{"id":2694,"date":"2018-03-05T11:10:41","date_gmt":"2018-03-05T10:10:41","guid":{"rendered":"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/?page_id=2694"},"modified":"2021-12-21T11:42:50","modified_gmt":"2021-12-21T10:42:50","slug":"2017-2","status":"publish","type":"page","link":"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/about-us\/publications-2-2-2\/2017-2\/","title":{"rendered":"2017"},"content":{"rendered":"
    \n
  1. 1Thouzeau V, Mennecier P, Verdu P, Austerlitz F. Genetic and linguistic histories in Central Asia inferred using approximate Bayesian computations. Proceedings of the Royal Society B-Biological Sciences 284: 20170706. doi: 10.1098\/Rspb.2017.0706; see<\/a><\/li>\n
  2. Aimeric Teyssier, Lieze Oscar Rouffaer, Noraine Saleh Hudin, Diederik Strubbe, Erik Matthysen, Luc Lens, Jo\u00ebl White; Inside the guts of the city: Urban-induced alterations of the gut microbiota in a wild passerine Science of The Total Environment Volume 612, 15 January 2018, Pages 1276-1286; doi : 10.1016\/j.scitotenv.2017.09.035; see<\/a><\/li>\n
  3. Pradiptajati Kusuma, Nicolas Brucato, Murray P Cox, Thierry Letellier, Abdul Manan, Chandra Nuraini, Philippe Grang\u00e9, Herawati Sudoyo & Fran\u00e7ois-Xavier Ricaut; The last sea nomads of the Indonesian archipelago: genomic origins and dispersal; European Journal of Human Genetic volume 25,pages 1004\u20131010 (2017); doi: 10.1038\/ejhg.2017.88; see<\/a><\/li>\n
  4. Andrea Benazzo, Emiliano Trucchi, James A. Cahill, Pierpaolo Maisano Delser, Stefano Mona, Matteo Fumagalli, Lynsey Bunnefeld, Luca Cornetti, Silvia Ghirotto, Matteo Girardi, Lino Ometto, Alex Panziera, Omar Rota-Stabelli, Enrico Zanetti, Alexandros Karamanlidis, Claudio Groff, Ladislav Paule, Leonardo Gentile, Carles Vil\u00e0, Saverio Vicario, Luigi Boitani, Ludovic Orlando, Silvia Fuselli, Cristiano Vernesi, Beth Shapiro, Paolo Ciucci, and Giorgio Bertorelle; Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers; PNAS November 7, 2017 114 (45) doi : 10.1073\/pnas.1707279114; see<\/a><\/li>\n
  5. S. Mona; On the role played by the carrying capacity and the ancestral population size during a range expansion; Heredity 118, pages 143\u2013153 (2017) doi: 10.1038\/hdy.2016.73; see<\/a><\/li>\n
  6. Etienne G.J. Danchin, Laetitia Perfus-Barbeoch, Corinne Rancurel, Peter Thorpe, Martine Da Rocha, Simon Bajew, Roy Neilson, Elena Sokolova (Guzeeva), Corinne Da Silva, Julie Guy, Karine Labadie, Daniel Esmenjaud, Johannes Helder, John T. Jones and Sebastian Eves-van den Akker; The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes. Genes (Basel). 8(10): 287. doi:10.3390\/genes8100287; see<\/a><\/li>\n
  7. Corinne Rancurel, Ludovic Legrand and Etienne G. J. Danchin. (2017) Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life. Genes, 8(10), 248; doi:10.3390\/genes8100248; see<\/a><\/li>\n
  8. Franck Cerutti, Ludovic Mallet, Ana\u00efs Painset, Claire Hoede<\/strong>, Annick Moisan, Christophe B\u00e9cavin, M\u00e9lodie Duval, Olivier Dussurget, Pascale Cossart, Christine Gaspin<\/strong> and H\u00e9l\u00e8ne Chiapello. Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria. BMC Genomics. 2017. doi: 10.1186\/s12864-017-4242-0 see<\/a><\/li>\n
  9. Bestion, E., Jacob, S., Zinger, L., Di Gesu, L., Richard, M., White, J., & Cote, J. Climate warming reduces gut microbiota diversity in a vertebrate ectotherm. Nature ecology & evolution, 1(6), 0161. DOI: 10.1038\/s41559-017-0161; see<\/a><\/li>\n
