Publications 2014

  • J Mariette, M Olteanu, J Boelaert, N Villa-Vialaneix. Bagged kernel SOM. 2014. Advances in Self-Organizing Maps and Learning Vector Quantization, 45-54. see
  • Morel, A, Teyssier C, Trontin J-F, Eliášová K, Pešek B, Beaufour M, Morabito D, Boizot N, Le Metté C, Belal-Bessai L, Reymond I, Harvengt L, Cadene M, Corbineau F,  Vágner M, Label P, Lelu-Walter M-A. Early molecular events involved in Pinus pinaster Ait. somatic embryo development under reduced water availability: transcriptomic and proteomic analyses. Physiologia Plantarum. 2014. Vol 152 Issue 1 pages 184-201. doi:10.1111/ppl.12158. see
  • Bouzid W, Verdenaud M, Klopp C, Ducancel F, Noirot C and Vétillard A. De Novo sequencing and transcriptome analysis for Tetramorium bicarinatum: a comprehensive venom gland transcriptome analysis from an ant species.    BMC Genomics 2014, 15:987. doi:10.1186/1471-2164-15-987. see
  • Kocher A, Kamilari M, Lhuillier E, Coissac E, Péneau J, Chave J, Murienne J. Shotgun assembly of the assassin bug Brontostoma colossus mitochondrial genome (Heteroptera, Reduviidae). Gene, Volume 552, Issue 1, 15 November 2014, Pages 184-194, ISSN 0378-1119. doi:10.1016/j.gene.2014.09.033. see
  • Marie P, Labas V, Brionne A, Harichaux G, Hennequet-Antiera C, Nysa Y, Gautrona J. Data set for the proteomic inventory and quantitative analysis of chicken uterine fluid during eggshell biomineralization. Data in brief. 2014. Volume 1, December 2014, Pages 65–69. doi:10.1016/j.dib.2014.09.006. see
  • Eves-van den Akker S., Lilley C., Danchin E.G.J., Rancurel C., Cock P., Urwin P., Jones J.T. The Transcriptome of Nacobbus aberrans Reveals Insights into the Evolution of Sedentary Endoparasitism in Plant-Parasitic Nematodes. Genome Biol Evol. 2014 Aug 13;6(9):2181-94. doi: 10.1093/gbe/evu171. Pubmed PMID:25123114. see
  • Habib Salami, Guillaume Croville, Olivier Kwiatek, Jérôme Mariette, Christophe Klopp, Sophie Valière, Jean-Luc Guérin, Moustapha Lo, Yaya Thiongane, Emmanuel Albina, Geneviève Libeau. Complete Genome Sequence of a Field Strain of Peste des Petits Ruminants Virus Isolated during 2010-2014 Epidemics in Senegal. Genome Announcements. 2014, vol.2 no.5 e00772-14. doi: 10.1128/genomA.00772-1. see
  • Philippe Bardou, Jérôme Mariette, Frédéric Escudié, Christophe Djemiel and Christophe Klopp. jvenn: an interactive Venn diagram viewer. BMC Bioinformatics 2014, 15:293 doi:10.1186/1471-2105-15-293. see
  • Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, Leroy P, Mangenot S, Guilhot N, Le Gouis J, Balfourier F, Alaux M, Jamilloux V, Poulain J, Durand C, Bellec A, Gaspin C, Safar J, Dolezel J, Rogers J, Vandepoele K, Aury JM, Mayer K, Berges H, Quesneville H, Wincker P, Feuillet C. Structural and functional partitioning of bread wheat chromosome 3B. Science. 2014 Jul 18;345(6194):1249721. doi: 10.1126/science.1249721. PubMed PMID: 25035497. see
  • Anthony Levasseur, Anne Lomascolo, Olivier Chabrol, Francisco J Ruiz-Dueñas, Eva Boukhris-Uzan, François Piumi, Ursula Kües, Arthur F Ram, Claude Murat, Mireille Haon, Isabelle Benoit, Yonathan Arfi, Didier Chevret, Elodie Drula, Min Jin Kwon, Philippe Gouret, Laurence Lesage-Meessen, Vincent Lombard, Jérôme Mariette, Céline Noirot, Joohae Park, Aleksandrina Patyshakuliyeva, Jean Claude Sigoillot, Ad Wiebenga, Han A Wösten, Francis Martin, Pedro M Coutinho, Ronald P de Vries, Angel T Martínez, Christophe Klopp, Pierre Pontarotti, Bernard Henrissat and Eric Record. The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown. BMC Genomics 2014, 15:486 doi:10.1186/1471-2164-15-486. see
