Publications 2015

  • Ferchaud A.-L., R. Eudeline, V. Arnal, M. Cheylan, G. Pottier, R. Leblois and P.-A. Crochet. 2015. Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard. Molecular Ecology 24 :  192–207 . doi : 10.1111/mec.13011. see
  • Mazet O, Rodríguez W, Grusea S, Boitard S and Chikhi L; On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference? Heredity advance online publication 9 December 2015; doi: 10.1038/hdy.2015.104. see
  • Mazet O, Rodríguez W, Chikhi L, Demographic inference using genetic data from a single individual: Separating population size variation from population structure, Theoretical Population Biology, Volume 104, September 2015, Pages 46-58, ISSN 0040-5809, doi: 10.1016/j.tpb.2015.06.003. see
  • Jousselin E., Clamens A.-L., Galan M., Bernard M., Maman S., Duport M.-G., Meseguer A., Calevro F. and Coeur d’acier A., 2015. An assessment of 16S rRNA amplicon Illumina sequencing procedure to study the microbiome of a symbiont-rich aphid genus. Molecular Ecology Resources. doi.org/10.1111/1755-0998.1247. see
  • Thiault N, Darrigues J, Adoue V, Gros M, Binet B, Perals C, Leobon B, Fazilleau N, Joffre OP, Robey EA, van Meerwijk JP, Romagnoli P.; Peripheral regulatory T lymphocytes recirculating to the thymus suppress the development of their precursors; Nature immunology. 2015 Jun;16(6):628-34. doi: 10.1038/ni.3150. Epub 2015 May 4. see
  • Dedeine F, Weinert LA, Bigot D, Josse T, Ballenghien M, Cahais V, et al. (2015) Comparative Analysis of Transcriptomes from Secondary Reproductives of Three Reticulitermes Termite Species. PLoS ONE 10(12): e0145596. doi:10.1371/journal.pone.0145596. see
  • Forneris NS, Legarra A, Vitezica ZG, Tsuruta S, Aguilar I, Misztal I, Cantet RJ. Quality control of genotypes using heritability estimates of gene content at the marker. Genetics. 2015 Mar;199(3):675-81. doi: 10.1534/genetics.114.173559. see
  • Legarra A, Christensen OF, Vitezica ZG, Aguilar I, Misztal I. Ancestral Relationships Using Metafounders: Finite Ancestral Populations and Across Population Relationships. Genetics. 2015 Jun;200(2):455-68. doi: 10.1534/genetics.115.177014. see
  • Legarra A, Croiseau P, Sanchez MP, Teyssèdre S, Sallé G, Allais S, Fritz S, Moreno CR, Ricard A, Elsen JM. A comparison of methods for whole-genome QTL mapping using dense markers in four livestock species. Genet Sel Evol. 2015 Feb 12;47:6. doi: 10.1186/s12711-015-0087-7. see
  • Legarra A. Comparing estimates of genetic variance across different relationship models. Theor Popul Biol. 2015 Sep 2. pii: S0040-5809(15)00083-0. doi: 10.1016/j.tpb.2015.08.005. see
  • Legarra A, Vitezica ZG. Genetic evaluation with major genes and polygenic inheritance when some animals are not genotyped using gene content multiple-trait BLUP. Genet Sel Evol. 2015 Nov 17;47(1):89.doi: 10.1186/s12711-015-0165-x. see
  • Jérôme Mariette, Frédéric Escudié, Philippe Bardou, Ibouniyamine Nabihoudine, Céline Noirot, Marie-Stéphane Trotard, Christine Gaspin and Christophe Klopp. Jflow: a workflow management system for web applications. Bioinformatics. 2015. doi 10.1093/bioinformatics/btv589. see
  • Lesur I, Le Provost G, Bento P, Da Silva C, Leplé JC, Murat F, Ueno S, Bartholomé J, Lalanne C, Ehrenmann F, Noirot C, Burban C, Léger V, Amselem J, Belser C, Quesneville H, Stierschneider M, Fluch S, Feldhahn L, Tarkka M, Herrmann S, Buscot F, Klopp C, Kremer A, Salse J, Aury JM, Plomion C. The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC Genomics. 2015 Feb 21;16:112. doi: 10.1186/s12864-015-1331-9. PubMed PMID: 25765701; PubMed Central PMCID: PMC4350297.see.
