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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, 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, no 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, no 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, 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, 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, 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, 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

Doctoral Dissertations and Habilitation Theses

  • 10G. Chapuis.

    Exploiter les capacités parallèles des architectures modernes en bioinformatique applications à la génétique, la comparaison de structures et l'analyse de larges graphes, École normale supérieure de Cachan - ENS Cachan, December 2013.

    http://hal.inria.fr/tel-00912553
  • 11N. Maillet.

    Comparaison de novo de données de séquençage issues de très grands échantillons métagénomiques : application sur le projet Tara Oceans, Université Rennes 1, December 2013.

    http://hal.inria.fr/tel-00941922

Articles in International Peer-Reviewed Journals

  • 12K. R. Bradnam, J. N. Fass, A. Alexandrov, P. Baranay, M. Bechner, I. Birol, S. Boisvert, J. Chapman, G. Chapuis, R. Chikhi, H. Chitsaz, W.-C. Chou, J. Corbeil, C. Del Fabbro, T. Roderick Docking, R. Durbin, D. Earl, S. Emrich, P. Fedotov, N. Fonseca, G. Ganapathy, R. Gibbs, S. Gnerre, É. Godzaridis, S. Goldstein, M. Haimel, G. Hall, D. Haussler, J. Hiatt, I. Ho, J. Howard, M. Hunt, S. Jackman, D. Jaffe, E. Jarvis, H. Jiang, S. Kazakov, P. Kersey, J. Kitzman, J. Knight, S. Koren, T.-W. Lam, D. Lavenier, F. Laviolette, Y. Li, Z. Li, B. Liu, Y. Liu, R. Luo, I. Maccallum, M. Macmanes, N. Maillet, S. Melnikov, D. Naquin, Z. Ning, T. Otto, B. Paten, O. Paulo, A. Phillippy, F. Pina-Martins, M. Place, D. Przybylski, X. Qin, C. Qu, F. Ribeiro, S. Richards, D. Rokhsar, G. Ruby, S. Scalabrin, M. Schatz, D. Schwartz, A. Sergushichev, T. Sharpe, T. Shaw, J. Shendure, Y. Shi, J. Simpson, H. Song, F. Tsarev, F. Vezzi, R. Vicedomini, B. Vieira, J. Wang, K. Worley, S. Yin, S.-M. Yiu, J. Yuan, G. Zhang, H. Zhang, S. Zhou, I. Korf1.

    Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species, in: GigaScience, July 2013, vol. 2, no 10. [ DOI : 10.1186/2047-217X-2-10 ]

    http://hal.inria.fr/hal-00908747
  • 13G. Chapuis, O. Filangi, D. Lavenier, J. M. Elsen, P. Leroy.

    Graphics Processing Unit-Accelerated Quantitative Trait Loci Detection, in: Journal of Computational Biology, September 2013, vol. 20, no 9, pp. 672-686. [ DOI : 10.1089/cmb.2012.0136 ]

    http://hal.inria.fr/hal-00903794
  • 14R. 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
  • 15E. Dordet-Frisoni, E. Baranowski, A. Barré, A. Blanchard, M. Breton, C. Couture, V. Dupuy, P. Gaurivaud, D. Jacob, C. Lemaitre, L. Manso-Silván, M. Nikolski, L.-X. Nouvel, F. Poumarat, P. Sirand-Pugnet, P. Thébault, S. Theil, F. Thiaucourt, C. Citti, F. Tardy.

    Draft Genome Sequences of Mycoplasma auris and Mycoplasma yeatsii, Two Species of the Ear Canal of Caprinae, in: Genome Announcements, 2013, vol. 1, no 3. [ DOI : 10.1128/genomeA.00280-13 ]

    http://hal.inria.fr/hal-00907449
  • 16V. Dupuy, P. Sirand-Pugnet, E. Baranowski, A. Barré, M. Breton, C. Couture, E. Dordet-Frisoni, P. Gaurivaud, D. Jacob, C. Lemaitre, L. Manso-Silván, M. Nikolski, L.-X. Nouvel, F. Poumarat, F. Tardy, P. Thébault, S. Theil, C. Citti, A. Blanchard, F. Thiaucourt.

    Complete Genome Sequence of Mycoplasma putrefaciens Strain 9231, One of the Agents of Contagious Agalactia in Goats, in: Genome Announcements, 2013, vol. 1, no 3. [ DOI : 10.1128/genomeA.00354-13 ]

    http://hal.inria.fr/hal-00907450
  • 17M. Federico, P. Peterlongo, N. Pisanti, M.-F. Sagot.

    Rime: Repeat identification, in: Discrete Applied Mathematics, March 2013. [ DOI : 10.1016/j.dam.2013.02.016 ]

    http://hal.inria.fr/hal-00802023
  • 18N. Glaser, A. Gallot, F. Legeai, N. Montagné, E. Poivet, M. Harry, P.-A. Calatayud, E. Jacquin-Joly.