  • Mariette J, Noirot C, Nabihoudine I, Bardou P, Hoede C, Djari A, Cabau C, Klopp C. (2014) RNAbrowse: RNA-Seq De Novo Assembly Results Browser. PLoS ONE 9(5): e96821. doi: 10.1371/journal.pone.0096821. see
  • Magnanou E, Klopp C, Noirot C, Besseau L, Falcón J. Generation and characterization of the sea bass Dicentrarchus labrax brain and liver transcriptomes. Gene. 2014 Jul 1;544(1):56-66. doi: 10.1016/j.gene.2014.04.032. Epub 2014 Apr 21.see
  • Hoede C, Arnoux S, Moisset M, Chaumier T, Inizan O, et al. (2014) PASTEC: An Automatic Transposable Element Classification Tool. PLoS ONE 9(5): e91929. doi:10.1371/journal.pone.0091929. see
  • Puchalska, P., Concepción García, M., & Luisa Marina, M. Identification of native angiotensin-I converting enzyme inhibitory peptides in commercial soybean based infant formulas using HPLC-Q-ToF-MS. Food chemistry, 157, 62-69. see
  • Berthelot C, Brunet F, Chalopin D, Juanchich A, Bernard M, Noel B, Bento P, Da Silva C, Labadie K, Albertii A, Aury JM, Louis A, Dehais P, Bardou P, Montfort J, Klopp C, Cabau C, Gaspin C, Thorgaard GH, Boussaha M, Quillet A, Guyomard R, galiana D, Bobe J, Volff JN, gene C, Wincker P, Jaillon O, Roest Crollius H, Guigen Y. The rainbow trout genome provides novel insights into evolution after whole-genome duplication invertebrates. NATURE COMMUNICATIONS, 5:3657, DOI: 10.103. see
  • Malé, P. J. G., Bardon, L., Besnard, G., Coissac, E., Delsuc, F., Engel, J., … & Chave, J. (2014). Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family. Molecular ecology resources. see
  • David Allouche, Jessica Davies, Simon de Givry, George Katsirelos, Thomas Schiex, Seydou Traoré, Isabelle André, Sophie Barbe, Steve Prestwich, Barry O’Sullivan. Computational protein design as an optimization problem. see
  • Laure Fresard, Sophie Leroux, Bertrand Servin, David Gourichon, Patrice Dehais, Magali San Cristobal, Nathalie Marsaud, Florence Vignoles, Bertrand Bedhom, Jean-Luc Coville, Farhad Hormozdiari, Catherine Beaumont, Tatiana Zerjal, Alain Vignal, Mireille Morisson, Sandrine Lagarrigue and Frederique Pitel. Transcriptome-wide investigation of genomic imprinting in chicken. Nucleic Acids Research, 2014, 1–15. doi:10.1093/nar/gkt1390. see 
  • Etienne Liais, Guillaume Croville, Jérôme Mariette, Maxence Delverdier, Marie-Noelle Lucas, Christophe Klopp, Jérôme Lluch, Cécile Donnadieu, James S. Guy, Léni Corrand, Mariette F. Ducatez, and Jean-Luc Guérin. Novel Avian Coronavirus and Fulminating Disease in Guinea Fowl, France. Emerg Infect Dis. see
  • Gschloessl B, Vogel H, Burban C, Heckel D, Streiff R, Kerdelhué C. 2014. Comparative analysis of two phenologically divergent populations of the pine processionary moth (Thaumetopoea pityocampa) by de novo transcriptome sequencing.  Insect Biochem Mol Biol. ;46:31-42. see
  • Vignaud, T. M., Maynard, J. A., Leblois, R., Meekan, M. G., Vázquez?Juárez, R., Ramírez?Macías, D., … & Planes, S. (2014). Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline. Molecular Ecology. see
  • F Assenza, JM Elsen, A Legarra, C Carré, G Sallé, C Robert-Granié, C Moreno. Genetic parameters for growth and faecal worm egg count following Haemonchus contortus experimental infestations using pedigree and molecular information. 2014. Genetics, Selection, Evolution,  46:13. see