  • Quelen C, Eloit Y, Noirot C, Bousquet M, Brousset P. RNA editing in acute myeloid leukaemia with normal karyotype. Br J Haematol. 2015 Aug 7. doi:10.1111/bjh.13631. [Epub ahead of print] PubMed PMID: 26251186.see
  • Esquerré T, Moisan A, Chiapello H, Arike L, Vilu R, Gaspin C, Cocaign-Bousquet M, Girbal L. Genome-wide investigation of mRNA lifetime determinants in Escherichia coli cells cultured at different growth rates. BMC Genomics. 2015 Apr 9;16:275. doi: 10.1186/s12864-015-1482-8. PubMed PMID: 25887031; PubMed Central PMCID: PMC4421995.
  • Higashi S, Fournier C, Gautier C, Gaspin C, Sagot MF. Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data. BMC Bioinformatics. 2015 May 29;16:179. doi: 10.1186/s12859-015-0594-0. PubMed PMID: 26022464; PubMed Central PMCID: PMC4448272.
  • Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Boudet N, Boury C, Canaguier A, Couloux A, Da Silva C, Duplessis S, Ehrenmann F, Estrada-Mairey B, Fouteau S, Francillonne N, Gaspin C, Guichard C, Klopp C, Labadie K, Lalanne C, Le Clainche I, Leplé JC, Le Provost G, Leroy T, Lesur I, Martin F, Mercier J, Michotey C, Murat F, Salin F, Steinbach D, Faivre-Rampant P, Wincker P, Salse J, Quesneville H, Kremer A. Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Mol Ecol Resour. 2015 May 6. doi: 10.1111/1755-0998.12425. [Epub ahead of print] PubMed PMID: 25944057.see.
  • Zedane L, Hong-Wa C, Murienne J, Jeziorski C, Baldwin BG, Besnard G. Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico. Biological Journal of the Linnean Society. 2015. doi:10.1111/bij.12509. see
  • Hinaux H, Blin M, Fumey J, Legendre L, Heuzé A, Casane D, Rétaux S. Lens defects in Astyanax mexicanus Cavefish: Evolution of crystallins and a role for alphaA-crystallin. Developmental Neurobiology. 2015. Vol 75, issue 5, page 505-521. doi:10.1002/dneu.22239; see
  • San Clemente H and Jamet E. WallProtDB, a database resource for plant cell wall proteomics. PlantMethods. 2015. 11:2. doi:10.1186/s13007-015-0045-y. see
  • Marie P, Labas V, Brionne A, Harichaux G, Hennequet-Antier C, Rodriguez-Navarro A.B, Nys Y, Gautron J. Data set for the proteomic inventory and quantitative analysis of chicken eggshell matrix proteins during the primary events of eggshell mineralization and the active growth phase of calcification. Data in Brief, Available online 7 July 2015, ISSN 2352-3409, doi:10.1016/j.dib.2015.06.019. see
  • Kocher A, Guilbert E, Lhuillier E, Murienne J. Sequencing of the mitochondrial genome of the avocado lace bug Pseudacysta perseae (Heteroptera, Tingidae) using a genome skimming approach. Comptes Rendus Biologies, Volume 338, Issue 3, March 2015, Pages 149-160, ISSN 1631-0691, doi:10.1016/j.crvi.2014.12.004. see
  • Pratlong M, Haguenauer A, Chabrol O, Klopp C, Pontarotti P and Aurelle D. The red coral (Corallium rubrum) transcriptome: a new resource for population genetics and local adaptation studies. 2015. doi: 10.1111/1755-0998.12383. see
  • Damian Smedley, Syed Haider, Steffen Durinck, Luca Pandini, Paolo Provero, James Allen, Olivier Arnaiz, Mohammad Hamza Awedh, Richard Baldock, Giulia Barbiera, Philippe Bardou, Tim Beck, Andrew Blake, Merideth Bonierbale, Anthony J Brookes, Gabriele Bucci, Iwan Buetti, Sarah Burge, Cédric Cabau, Joseph W Carlson, Claude Chelala, Charalambos Chrysostomou, Davide Cittaro, Olivier Collin, Raul Cordova, Rosalind J Cutts, Erik Dassi, Alex Di Genova, Anis Djari, Anthony Esposito, Heather Estrella, Eduardo Eyras, Julio Fernandez-Banet, Simon Forbes, Robert C Free, Takatomo Fujisawa, Emanuela Gadaleta, Jose M Garcia-Manteiga, David Goodstein, Kristian Gray, José Afonso Guerra-Assunção, Bernard Haggarty, Dong-Jin Han, Byung Woo Han, Todd