    Candidate chemosensory genes in the Stemborer Sesamia nonagrioides, in: Int J Biol Sci, 2013, vol. 9, no 5, pp. 481-95. [ DOI : 10.7150/ijbs.6109 ]

    http://hal.inria.fr/hal-00916961
  • 19J. Jaquiéry, C. Rispe, D. Roze, F. Legeai, G. Le Trionnaire, S. Stoeckel, L. Mieuzet, C. Da Silva, J. Poulain, N. Prunier-Leterme, B. Ségurens, D. Tagu, J.-C. Simon.

    Masculinization of the x chromosome in the pea aphid, in: PLoS Genetics, August 2013, vol. 9, no 8. [ DOI : 10.1371/journal.pgen.1003690 ]

    http://hal.inria.fr/hal-00916967
  • 20C. Lavor, L. Liberti, A. Mucherino.

    The interval Branch & Prune Algorithm for the Discretizable Molecular Distance Geometry Problem with Inexact Distances, in: Journal of Global Optimization, 2013, vol. 56, no 3, pp. 855-871.

    http://hal.inria.fr/hal-00912660
  • 21L. Manso-Silván, F. Tardy, E. Baranowski, A. Barré, A. Blanchard, M. Breton, C. Couture, C. Citti, E. Dordet-Frisoni, V. Dupuy, P. Gaurivaud, D. Jacob, C. Lemaitre, M. Nikolski, L.-X. Nouvel, F. Poumarat, P. Thébault, S. Theil, F. Thiaucourt, P. Sirand-Pugnet.

    Draft Genome Sequences of Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma bovigenitalium, Three Species with Equivocal Pathogenic Status for Cattle, in: Genome Announcements, 2013, vol. 1, no 3. [ DOI : 10.1128/genomeA.00348-13 ]

    http://hal.inria.fr/hal-00907454
  • 22E. Poivet, A. Gallot, N. Montagné, N. Glaser, F. Legeai, E. Jacquin-Joly.

    A comparison of the olfactory gene repertoires of adults and larvae in the noctuid moth Spodoptera littoralis, in: PLoS ONE, 2013, vol. 8, no 4. [ DOI : 10.1371/journal.pone.0060263 ]

    http://hal.inria.fr/hal-00916952
  • 23E. Quillery, O. Quenez, P. Peterlongo, O. Plantard.

    Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of Single Nucleotide Polymorphisms, in: Molecular Ecology Ressources, October 2013, epub ahead of print. [ DOI : 10.1111/1755-0998.12179 ]

    http://hal.inria.fr/hal-00880072
  • 24G. Rizk, D. Lavenier, R. Chikhi.

    DSK: k-mer counting with very low memory usage, in: Bioinformatics, January 2013, vol. 29, no 5, pp. 652-653, Bioinformatics journal requires that we post only the pre-print, which does not include modifications suggested by the reviewers. [ DOI : 10.1093/bioinformatics/btt020 ]

    http://hal.inria.fr/hal-00778473

International Conferences with Proceedings

  • 25R. Alves, A. Cassioli, A. Mucherino, C. Lavor, L. Liberti.

    Adaptive Branching in iBP with Clifford Algebra, in: Distance Geometry and Applications (DGA13), Manaus, Amazonas, Brazil, 2013, pp. 65-69.

    http://hal.inria.fr/hal-00912698
  • 26G. Chapuis, M. Le Boudic-Jamin, R. Andonov, H. Djidjev, D. Lavenier.

    Parallel seed-based approach to protein structure similarity detection, in: PPAM 2013, Varsovie, Poland, R. Wyrzykowski (editor), Springer, May 2013.

    http://hal.inria.fr/hal-00881507
  • 27V. Costa, A. Mucherino, L. Carvalho, N. Maculan.

    On the Discretization of iDMDGP instances regarding Protein Side Chains with Rings, in: Distance Geometry and Applications (DGA13), Manaus, Amazonas, Brazil, 2013, pp. 99-102.

    http://hal.inria.fr/hal-00912702
  • 28D. Gonçalves, A. Mucherino, C. Lavor.

    Energy-based Pruning Devices for the BP algorithm for Distance Geometry, in: Workshop on Computational Optimization, Krakow, Poland, IEEE, 2013, pp. 335-340.

    http://hal.inria.fr/hal-00912670
  • 29W. Gramacho, D. Gonçalves, A. Mucherino, N. Maculan.

    A new Algorithm to Finding Discretizable Orderings for Distance Geometry, in: Distance Geometry and Applications (DGA13), Manaus, Amazonas, Brazil, 2013, pp. 149-152.

    http://hal.inria.fr/hal-00912706
  • 30F. Moreews, D. Lavenier.