  10. Pau Boher, Mar\u00e7al Soler, Anna S\u00e1nchez, Claire Hoede<\/strong>, C\u00e9line Noirot<\/strong>, Jorge Almiro Pinto Paiva, Olga Serra, Merc\u00e8 Figueras. A comparative transcriptomic approach to understanding the formation of cork. Plant Molecular Biology. 2017. doi: 10.1007\/s11103-017-0682-9 see<\/a><\/li>\n
  11. Jorge Urrestarazu, H\u00e9l\u00e8ne Muranty, Caroline Denanc\u00e9, Diane Leforestier, Elisa Ravon, Arnaud Guyader, Remi Guisnel, Laurence Feugey, Sebastien Aubourg, Jean-Marc Celton, Nicolas Daccord, Luca Dondini, Roberto Gregori, Marc Lateur, Patrick Houben, Matthew Ordidge, Frantisek Paprstein, Jiri Sedlak, Hilde Nybom, Larisa Garkava- Gustavson, Michela Troggio, Luca Bianco, Riccardo Velasco, Charles Poncet, Anthony Theron, Shigeki Moriya, Marco C.a.m. Bink, Fran\u00e7ois Laurens, Stefano Tartarini, Charles-Eric Durel, 2017. Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple. Frontiers in Plant Science.; doi: 10.3389\/fpls.2017.01923 see<\/a><\/li>\n
  12. Mariette, J.<\/strong> and Villa-Vialaneix, N. Unsupervised multiple kernel learning for heterogeneous data integration. Bioinformatics. 2017. btx682. doi: 10.1093\/bioinformatics\/btx682 see<\/a><\/li>\n
  13. P\u00e9rez-Pascual D, Lunazzi A, Magdelenat G, Rouy Z, Roulet A, Lopez-Roques C, Larocque R, Barbeyron T, Gobet A, Michel G, Bernardet JF, Duchaud E, The Complete Genome Sequence of the Fish Pathogen Tenacibaculum maritimum Provides Insights into Virulence Mechanisms. Front Microbiol. 2017 Aug 16;8:1542. doi: 10.3389\/fmicb.2017.01542 see<\/a><\/li>\n
  14. Caldelari I, Chane-Woon-Ming B, Noirot C<\/strong>, Moreau K, Romby P, Gaspin C<\/strong>, Marzi S. Complete Genome Sequence and Annotation of the Staphylococcus aureus Strain HG001. Genome Announc. 2017 Aug 10;5(32). pii: e00783-17. doi: 10.1128\/genomeA.00783-17 see<\/a><\/li>\n
  15. Durrens P, Klopp C<\/strong>, Biteau N, Fitton-Ouhabi V, Dementhon K, Accoceberry I, Sherman DJ, No\u00ebl T. Genome Sequence of the Yeast Clavispora lusitaniae Type Strain CBS 6936. Genome Announc. 2017 Aug 3;5(31). pii: e00724-17. doi: 10.1128\/genomeA.00724-17. see<\/a><\/li>\n
  16. Auer L, Mariadassou M, O’Donohue M, Klopp C<\/strong>, Hernandez-Raquet G. Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description. Mol Ecol Resour. 2017 Jul 11. doi: 10.1111\/1755-0998.12700. see<\/a><\/li>\n
  17. Belkorchia A, Pombert JF, Polonais V, Parisot N, Delbac F, Brug\u00e8re JF, Peyret P, Gaspin C<\/strong>, Peyretaillade E. Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes. DNA Res. 2017 Jun 1;24(3):251-260. see<\/a><\/li>\n
  18. Urriza MG, Gassie C, Bouchez O, Klopp C<\/strong>, Guyoneaud R. Draft Genome Sequence of Desulfovibrio BerOc1, a Mercury-Methylating Strain. Genome Announc. 2017;5: e01483-16. doi:10.1128\/genomeA.01483-16 see<\/a><\/li>\n
  19. Patrascu O, B\u00e9guet-Crespel F, Marinelli L, Chatelier EL, Abraham A-L, Leclerc M, et al. A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic. Scientific Reports. 2017;7: 40248. doi:10.1038\/srep40248 see<\/a><\/li>\n
  20. Panicz R, Klopp C<\/strong>, Igielski R, Hofsoe P, Sadowski J, Coller Jr JA. Tench (Tinca tinca) high-throughput transcriptomics reveal feed dependent gut profiles. Aquaculture. 2017;479: 200\u2013207. doi:10.1016\/j.aquaculture.2017.05.047 see<\/a><\/li>\n
  21. Nouwen N, Arrighi J-F, Cartieaux F, Chaintreuil C, Gully D, Klopp C<\/strong>, et al. The role of rhizobial (NifV) and plant (FEN1) homocitrate synthases in Aeschynomene \/photosynthetic Bradyrhizobium symbiosis. Scientific Reports. 2017;7: 448. doi:10.1038\/s41598-017-00559-0 see<\/a><\/li>\n
