Publications

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

2015

1. Allouche, D., Givry, S. de, Katsirelos, G., Schiex, T., and Zytnicki, M. (2015). Anytime Hybrid Best-First Search with Tree Decomposition for Weighted CSP. In Principles and Practice of Constraint Programming, G. Pesant, ed. (Springer International Publishing), pp. 12–29. https://doi.org/10.1007/978-3-319-23219-5_2.

2. 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. (2016). Genome-wide association links candidate genes to resistance to Plum Pox Virus in apricot (Prunus armeniaca). New Phytologist 209, 773–784. https://doi.org/10.1111/nph.13627.

3. Simoncini, D., Allouche, D., Givry, S. de, Delmas, C., Barbe, S., and Schiex, T. (2015). Guaranteed Discrete Energy Optimization on Large Protein Design Problems. Journal of Chemical Theory and Computation 11, 5980–5989. https://doi.org/10.1021/acs.jctc.5b00594.

4. Pringault, O., Aube, J., Bouchez, O., Klopp, C., Mariette, J., Escudie, F., Senin, P., and Goni-Urriza, M. (2015). Contrasted effects of natural complex mixtures of PAHs and metals on oxygen cycle in a microbial mat. Chemosphere 135, 189–201. https://doi.org/10.1016/j.chemosphere.2015.04.037.

5. Bonhomme, M., Boitard, S., San Clemente, H., Dumas, B., Young, N., and Jacquet, C. (2015). Genomic Signature of Selective Sweeps Illuminates Adaptation of Medicago truncatula to Root-Associated Microorganisms. Molecular Biology and Evolution 32, 2097–2110. https://doi.org/10.1093/molbev/msv092.

6. Lauressergues, D., Couzigou, J.-M., Clemente, H.S., Martinez, Y., Dunand, C., Bécard, G., and Combier, J.-P. (2015). Primary transcripts of microRNAs encode regulatory peptides. Nature 520, 90–93. https://doi.org/10.1038/nature14346.

7. San Clemente, H., and Jamet, E. (2015). WallProtDB, a database resource for plant cell wall proteomics. Plant Methods 11, 2. https://doi.org/10.1186/s13007-015-0045-y.

8. Duhoux, A., Carrère, S., Gouzy, J., Bonin, L., and Délye, C. (2015). RNA-Seq analysis of rye-grass transcriptomic response to an herbicide inhibiting acetolactate-synthase identifies transcripts linked to non-target-site-based resistance. Plant Molecular Biology 87, 473–487. https://doi.org/10.1007/s11103-015-0292-3.

9. Lesur, I., Bechade, A., Lalanne, C., Klopp, C., Noirot, C., Leplé, J.-C., Kremer, A., Plomion, C., and Le Provost, G. (2015). A unigene set for European beech (Fagus sylvatica L.) and its use to decipher the molecular mechanisms involved in dormancy regulation. Molecular Ecology Resources 15, 1192–1204. https://doi.org/10.1111/1755-0998.12373.

10. Bourret, V., Croville, G., Mansuy, J.-M., Mengelle, C., Mariette, J., Klopp, C., Genthon, C., Izopet, J., and Guérin, J.-L. (2015). Intra-host viral variability in children clinically infected with H1N1 (2009) pandemic influenza. Infection, Genetics and Evolution 33, 47–54. https://doi.org/10.1016/j.meegid.2015.04.009.