    Seamless Coarse Grained Parallelism Integration in Intensive Bioinformatics Workflows, in: Proceedings of the 20th European MPI Users' Group Meeting, New York, NY, United States, EuroMPI '13, ACM, 2013, pp. 277–282. [ DOI : 10.1145/2488551.2488588 ]

    http://hal.inria.fr/hal-00908842
  • 31A. Mucherino.

    On the Identification of Discretization Orders for Distance Geometry with Intervals, in: Geometric Science of Information (GSI13), Paris, France, Springer, 2013, pp. 231-238.

    http://hal.inria.fr/hal-00912677
  • 32S. C. Varma, P. Kolin, M. Balakrishnan, D. Lavenier.

    FAssem : FPGA based Acceleration of De Novo Genome Assembly, in: Proceeding of The 21st Annual International IEEE Symposium on Field Programmable Custom Computing Machines, Seattle, United States, April 2013, FCCM'2013.

    http://hal.inria.fr/hal-00829055

National Conferences with Proceedings

  • 33A. Bretaudeau, O. Dameron, F. Legeai, Y. Rahbé.

    AphidAtlas : avancées récentes, in: Proceedings of BAPOA 2013 MOP. INRA, CIRAD, Montpellier, France, M. Uzest (editor), 2013, [In French].

    http://hal.inria.fr/hal-00913155
  • 34A. Gouin, P. Nouhaud, F. Legeai, G. Rizk, J.-C. Simon, C. Lemaitre.

    Whole genome re-sequencing : lessons from unmapped reads, in: Journées Ouvertes Biologie Informatique Mathématiques, Toulouse, France, July 2013.

    http://hal.inria.fr/hal-00907446

Conferences without Proceedings

  • 35G. 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.

    http://hal.inria.fr/hal-00905738

Scientific Books (or Scientific Book chapters)

  • 36L. Liberti, C. Lavor, A. Mucherino.

    The Discretizable Molecular Distance Geometry Problem seems Easier on Proteins, in: Distance Geometry: Theory, Methods and Applications, A. Mucherino, C. Lavor, L. Liberti, N. Maculan (editors), Springer, 2013, pp. 47-60.

    http://hal.inria.fr/hal-00912689
  • 37T. E. Malliavin, A. Mucherino, M. Nilges.

    Distance Geometry in Structural Biology, in: Distance Geometry: Theory, Methods and Applications, A. Mucherino, C. Lavor, L. Liberti, N. Maculan (editors), Springer, 2013, pp. 329-350.

    http://hal.inria.fr/hal-00912683
  • 38A. Mucherino, C. Lavor, L. Liberti, N. Maculan.

    Distance Geometry: Theory, Methods and Applications, Springer, 2013, 410 p.

    http://hal.inria.fr/hal-00912679
  • 39A. Mucherino, L. Liberti.

    A VNS-based Heuristic for Feature Selection in Data Mining, in: Hybrid Metaheuristics, E.-G. Talbi (editor), Springer, 2013, pp. 353-368.

    http://hal.inria.fr/hal-00912692

Internal Reports

  • 40M. C. De Cola, A. Mucherino, G. Felice, L. Liberti.

    A Branch-and-Prune Algorithm for the Sensor Network Localization Problem, 2013.

    http://hal.inria.fr/hal-00912710
  • 41A. Rousseau, A. Darnaud, B. Goglin, C. Acharian, C. Leininger, C. Godin, C. Holik, C. Kirchner, D. Rives, E. Darquie, E. Kerrien, F. Neyret, F. Masseglia, F. Dufour, G. Berry, G. Dowek, H. Robak, H. Xypas, I. Illina, I. Gnaedig, J. Jongwane, J. Ehrel, L. Viennot, L. Guion, L. Calderan, L. Kovacic, M. Collin, M.-A. Enard, M.-H. Comte, M. Quinson, M. Olivi, M. Giraud, M. Dorémus, M. Ogouchi, M. Droin, N. Lacaux, N. Rougier, N. Roussel, P. Guitton, P. Peterlongo, R.-M. Cornus, S. Vandermeersch, S. Maheo, S. Lefebvre, S. Boldo, T. Viéville, V. Poirel, A. Chabreuil, A. Fischer, C. Farge, C. Vadel, I. Astic, J.-P. Dumont, L. Féjoz, P. Rambert, P. Paradinas, S. De Quatrebarbes, S. Laurent.

    Médiation Scientifique : une facette de nos métiers de la recherche, March 2013, 34 p.

    http://hal.inria.fr/hal-00804915

Other Publications

  • 42G. Collet, G. Rizk, R. Chikhi, D. Lavenier.

    MINIA on a Raspberry Pi, Assembling a 100 Mbp Genome on a Credit Card Sized Computer, in: JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques, Toulouse, France, July 2013.

    http://hal.inria.fr/hal-00842027


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