  • A. Legarra, G. Baloche, F.Barillet, J.M. Astruc, C. Soulas, X. Aguerre, F. Arrese, L.Mintegi, M. Lasarte, F. Maeztu|, I. Beltrán de Heredia, E. Ugarte. 2014. Within and across-breed genomic predictions and genomic relationships for Western Pyrenees breeds of dairy sheep Latxa, Manech and Basco-Bearnaise. Journal of Dairy Science, 3200-3212. see
  • J Ertl, A Legarra, ZG Vitezica, L Varona, C Edel, R Emmerling, KU Götz., 2014 Genomic analysis of dominance effects in milk production and conformation traits of Fleckvieh cattle. Genetics Selection Evolution, 46:40. see
  • Sanu Shameer, Flora J. Logan-Klumpler, Florence Vinson, Ludovic Cottret, Benjamin Merlet, Fiona Achcar, Michael Boshart, Matthew Berriman, Rainer Breitling, Frédéric Bringaud, Peter Bütikofer, Amy M. Cattanach, Bridget Bannerman-Chukualim, Darren J. Creek, Kathryn Crouch, Harry P. de Koning, Hubert Denise, Charles Ebikeme, Alan H. Fairlamb, Michael A. J. Ferguson, Michael L. Ginger, Christiane Hertz-Fowler, Eduard J. Kerkhoven, Pascal Mäser, Paul A. M. Michels, Archana Nayak, David W. Nes, Derek P. Nolan, Christian Olsen, Fatima Silva-Franco, Terry K. Smith, Martin C. Taylor, Aloysius G. M. Tielens, Michael D. Urbaniak, Jaap J. van Hellemond, Isabel M. Vincent, Shane R. Wilkinson, Susan Wyllie, Fred R. Opperdoes, Michael P. Barrett, and Fabien Jourdan, TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei Nucl. Acids Res. first published online October 9, 2014 doi:10.1093/nar/gku944. see
  • Vignaud T. M., J. Mourier, J. A. Maynard, R. Leblois, J. Spaet, E. Clua, V. Neglia, S. Planes. 2014. Blacktip reef sharks, Carcharhinus melanopterus, have high genetic structure and varying demographic histories in their Indo-Pacific range. Molecular Ecology, 23: 5193-5207. doi : 10.1111/mec.12936. see
  • Leblois R., P. Pudlo, J. Néron, F. Bertaux, C. Reddy Beeravolu, R. Vitalis, F. Rousset. 2014. Maximum likelihood inference of population size contractions from microsatellite data. Molecular Biology and Evolution 31: 2805-2823. doi: 10.1093/molbev/msu212. see
  • Marçal Soler, Eduardo Leal Oliveira Camargo, Victor Carocha, Hua Cassan-Wang, Hélène San Clemente, Bruno Savelli, Charles A. Hefer4, Jorge A. Pinto Paiva, Alexander A. Myburg and Jacqueline Grima-Pettenati, The Eucalyptus grandis R2R3-MYB transcription factor family: evidence for woody growth-related evolution and function, New Phytol., DOI: 10.1111/nph.13039, sept 201. see
  • Hong Yu, Marc¸al Soler, Isabelle Mila, He lene San Clemente, Bruno Savelli, Christophe Dunand, Jorge A. P. Paiva, Alexander A. Myburg, Mondher Bouzayen, Jacqueline Grima-Pettenati, Hua Cassan-Wan, Genome-Wide Characterization and Expression Profiling of the AUXIN RESPONSE FACTOR (ARF) Gene Family in Eucalyptus grandi, PloS One, volume 9, issue 9, e108906,sept  2014, DOI: 10.1371/journal.pone.010890. see
  • Hong et al, Comprehensive Genome-wide Analysis of the Aux/IAA Gene Family in Eucalyptus: Evidence for the Role of EgrIAA4 in Wood Formation, Plant and Cell Physiology (PCP), dec 2014, doi: 10.1093/pcp/pcu215. see
  • David Allouche, Christine Cierco-Ayrolles, Simon de Givry, G Guillermin, Brigitte Mangin, Thomas Schiex, Jimmy Vandel, and Matthieu Vignes; Gene Network Inference, chapter A Panel of Learning Methods for the Reconstruction of Gene Regulatory Networks in a Systems Genetics Contex; Springer, 2014
  • N Briot, A Chateau, R Coletta, S de Givry, P Leleux, and T Schiex; An integer linear programming approach for genome scaffolding; In CP-14 workshop on Constraint-Based Methods for Bioinformatics, Lyon, France, 2014