwards (editor), Methods in Molecular Biology, Humana Press - Springer Science+Business Media, November 2015, no 1374, 365 p. [ DOI : 10.1007/978-1-4939-3167-5_17 ]

    https://hal.inria.fr/hal-01228488

Scientific Popularization

Other Publications

  • 39G. Benoit, P. Peterlongo, D. Lavenier, C. Lemaitre.

    Simka: fast kmer-based method for estimating the similarity between numerous metagenomic datasets, July 2015, JOBIM 2015, Poster. [ DOI : 10.1093/Bioinforma-cs/btu406 ]

    https://hal.inria.fr/hal-01180603
  • 40A. Bodrug.

    Test and Benchmarking of A New Scaffolding Methodology, University of Rennes 1, July 2015.

    https://hal.inria.fr/hal-01251303
  • 41A. Gouin, A. Bretaudeau, E. D'Alençon, C. Lemaitre, F. Legeai.

    Improvement of the assembly of heterozygous genomes of non-model organisms, October 2015, Genome Informatics, Poster.

    https://hal.inria.fr/hal-01231793
  • 42A. Gouin, A. Bretaudeau, K. Labadie, J.-M. Aury, E. D'Alençon, C. Lemaitre, F. Legeai.

    Improvement of the assembly of heterozygous genomes of non-model organisms, a case study of the genomes of two Spodoptera frugiperda host strains, June 2015, Arthropod Genomics 2015, Poster.

    https://hal.inria.fr/hal-01240443
  • 43A. Limasset, P. Peterlongo.

    BGREAT: A De Bruijn graph read mapping tool, July 2015, JOBIM 2015, Poster.

    https://hal.inria.fr/hal-01192857
  • 44C. Riou, C. Lemaitre, P. Peterlongo.

    VCF_creator: Mapping and VCF Creation features in DiscoSnp++, July 2015, JOBIM 2015, Poster.

    https://hal.inria.fr/hal-01176492


previous Previous | up Home