Harris, Jayson Harshbarger, Robert K Hastings, Richard D Hayes, Claire Hoede, Shen Hu, Zhi-Liang Hu, Lucie Hutchins, Zhengyan Kan, Hideya Kawaji, Aminah Keliet, Arnaud Kerhornou, Sunghoon Kim, Rhoda Kinsella, Christophe Klopp, Lei Kong, Daniel Lawson, Dejan Lazarevic, Ji-Hyun Lee, Thomas Letellier, Chuan-Yun Li, Pietro Lio, Chu-Jun Liu, Jie Luo, Alejandro Maass, Jerome Mariette, Thomas Maurel, Stefania Merella, Azza Mostafa Mohamed, Francois Moreews, Ibounyamine Nabihoudine, Nelson Ndegwa, Céline Noirot, Cristian Perez-Llamas, Michael Primig, Alessandro Quattrone, Hadi Quesneville, Davide Rambaldi, James Reecy, Michela Riba, Steven Rosanoff, Amna Ali Saddiq, Elisa Salas, Olivier Sallou, Rebecca Shepherd, Reinhard Simon, Linda Sperling, William Spooner, Daniel M Staines, Delphine Steinbach, Kevin Stone, Elia Stupka, Jon W Teague, Abu Z Dayem Ullah, Jun Wang, Doreen Ware, Marie Wong-Erasmus, Ken Youens-Clark, Amonida Zadissa, Shi-Jian Zhang, Arek Kasprzyk. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acid Research. 2015, doi: 10.1093/nar/gkv350. see
  • Vincent Bourret, Guillaume Croville, Jean-Michel Mansuy, Catherine Mengelle, Jérôme Mariette, Christophe Klopp, Clémence Genthon, Jacques Izopet, Jean-Luc Guérin. Intra-host viral variability in children clinically infected with H1N1 (2009) pandemic influenza. Infection, Genetics and Evolution. 2015, doi:10.1016/j.meegid.2015.04.009. see
  • Lesur I, Bechade A, Lalanne C, Klopp C, Noirot C, Leplé JC, Kremer A, Plomion C, Le Provost G. A unigene set for European beech (Fagus sylvatica L.) and its use to decipher the molecular mechanisms involved in dormancy regulation. Mol Ecol Resour. 2015 Jan 16. doi: 10.1111/1755-0998.12373. see
  • Duhoux A, Carrère S, Gouzy J, Bonin L, Délye C. RNA-Seq analysis of rye-grass transcriptomic response to an herbicide inhibiting acetolactate-synthase identifies transcripts linked to non-target-site-based resistance. Plant Mol Biol. 2015 Jan 31. doi:10.1007/s11103-015-0292-3. see
  • San Clemente H, Jamet E, WallProtDB, a database resource for plant cell wall proteomic, Plant methods 2015, 11:2, doi:10.1186/s13007-015-0045-y. see
  • Lauressergues D, Couzigou JM, San Clemente H, Martinez Y, Dunand C, Bécard G, Combier JP, Primary transcripts of microRNAs encode regulatory peptide, Nature 520, 90–93 (02 April 2015), doi:10.1038/nature14346. see
  • Bonhomme M, Boitard S, San Clemente H, Dumas B, Young N and Jacquet C, Genomic signature of selective sweeps illuminates adaptation of Medicago truncatula to root-associated microorganism, Molecular Biology and Evolution, avril 2015, doi: 10.1093/molbev/msv092. see
  • O Pringault, J Aube, O Bouchez, C Klopp, J Mariette, F Escudie, P Senin, M Goni-Urriza, Contrasted effects of natural complex mixtures of PAHs and metals on oxygen cycle in a microbial mat. Chemosphere. 2015. doi:10.1016/j.chemosphere.2015.04.037. see
  • David Simoncini, David Allouche, Simon de Givry, Céline Delmas, Sophie Barbe, and Thomas Schiex, J. Chem. Theory Comput., Just Accepted Manuscript, DOI: 10.1021/acs.jctc.5b00594, Publication Date (Web): November 11, 2015. see
  • Mariette, S., Wong Jun Tai, F., Roch, G., Barre, A., Chague, A., Decroocq, S., Groppi, A., Laizet, Y., Lambert, P., Tricon, D., Nikolski, M., Audergon, J.-M., Abbott, A. G. and Decroocq, V. (July 2015), Genome-wide association links candidate genes to resistance to Plum Pox Virus in apricot (Prunus armeniaca). New Phytol, 209: 773–784. doi:10.1111/nph.13627. see
  • Allouche, D., de Givry, S., Katsirelos, G., Schiex, T., Zytnicki, M.: Anytime Hybrid Best-First Search with Tree Decomposition for Weighted CSP. In: Proc. of CP-15. pp. 12–28. Cork, Ireland (2015). see