Publications 2017

  1. Thouzeau 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
  2. Aimeric Teyssier, Lieze Oscar Rouffaer, Noraine Saleh Hudin, Diederik Strubbe, Erik Matthysen, Luc Lens, Joël 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
  3. Pradiptajati Kusuma, Nicolas Brucato, Murray P Cox, Thierry Letellier, Abdul Manan, Chandra Nuraini, Philippe Grangé, Herawati Sudoyo & François-Xavier Ricaut; The last sea nomads of the Indonesian archipelago: genomic origins and dispersal; European Journal of Human Genetic volume 25,pages 1004–1010 (2017); doi: 10.1038/ejhg.2017.88; see
  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 Vilà, 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
  5. S. Mona; On the role played by the carrying capacity and the ancestral population size during a range expansion; Heredity 118, pages 143–153 (2017) doi: 10.1038/hdy.2016.73; see
  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
  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
  8. Franck Cerutti, Ludovic Mallet, Anaïs Painset, Claire Hoede, Annick Moisan, Christophe Bécavin, Mélodie Duval, Olivier Dussurget, Pascale Cossart, Christine Gaspin and Hélène 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
  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
  10. Pau Boher, Marçal Soler, Anna Sánchez, Claire Hoede, Céline Noirot, Jorge Almiro Pinto Paiva, Olga Serra, Mercè Figueras. A comparative transcriptomic approach to understanding the formation of cork. Plant Molecular Biology. 2017. doi: 10.1007/s11103-017-0682-9 see
  11. Jorge Urrestarazu, Hélène Muranty, Caroline Denancé, 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, François 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
  12. Mariette, J. and Villa-Vialaneix, N. Unsupervised multiple kernel learning for heterogeneous data integration. Bioinformatics. 2017. btx682. doi: 10.1093/bioinformatics/btx682 see
  13. Pérez-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
  14. Caldelari I, Chane-Woon-Ming B, Noirot C, Moreau K, Romby P, Gaspin C, 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
  15. Durrens P, Klopp C, Biteau N, Fitton-Ouhabi V, Dementhon K, Accoceberry I, Sherman DJ, Noël 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
  16. Auer L, Mariadassou M, O’Donohue M, Klopp C, 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
  17. Belkorchia A, Pombert JF, Polonais V, Parisot N, Delbac F, Brugère JF, Peyret P, Gaspin C, 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
  18. Urriza MG, Gassie C, Bouchez O, Klopp C, 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
  19. Patrascu O, Béguet-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
  20. Panicz R, Klopp C, Igielski R, Hofsoe P, Sadowski J, Coller Jr JA. Tench (Tinca tinca) high-throughput transcriptomics reveal feed dependent gut profiles. Aquaculture. 2017;479: 200–207. doi:10.1016/j.aquaculture.2017.05.047 see
  21. Nouwen N, Arrighi J-F, Cartieaux F, Chaintreuil C, Gully D, Klopp C, 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
  22. Murat F, Armero A, Pont C, Klopp C, Salse J. Reconstructing the genome of the most recent common ancestor of flowering plants. Nat Genet. 2017;49: 490–496. doi:10.1038/ng.3813 see
  23. Mercière M, Boulord R, Carasco-Lacombe C, Klopp C, 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
  24. Jean-Yves Mazzitelli, Elsa Bonnafe, Christophe Klopp, Frédéric 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: 127–140. doi:10.1007/s10646-016-1748-1 see
  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
  26. Cabau C, Escudié F, Djari A, Guiguen Y, Bobe J, Klopp C. Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies. PeerJ. 2017;5: e2988. doi:10.7717/peerj.2988 see
  27. Jadwiga Rzeznik-Orignac, Dimitri Kalenitchenko, Jérôme Mariette, 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
  28. Christophe Bécavin, Mikael Koutero, Nicolas Tchitchek, Franck Cerutti, Pierre Lechat, Nicolas Maillet, Claire Hoede, Hélène Chiapello, Christine Gaspin, 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
  29. Carolina A. Garcia‑Baccino, 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‑step genomic evaluations; Genet Sel Evol (2017) 49:34; DOI 10.1186/s12711-017-0309-2. see
  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 109–118. DOI: 10.1111/jbg.12236. see
  31. Felipe Freitas Castro, Patricia C. Ruy, Karina Nogueira Zeviani, Ramon Freitas Santos, Juliano Simões 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
  32. Hélène Badouin, Jérôme Gouzy, Christopher J. Grassa, Florent Murat, S. Evan Staton, Ludovic Cottret, Christine Lelandais-Brière, Gregory L. Owens, Sébastien Carrère, Baptiste Mayjonade, Ludovic Legrand, Navdeep Gill, Nolan C. Kane, John E. Bowers, Sariel Hubner, Arnaud Bellec, Aurélie Bérard, Hélène Bergès, Nicolas Blanchet, Marie-Claude Boniface, Dominique Brunel, Olivier Catrice, Nadia Chaidir, Clotilde Claudel, Cécile 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, Gwenaëlle 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, Céline Vandecasteele, Didier Varès, Felicity Vear, Sonia Vautrin, Martin Crespi, Brigitte Mangin, John M. Burke Jérôme Salse, Stéphane Muños, Patrick Vincourt, Loren H. Rieseberg & Nicolas B. Langlade; The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution; Nature 546, 148–152 (01 June 2017); doi:10.1038/nature22380; see
  33. Laura Payton, Mickael Perrigault, Claire Hoede, Jean-Charles Massabuau, Mohamedou Sow, Arnaud Huvet, Floriane Boullot, Caroline Fabioux, Hélène 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
  34. Kocher, A., Gantier, J.-C., Gaborit, P., Zinger, L., Holota, H., Valiere, S., Dusfour, I., Girod, R., Bañuls, A.-L. and Murienne, J.; Vector soup: high-throughput identification of Neotropical phlebotomine sand flies using metabarcoding; Mol Ecol Resour, 17: 172–182. doi:10.1111/1755-0998.12556; see
  35. Ludovic Mallet, Tristan Bitard-Feildel, Franck Cerutti, Hélène Chiapello; PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies. Bioinformatics 2017 btx396. doi: 10.1093/bioinformatics/btx396; see
  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: 852–858. doi:10.1002/prot.25244; see
  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
  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: 142–162. doi:10.1111/mec.13664; see
  39. Jean Peccoud, Vincent Loiseau, Richard Cordaux, and Clément Gilbert; Massive horizontal transfer of transposable elements in insects; PNAS vol. 114 no. 18 4721-4726; doi: 10.1073/pnas.1621178114; see
  40. Sophie Comtet-Marre, Nicolas Parisot, Pascale Lepercq, Frédérique 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
  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.