  22. Murat F, Armero A, Pont C, Klopp C<\/strong>, Salse J. Reconstructing the genome of the most recent common ancestor of flowering plants. Nat Genet. 2017;49: 490\u2013496. doi:10.1038\/ng.3813 see<\/a><\/li>\n
  23. Merci\u00e8re M, Boulord R, Carasco-Lacombe C, Klopp C<\/strong>, Lee Y-P, Tan JS, et al. About Ganoderma boninense in oil palm plantations of Sumatra and peninsular Malaysia: Ancient population expansion, extensive gene flow and large scale dispersion ability. Fungal Biology. 2017; doi:10.1016\/j.funbio.2017.01.001 see<\/a><\/li>\n
  24. Jean-Yves Mazzitelli, Elsa Bonnafe, Christophe Klopp<\/strong>, Fr\u00e9d\u00e9ric Escudier and Florence Geret. De novo transcriptome sequencing and analysis of freshwater snail (Radix balthica) to discover genes and pathways affected by exposure to oxazepam. Ecotoxicology. 2017;26: 127\u2013140. doi:10.1007\/s10646-016-1748-1 see<\/a><\/li>\n
  25. Ciabrelli F, Comoglio F, Fellous S, Bonev B, Ninova M, Szabo Q, et al. Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila. Nat Genet. 2017;advance online publication. doi:10.1038\/ng.3848 see<\/a><\/li>\n
  26. Cabau C, Escudi\u00e9 F, Djari A, Guiguen Y, Bobe J, Klopp C<\/strong>. Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies. PeerJ. 2017;5: e2988. doi:10.7717\/peerj.2988 see<\/a><\/li>\n
  27. Jadwiga Rzeznik-Orignac, Dimitri Kalenitchenko, J\u00e9r\u00f4me Mariette<\/strong>, Jean-Yves Bodiou, Nadine Le Bris, Evelyne Derelle. Comparison of meiofaunal diversity by combined morphological and molecular approaches in a shallow Mediterranean sediment. Marine Biology. 2017; 164:40. doi:10.1007\/s00227-017-3074-4. see<\/a><\/li>\n
  28. Christophe B\u00e9cavin, Mikael Koutero, Nicolas Tchitchek, Franck Cerutti, Pierre Lechat, Nicolas Maillet, Claire Hoede<\/strong>, H\u00e9l\u00e8ne Chiapello, Christine Gaspin<\/strong>, Pascale Cossart. Listeriomics: an Interactive Web Platform for Systems Biology of Listeria. mSystems Mar 2017, 2 (2) e00186-16; DOI: 10.1128\/mSystems.00186-16. see<\/a><\/li>\n
  29. Carolina A. Garcia\u2011Baccino, Andres Legarra, Ole F. Christensen, Ignacy Misztal, Ivan Pocrnic, Zulma G. Vitezica and Rodolfo J. C. Cantet; Metafounders are related to Fst fixation indices and reduce bias in single\u2011step genomic evaluations; Genet Sel Evol (2017) 49:34; DOI 10.1186\/s12711-017-0309-2. see<\/a><\/li>\n
  30. C.A. Garcia-Baccino, S. Munilla, A. Legarra, Z.G. Vitezica, N.S. Forneris, R.O. Bates, C.W. Ernst, N.E. Raney, J.P. Steibel & R.J.C. Cantet; Estimates of the actual relationship between half-sibs in a pig population; J. Anim. Breed. Genet. Volume 134, Issue 2, April 2017, Pages 109\u2013118. DOI: 10.1111\/jbg.12236. see<\/a><\/li>\n
  31. Felipe Freitas Castro, Patricia C. Ruy, Karina Nogueira Zeviani, Ramon Freitas Santos, Juliano Sim\u00f5es Toledo, Angela Kaysel Cruz, Evidence of putative non-coding RNAs from Leishmania untranslated regions, Molecular and Biochemical Parasitology, Volume 214, June 2017, Pages 69-74, DOI:10.1016\/j.molbiopara.2017.04.002 see<\/a><\/li>\n
