Publications 2017

This list includes publications for which the GenoToul Bioinformatics facility has been used (hardware infrastructure / Funding / Staff members). All Sigenae’s publications have used the GenoToul Bioinformatics hardware infrastructure.

  • 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.
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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.
  • Simon de Givry and George Katsirelos. Clique Cuts in Weighted Constraint Satisfaction. In Proc. of CP-17, Melbourne, Australia.
  • 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
  • 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
  • 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
  • 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
  • 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
  • Seydou Traoré, David Allouche, Isabelle André, Thomas Schiex, Sophie Barbe; Deterministic Search Methods for Computational Protein Design; Computational Protein Design pp 107-123. see
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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