11. Smedley, D., Haider, S., Durinck, S., Pandini, L., Provero, P., Allen, J., Arnaiz, O., Awedh, M.H., Baldock, R., Barbiera, G., Bardou, P., Beck, T., Blake, A., Bonierbale, M., Brookes, A.J., Bucci, G., Buetti, I., Burge, S., Cabau, C., Carlson, J.W., Chelala, C., Chrysostomou, C., Cittaro, D., Collin, O., Cordova, R., Cutts, R.J., Dassi, E., Genova, A.D., Djari, A., Esposito, A., Estrella, H., Eyras, E., Fernandez-Banet, J., Forbes, S., Free, R.C., Fujisawa, T., Gadaleta, E., Garcia-Manteiga, J.M., Goodstein, D., Gray, K., Guerra-Assunção, J.A., Haggarty, B., Han, D.-J., Han, B.W., Harris, T., Harshbarger, J., Hastings, R.K., Hayes, R.D., Hoede, C., Hu, S., Hu, Z.-L., Hutchins, L., Kan, Z., Kawaji, H., Keliet, A., Kerhornou, A., Kim, S., Kinsella, R., Klopp, C., Kong, L., Lawson, D., Lazarevic, D., Lee, J.-H., Letellier, T., Li, C.-Y., Lio, P., Liu, C.-J., Luo, J., Maass, A., Mariette, J., Maurel, T., Merella, S., Mohamed, A.M., Moreews, F., Nabihoudine, I., Ndegwa, N., Noirot, C., Perez-Llamas, C., Primig, M., Quattrone, A., Quesneville, H., Rambaldi, D., Reecy, J., Riba, M., Rosanoff, S., Saddiq, A.A., Salas, E., Sallou, O., Shepherd, R., Simon, R., Sperling, L., Spooner, W., Staines, D.M., Steinbach, D., Stone, K., Stupka, E., Teague, J.W., Dayem Ullah, A.Z., Wang, J., Ware, D., Wong-Erasmus, M., Youens-Clark, K., Zadissa, A., Zhang, S.-J., and Kasprzyk, A. (2015). The BioMart community portal: An innovative alternative to large, centralized data repositories. Nucleic Acids Research 43, W589–W598. https://doi.org/10.1093/nar/gkv350.

12. Pratlong, M., Haguenauer, A., Chabrol, O., Klopp, C., Pontarotti, P., and Aurelle, D. (2015). The red coral (Corallium rubrum) transcriptome: A new resource for population genetics and local adaptation studies. Molecular Ecology Resources 15, 1205–1215. https://doi.org/10.1111/1755-0998.12383.

13. Kocher, A., Guilbert, É., Lhuillier, É., and Murienne, J. (2015). Sequencing of the mitochondrial genome of the avocado lace bug Pseudacysta perseae (Heteroptera, Tingidae) using a genome skimming approach. Comptes Rendus Biologies 338, 149–160. https://doi.org/10.1016/j.crvi.2014.12.004.

14. Marie, P., Labas, V., Brionne, A., Harichaux, G., Hennequet-Antier, C., Rodriguez-Navarro, A.B., Nys, Y., and Gautron, J. (2015). 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 4, 430–436. https://doi.org/10.1016/j.dib.2015.06.019.

15. Hinaux, H., Blin, M., Fumey, J., Legendre, L., Heuzé, A., Casane, D., and Rétaux, S. (2015). Lens defects in Astyanax mexicanus Cavefish: Evolution of crystallins and a role for alphaA-crystallin. Developmental Neurobiology 75, 505–521. https://doi.org/10.1002/dneu.22239.

16. Zedane, L., Hong-Wa, C., Murienne, J., Jeziorski, C., Baldwin, B.G., and Besnard, G. (2016). 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 117, 44–57. https://doi.org/10.1111/bij.12509.

17. Plomion, C., Aury, J.-M., 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, J.-C., 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., and Kremer, A. (2016). Decoding the oak genome: Public release of sequence data, assembly, annotation and publication strategies. Molecular Ecology Resources 16, 254–265. https://doi.org/10.1111/1755-0998.12425.

18. Quelen, C., Eloit, Y., Noirot, C., Bousquet, M., and Brousset, P. (2016). RNA editing in acute myeloid leukaemia with normal karyotype. British Journal of Haematology 173, 788–790. https://doi.org/10.1111/bjh.13631.

19. Lesur, I., Le Provost, G., Bento, P., Da Silva, C., Leplé, J.-C., 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, J.-M., and Plomion, C. (2015). The oak gene expression atlas: Insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC Genomics 16, 112. https://doi.org/10.1186/s12864-015-1331-9.

20. Mariette, J., Escudié, F., Bardou, P., Nabihoudine, I., Noirot, C., Trotard, M.-S., Gaspin, C., and Klopp, C. (2016). Jflow: A workflow management system for web applications. Bioinformatics 32, 456–458. https://doi.org/10.1093/bioinformatics/btv589.