  32. H\u00e9l\u00e8ne Badouin, J\u00e9r\u00f4me Gouzy, Christopher J. Grassa, Florent Murat, S. Evan Staton, Ludovic Cottret, Christine Lelandais-Bri\u00e8re, Gregory L. Owens, S\u00e9bastien Carr\u00e8re, Baptiste Mayjonade, Ludovic Legrand, Navdeep Gill, Nolan C. Kane, John E. Bowers, Sariel Hubner, Arnaud Bellec, Aur\u00e9lie B\u00e9rard, H\u00e9l\u00e8ne Berg\u00e8s, Nicolas Blanchet, Marie-Claude Boniface, Dominique Brunel, Olivier Catrice, Nadia Chaidir, Clotilde Claudel, C\u00e9cile Donnadieu, Thomas Faraut, Ghislain Fievet, Nicolas Helmstetter, Matthew King, Steven J. Knapp, Zhao Lai, Marie-Christine Le Paslier, Yannick Lippi, Lolita Lorenzon, Jennifer R. Mandel, Gwenola Marage, Gwena\u00eblle Marchand, Elodie Marquand, Emmanuelle Bret-Mestries, Evan Morien, Savithri Nambeesan, Thuy Nguyen, Prune Pegot-Espagnet, Nicolas Pouilly, Frances Raftis, Erika Sallet, Thomas Schiex, Justine Thomas, C\u00e9line Vandecasteele, Didier Var\u00e8s, Felicity Vear, Sonia Vautrin, Martin Crespi, Brigitte Mangin, John M. Burke J\u00e9r\u00f4me Salse, St\u00e9phane Mu\u00f1os, Patrick Vincourt, Loren H. Rieseberg & Nicolas B. Langlade; The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution; Nature 546, 148\u2013152 (01 June 2017); doi:10.1038\/nature22380; see<\/a><\/li>\n
  33. Laura Payton, Mickael Perrigault, Claire Hoede<\/strong>, Jean-Charles Massabuau, Mohamedou Sow, Arnaud Huvet, Floriane Boullot, Caroline Fabioux, H\u00e9l\u00e8ne Hegaret & Damien Tran; Remodeling of the cycling transcriptome of the oyster Crassostrea gigas by the harmful algae Alexandrium minutum; Scientific Reports | 7: 3480 | DOI:10.1038\/s41598-017-03797; see<\/a><\/li>\n
  34. Kocher, A., Gantier, J.-C., Gaborit, P., Zinger, L., Holota, H., Valiere, S., Dusfour, I., Girod, R., Ba\u00f1uls, A.-L. and Murienne, J.; Vector soup: high-throughput identification of Neotropical phlebotomine sand flies using metabarcoding; Mol Ecol Resour, 17: 172\u2013182. doi:10.1111\/1755-0998.12556; see<\/a><\/li>\n
  35. Ludovic Mallet, Tristan Bitard-Feildel, Franck Cerutti, H\u00e9l\u00e8ne Chiapello; PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies. Bioinformatics 2017 btx396. doi: 10.1093\/bioinformatics\/btx396; see<\/a><\/li>\n
  36. Simoncini, D., Schiex, T. and Zhang, K. Y.J.; Balancing exploration and exploitation in population-based sampling improves fragment-based de novo protein structure prediction. Proteins, 85: 852\u2013858. doi:10.1002\/prot.25244; see<\/a><\/li>\n
  37. Laurent, B., Palaiokostas, C., Spataro, C., Moinard, M., Zehraoui, E., Houston, R. D. and Foulongne-Oriol, M.; High-resolution mapping of the recombination landscape of the phytopathogen Fusarium graminearum suggests two-speed genome evolution. Molecular Plant Pathology. doi:10.1111\/mpp.12524; see<\/a><\/li>\n
  38. Rougemont, Q., Gagnaire, P.-A., Perrier, C., Genthon, C., Besnard, A.-L., Launey, S. and Evanno, G.; Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes. Mol Ecol, 26: 142\u2013162. doi:10.1111\/mec.13664; see<\/a><\/li>\n
  39. Jean Peccoud, Vincent Loiseau, Richard Cordaux, and Cl\u00e9ment Gilbert; Massive horizontal transfer of transposable elements in insects; PNAS vol. 114 no. 18 4721-4726; doi: 10.1073\/pnas.1621178114; see<\/a><\/li>\n
  40. Sophie Comtet-Marre, Nicolas Parisot, Pascale Lepercq, Fr\u00e9d\u00e9rique Chaucheyras-Durand, Pascale Mosoni, Eric Peyretaillade, Ali R. Bayat, Kevin J. Shingfield, Pierre Peyret, and Evelyne Forano; Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet; Front Microbiol.; 8: 67. doi: 10.3389\/fmicb.2017.00067. see<\/a><\/li>\n
  41. Abdelkader Ouali; David Allouche; Simon de Givry; Samir Loudni; Yahia Lebbah; Lakhdar Loukil. Iterative Decomposition Guided Variable Neighborhood Search for Graphical Model Energy Minimization. In Proc. of UAI-17, Sydney, Australia.<\/li>\n
  42. Simon de Givry and George Katsirelos. Clique Cuts in Weighted Constraint Satisfaction. In Proc. of CP-17, Melbourne, Australia.<\/li>\n