  42. Simon de Givry and George Katsirelos. Clique Cuts in Weighted Constraint Satisfaction. In Proc. of CP-17, Melbourne, Australia.
  43. Kocher, A., de Thoisy, B., Catzeflis, F., Huguin, M., Valière, S., Zinger, L., Bañuls, 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
  44. Noé Cochetel, Frédéric Escudié, Sarah Jane Cookson, Zhanwu Dai, Philippe Vivin, Pierre-François Bert, Mindy Stephania Muñoz, Serge Delrot, Christophe Klopp, 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
  45. Nicolas Blanc, Xavier Frank, Claire Mayer-Laigle, Farhang Radjaï 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
  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
  47. Blanc-Mathieu R, Perfus-Barbeoch L, Aury J-M, Da Rocha M, Gouzy J, Sallet E, et al.; Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes; PLoS Genet 13(6); doi: 10.1371/journal.pgen.1006777. see
  48. Seydou Traoré, David Allouche, Isabelle André, Thomas Schiex, Sophie Barbe; Deterministic Search Methods for Computational Protein Design; Computational Protein Design pp 107-123. see
  49. Leroy, T., Roux, C., Villate, L., Bodénès, 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: 865–878; doi:10.1111/nph.14413. see
  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
  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
  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
  53. Raphael Ployet, Marçal Soler, Victor Carocha, Nathalie Ladouce, Ana Alves, José-Carlos Rodrigues, Luc Harvengt, Christiane Marque, Chantal Teulières, 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
  54. Karsta Heinze, Xavier Frank, Valérie 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
  55. Tannous, J., Snini, S.P., El Khoury, R., Canlet, C., Pinton, P., Lippi, Y., Alassane-Kpembi, I., Gauthier, T., El Khoury, A., Atoui, A. and Zhou, T., Patulin transformation products and last intermediates in its biosynthetic pathway, E-and Z-ascladiol, are not toxic to human cells. Archives of toxicology, 91(6), pp.2455-2467.; doi:10.1007/s00204-016-1900-y. see
  56. Brucato, N., Kusuma, P., Beaujard, P., Sudoyo, H., Cox, M.P. and Ricaut, F.X., Genomic admixture tracks pulses of economic activity over 2,000 years in the Indian Ocean trading network. Scientific Reports, 7.; doi:10.1038/s41598-017-03204-y. see
  57. Mariette, J., Olteanu, M. and Villa-Vialaneix, N., Efficient interpretable variants of online SOM for large dissimilarity data. Neurocomputing, 225, pp.31-48.; doi:10.1016/j.neucom.2016.11.014. see
  58. Roselli, S., Olry, A., Vautrin, S., Coriton, O., Ritchie, D., Galati, G., Navrot, N., Krieger, C., Vialart, G., Bergès, H. and Bourgaud, F.,. A bacterial artificial chromosome (BAC) genomic approach reveals partial clustering of the furanocoumarin pathway genes in parsnip. The Plant Journal, 89(6), pp.1119-1132; doi: 10.1111/tpj.13450 see
  59. Fernández, E.N., Sánchez, J.P., Martínez, R., Legarra, A. and Baselga, M., 2017. Role of inbreeding depression, non‐inbred dominance deviations and random year‐season effect in genetic trends for prolificacy in closed rabbit lines. Journal of Animal Breeding and Genetics.; doi: 10.1111/jbg.12284 see
  60. Wereszczuk A., R. Leblois, A. Zalewski. 2017. Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural-urban habitats. BMC ecology 17:46; doi: 10.1186/s12898-017-0156-6; see
  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
  62. Bonnet T., R. Leblois, F. Rousset, P.-A. Crochet. 2017. A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes. Evolution 71:2140-2158.; doi: 10.1111/evo.13296; see
  63. Navascués M., R. Leblois, C. Burgarella. 2017. Demographic inference through approximate-Bayesian-computation skyline plots. PeerJ 5:e3530.; DOI: 10.7717/peerj.3530 ; see
  64. Lippens C., A. Estoup, K. Hima, A. Loiseau, C. Tatard, A. Dalecky, K. Bâ, M. Kane, M. Diallo, A. Sow, S. Piry, R. Leblois, J.-M. Duplantier, C. Brouat. 2017. Genetic structure and invasion history of the house mouse (Mus musculus domesticus) in Senegal : a legacy of colonial times? Heridity 119 :64-75.; doi: 10.1038/hdy.2017.18; see
  65. Merle C., R. Leblois, F. Rousset, P. Pudlo. 2017. Resampling: an improvement of Importance Sampling in varying population size models. Theoretical Population Biology 114:70-87.; DOI: 10.1016/j.tpb.2016.09.002 ; see