21. Legarra, A., and Vitezica, Z.G. (2015). Genetic evaluation with major genes and polygenic inheritance when some animals are not genotyped using gene content multiple-trait BLUP. Genetics Selection Evolution 47, 89. https://doi.org/10.1186/s12711-015-0165-x.

22. Legarra, A. (2016). Comparing estimates of genetic variance across different relationship models. Theoretical Population Biology 107, 26–30. https://doi.org/10.1016/j.tpb.2015.08.005.

23. Forneris, N.S., Legarra, A., Vitezica, Z.G., Tsuruta, S., Aguilar, I., Misztal, I., and Cantet, R.J.C. (2015). Quality Control of Genotypes Using Heritability Estimates of Gene Content at the Marker. Genetics 199, 675–681. https://doi.org/10.1534/genetics.114.173559.

24. Dedeine, F., Weinert, L.A., Bigot, D., Josse, T., Ballenghien, M., Cahais, V., Galtier, N., and Gayral, P. (2015). Comparative Analysis of Transcriptomes from Secondary Reproductives of Three Reticulitermes Termite Species. PLOS ONE 10, e0145596. https://doi.org/10.1371/journal.pone.0145596.

25. Thiault, N., Darrigues, J., Adoue, V., Gros, M., Binet, B., Perals, C., Leobon, B., Fazilleau, N., Joffre, O.P., Robey, E.A., Meerwijk, J.P.M. van, and Romagnoli, P. (2015). Peripheral regulatory T lymphocytes recirculating to the thymus suppress the development of their precursors. Nature Immunology 16, 628–634. https://doi.org/10.1038/ni.3150.

26. Jousselin, E., Clamens, A.-L., Galan, M., Bernard, M., Maman, S., Gschloessl, B., Duport, G., Meseguer, A.S., Calevro, F., and Coeur d’acier, A. (2016). Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus. Molecular Ecology Resources 16, 628–640. https://doi.org/10.1111/1755-0998.12478.

27. Mazet, O., Rodríguez, W., and Chikhi, L. (2015). Demographic inference using genetic data from a single individual: Separating population size variation from population structure. Theoretical Population Biology 104, 46–58. https://doi.org/10.1016/j.tpb.2015.06.003.

28. Ferchaud, A.-L., Eudeline, R., Arnal, V., Cheylan, M., Pottier, G., Leblois, R., and Crochet, P.-A. (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. https://doi.org/10.1111/mec.13011.

29. Higashi, S., Fournier, C., Gautier, C., Gaspin, C., and Sagot, M.-F. (2015). Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data. BMC Bioinformatics 16, 179. https://doi.org/10.1186/s12859-015-0594-0.

30. Esquerré, T., Moisan, A., Chiapello, H., Arike, L., Vilu, R., Gaspin, C., Cocaign-Bousquet, M., and Girbal, L. (2015). Genome-wide investigation of mRNA lifetime determinants in Escherichia coli cells cultured at different growth rates. BMC Genomics 16, 275. https://doi.org/10.1186/s12864-015-1482-8.

31. Mazet, O., Rodríguez, W., Grusea, S., Boitard, S., and Chikhi, L. (2016). On the importance of being structured: Instantaneous coalescence rates and human evolution—lessons for ancestral population size inference? Heredity 116, 362–371. https://doi.org/10.1038/hdy.2015.104.

32. Legarra, A., Christensen, O.F., Vitezica, Z.G., Aguilar, I., and Misztal, I. (2015). Ancestral Relationships Using Metafounders: Finite Ancestral Populations and Across Population Relationships. Genetics 200, 455–468. https://doi.org/10.1534/genetics.115.177014.

33. Legarra, A., Croiseau, P., Sanchez, M.P., Teyssèdre, S., Sallé, G., Allais, S., Fritz, S., Moreno, C.R., Ricard, A., and Elsen, J.-M. (2015). A comparison of methods for whole-genome QTL mapping using dense markers in four livestock species. Genetics Selection Evolution 47, 6. https://doi.org/10.1186/s12711-015-0087-7.