  43. Kocher, A., de Thoisy, B., Catzeflis, F., Huguin, M., Vali\u00e8re, S., Zinger, L., Ba\u00f1uls, A.-L. and Murienne, J.; Evaluation of short mitochondrial metabarcodes for the identification of Amazonian mammals; Methods Ecol Evol.; doi: 10.1111\/2041-210X.12729. see<\/a><\/li>\n
  44. No\u00e9 Cochetel, Fr\u00e9d\u00e9ric Escudi\u00e9<\/strong>, Sarah Jane Cookson, Zhanwu Dai, Philippe Vivin, Pierre-Fran\u00e7ois Bert, Mindy Stephania Mu\u00f1oz, Serge Delrot, Christophe Klopp<\/strong>, Nathalie Ollat, Virginie Lauvergeat; Root transcriptomic responses of grafted grapevines to heterogeneous nitrogen availability depend on rootstock genotype. J Exp Bot; doi: 10.1093\/jxb\/erx224. see<\/a><\/li>\n
  45. Nicolas Blanc, Xavier Frank, Claire Mayer-Laigle, Farhang Radja\u00ef and Jean-Yves Delenne; Peridynamics simulation of the comminution of particles containing microcraks; EPJ Web of Conferences 140, 07018; doi: 10.1051\/epjconf\/201714007018. see<\/a><\/li>\n
  46. Xavier Frank, Jean-Yves Delenne and Farhang Radjai; Numerical study of the failure of materials embedding soft to hard particles; EPJ Web Conf. 140 02029; doi: 10.1051\/epjconf\/201714002029. see<\/a><\/li>\n
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  49. Leroy, T., Roux, C., Villate, L., Bod\u00e9n\u00e8s, C., Romiguier, J., Paiva, J. A. P., Dossat, C., Aury, J.-M., Plomion, C. and Kremer, A.; Extensive recent secondary contacts between four European white oak species; New Phytol, 214: 865\u2013878; doi:10.1111\/nph.14413. see<\/a><\/li>\n
  50. Marc Krasovec, Adam Eyre-Walker, Sophie Sanchez-Ferandin, Gwenael Piganeau; Spontaneous Mutation Rate in the Smallest Photosynthetic Eukaryotes. Mol Biol Evol; 34 (7): 1770-1779; doi:10.1093\/molbev\/msx119. see<\/a><\/li>\n
  51. Delrieu-Trottin, E. et al.; Population expansions dominate demographic histories of endemic and widespread Pacific reef fishes; Sci. Rep. 7, 40519; doi:10.1038\/srep40519. see<\/a><\/li>\n
  52. Xiang, T., O. F. Christensen, and A. Legarra; Technical note: Genomic evaluation for crossbred performance in a single-step approach with metafounders; J. Anim. Sci. 95:1472-1480; doi:10.2527\/jas.2016.1155. see<\/a><\/li>\n
  53. Raphael Ployet, Mar\u00e7al Soler, Victor Carocha, Nathalie Ladouce, Ana Alves, Jos\u00e9-Carlos Rodrigues, Luc Harvengt, Christiane Marque, Chantal Teuli\u00e8res, Jacqueline Grima-Pettenati, Fabien Mounet; Long cold exposure induces transcriptional and biochemical remodelling of xylem secondary cell wall in Eucalyptus. Tree Physiol 1-14; doi:10.1093\/treephys\/tpx062. see<\/a><\/li>\n
  54. Karsta Heinze, Xavier Frank, Val\u00e9rie Lullien-Pellerin, Matthieu George, Farhang Radjai and Jean-Yves Delenne; Numerical modeling of the tensile strength of a biological granular aggregate: Effect of the particle size distribution; EPJ Web Conf., 140 08013; doi:10.1051\/epjconf\/201714008013. see<\/a><\/li>\n
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  61. Wereszczuk A., Leblois R., M. Gautier, A. Rohfritsch, J. Foucaud, C. Burban, M. Galan, A. Loiseau, L. Saune, M. Branco, K. Gharbi, R. Vitalis, C. Kerdelhue. 2017. Deciphering the evolutionary history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa. Molecular Ecology 2017: 1-15.; doi: 10.1111\/mec.14411; see<\/a><\/li>\n
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    1Thouzeau V, Mennecier P, Verdu P, Austerlitz F. Genetic and linguistic histories in Central Asia inferred using approximate Bayesian computations. 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