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.

  • 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. 2017; 8: 67. doi: 10.3389/fmicb.2017.00067. see