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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, no 4, p. 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, no 1, p. 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: WABI 2012, Ljubljana, Slovenia, September 2012, vol. 7534, p. 236-248. [ DOI : 10.1007/978-3-642-33122-0_19 ]

    http://hal.inria.fr/hal-00753930
  • 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, no 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, p. 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, 329 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, no 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, no 20, p. 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

Doctoral Dissertations and Habilitation Theses

  • 10R. Chikhi.

    Computational methods for de novo assembly of next-generation genome sequencing data, École normale supérieure de Cachan - ENS Cachan, July 2012.

    http://hal.inria.fr/tel-00752033

Articles in International Peer-Reviewed Journals

  • 11J. Jaquiéry, S. Stoeckel, P. Nouhaud, L. Mieuzet, F. Mahéo, F. Legeai, N. Bernard, A. Bonvoisin, R. Vitalis, J. C. Simon.

    Genome scans reveal candidate regions involved in the adaptation to host plant in the pea aphid complex., in: Molecular Ecology, November 2012, vol. 21, no 21, p. 5251-64. [ DOI : 10.1111/mec.12048 ]

    http://hal.inria.fr/hal-00753439
  • 12G. Le Trionnaire, S. Jaubert-Possamai, J. Bonhomme, J.-P. Gauthier, G. Guernec, A. Le Cam, F. Legeai, J. Monfort, D. Tagu.

    Transcriptomic profiling of the reproductive mode switch in the pea aphid in response to natural autumnal photoperiod., in: Journal of Insect Physiology, December 2012, vol. 58, no 12, p. 1517–1524. [ DOI : 10.1016/j.jinsphys.2012.07.009 ]

    http://hal.inria.fr/hal-00753429
  • 13P. Leroy, N. Guilhot, H. Sakai, A. Bernard, F. Choulet, S. Theil, S. Reboux, N. Amano, T. Flutre, C. Pelegrin, H. Ohyanagi, M. Seidel, F. Giacomoni, M. Reichstadt, M. Alaux, E. Gicquello, F. Legeai, L. Cerutti, H. Numa, T. Tanaka, K. Mayer, T. Itoh, H. Quesneville, C. Feuillet.

    TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes., in: Front Plant Sci, 2012, vol. 3, 5 p. [ DOI : 10.3389/fpls.2012.00005 ]

    http://hal.inria.fr/hal-00753407
  • 14A. Mucherino, C. Lavor, L. Jon, J. Lee S., L. Liberti, M. Sviridenko.

    Discretization Orders for Distance Geometry Problems, in: Optimization Letters, 2012, vol. 6, no 4, p. 783-796.

    http://hal.inria.fr/hal-00756941
  • 15A. Mucherino, C. Lavor, L. Liberti, N. Maculan.

    Recent Advances on the Discretizable Molecular Distance Geometry Problem, in: European Journal of Operational Research, 2012, vol. 219, p. 698-706.

    http://hal.inria.fr/hal-00756942
  • 16A. Mucherino, C. Lavor, L. Liberti, N. Maculan.

    The Discretizable Molecular Distance Geometry Problem, in: Computational Optimization and Applications, 2012, vol. 52, p. 115-146.

    http://hal.inria.fr/hal-00756940
  • 17A. Mucherino, C. Lavor, L. Liberti.

    Exploiting Symmetry Properties of the Discretizable Molecular Distance Geometry Problem, in: Journal of Bioinformatics and Computational Biology, 2012, vol. 10, no 3, 1242009(1-15).

    http://hal.inria.fr/hal-00756939
  • 18A. Mucherino, C. Lavor, L. Liberti.

    The Discretizable Distance Geometry Problem, in: Optimization Letters, 2012, vol. 6, no 8, p. 1671-1686.

    http://hal.inria.fr/hal-00756943
  • 19M. Ollivier, T. Gabaldón, J. Poulain, F. Gavory, N. Leterme, J.-P. Gauthier, F. Legeai, D. Tagu, J. C. Simon, C. Rispe.

    Comparison of gene repertoires and patterns of evolutionary rates in eight aphid species that differ by reproductive mode., in: Genome Biol Evol, 2012, vol. 4, no 2, p. 155-67. [ DOI : 10.1093/gbe/evr140 ]

    http://hal.inria.fr/hal-00753402
  • 20P. 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
  • 21G. 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
  • 22I. Wohlers, R. Andonov, G. W. Klau.

    Optimal DALI protein structure alignment, in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, November 2012, 20 p.

    http://hal.inria.fr/hal-00685824
  • 23I. Wohlers, N. Malod-Dognin, R. Andonov, G. W. Klau.

    CSA: Comprehensive comparison of pairwise protein structure alignments, in: Nucleic Acids Research, 2012, p. 303-309, Preprint, submitted to Nucleic Acids Research.

    http://hal.inria.fr/hal-00667920

International Conferences with Proceedings

  • 24R. Chikhi, G. Rizk.

    Space-efficient and exact de Bruijn graph representation based on a Bloom filter, in: WABI 2012, Ljubljana, Slovenia, September 2012, vol. 7534, p. 236-248. [ DOI : 10.1007/978-3-642-33122-0_19 ]

    http://hal.inria.fr/hal-00753930
  • 25N. Maillet, C. Lemaitre, R. Chikhi, D. Lavenier, P. Peterlongo.

    Compareads: comparing huge metagenomic experiments, in: RECOMB Comparative Genomics 2012, Niterói, Brazil, October 2012.

    http://hal.inria.fr/hal-00720951
  • 26A. Mucherino, C. Lavor, L. Liberti, N. Maculan.

    Finding Low-Energy Homopolymer Conformations by a Discrete Approach, in: Global Optimization Workshop 2012 (GOW12), Natal, Brazil, 2012.

    http://hal.inria.fr/hal-00756946
  • 27A. Mucherino, C. Lavor, L. Liberti, N. Maculan.

    On the Discretization of Distance Geometry Problems, in: Mathematics of Distances and Applications 2012 (MDA12), Varna, Bulgaria, 2012.

    http://hal.inria.fr/hal-00756945
  • 28A. Mucherino, C. Virginia, C. Luiz Mariano, C. Lavor, N. Maculan.

    On Suitable Orders for Discretizing Molecular Distance Geometry Problems related to Protein Side Chains, in: IEEE Conference Proceedings, Federated Conference on Computer Science and Information Systems (FedCSIS12), Workshop on Computational Optimization (WCO12), Warsaw, Poland, 2012.

    http://hal.inria.fr/hal-00756944
  • 29A. Mucherino, G. Warley, C. Lavor, N. Maculan.

    A Parallel BP Algorithm for the Discretizable Distance Geometry Problem, in: Workshop on Parallel Computing and Optimization (PCO12), 26th IEEE International Parallel & Distributed Processing Symposium (IPDPS12), Shanghai, China, 2012.

    http://hal.inria.fr/hal-00756947

National Conferences with Proceeding

  • 30M. Le Boudic-Jamin, A. Mucherino, R. Andonov.

    Modeling protein flexibility by distance geometry, in: ROADEF 2012, Angers, France, Université d'Angers, 2012.

    http://hal.inria.fr/hal-00757717

Conferences without Proceedings

  • 31G. Holley, P. Peterlongo.

    BlastGraph: intensive approximate pattern matching in string graphs and de-Bruijn graphs, in: PSC 2012, Prague, Czech Republic, August 2012.

    http://hal.inria.fr/hal-00711911