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.

2016

1. Lalis, A., Leblois, R., Stoetzel, E., Benazzou, T., Souttou, K., Denys, C., and Nicolas, V. (2016). Phylogeography and demographic history of Shaw’s Jird (Meriones shawii complex) in North Africa. Biological Journal of the Linnean Society 118, 262–279. https://doi.org/10.1111/bij.12725.

2. Hurley, B., O’Sullivan, B., Allouche, D., Katsirelos, G., Schiex, T., Zytnicki, M., and Givry, S.D. (2016). Multi-language evaluation of exact solvers in graphical model discrete optimization. Constraints 21, 413–434. https://doi.org/10.1007/s10601-016-9245-y.

3. Guellerin, M., Passerini, D., Fontagné-Faucher, C., Robert, H., Gabriel, V., Loux, V., Klopp, C., Le Loir, Y., Coddeville, M., Daveran-Mingot, M.-L., Ritzenthaler, P., and Le Bourgeois, P. (2016). Complete Genome Sequence of Lactococcus lactis subsp. Lactis A12, a Strain Isolated from Wheat Sourdough. Genome Announcements 4, 10.1128/genomea.00692–16. https://doi.org/10.1128/genomea.00692-16.

4. Hammoumi, S., Vallaeys, T., Santika, A., Leleux, P., Borzym, E., Klopp, C., and Avarre, J.-C. (2016). Targeted genomic enrichment and sequencing of CyHV-3 from carp tissues confirms low nucleotide diversity and mixed genotype infections. PeerJ 4, e2516. https://doi.org/10.7717/peerj.2516.

5. Mazzitelli, J.-Y., Bonnafe, E., Klopp, C., Escudier, F., and Geret, F. (2017). De novo transcriptome sequencing and analysis of freshwater snail (Radix balthica) to discover genes and pathways affected by exposure to oxazepam. Ecotoxicology 26, 127–140. https://doi.org/10.1007/s10646-016-1748-1.

6. Satgé, C., Moreau, S., Sallet, E., Lefort, G., Auriac, M.-C., Remblière, C., Cottret, L., Gallardo, K., Noirot, C., Jardinaud, M.-F., and Gamas, P. (2016). Reprogramming of DNA methylation is critical for nodule development in Medicago truncatula. Nature Plants 2, 16166. https://doi.org/10.1038/nplants.2016.166.

7. Magnanou, E., Noirot, C., Falcón, J., and Jørgensen, E.H. (2016). Sequencing and characterization of a multi-organ Arctic charr transcriptome: A toolbox for investigating polymorphism and seasonal life in a high Arctic fish. Marine Genomics 29, 45–53. https://doi.org/10.1016/j.margen.2016.04.006.

8. Berthier, K., Garba, M., Leblois, R., Navascués, M., Tatard, C., Gauthier, P., Gagaré, S., Piry, S., Brouat, C., Dalecky, A., Loiseau, A., and Dobigny, G. (2016). Black rat invasion of inland Sahel: Insights from interviews and population genetics in south-western Niger. Biological Journal of the Linnean Society 119, 748–765. https://doi.org/10.1111/bij.12836.

9. Merle, C., Leblois, R., Rousset, F., and Pudlo, P. (2017). Resampling: An improvement of importance sampling in varying population size models. Theoretical Population Biology 114, 70–87. https://doi.org/10.1016/j.tpb.2016.09.002.

10. Bétous, R., Renoud, M.-L., Hoede, C., Gonzalez, I., Jones, N., Longy, M., Sensebé, L., Cazaux, C., and Hoffmann, J.-S. (2017). Human Adipose-Derived Stem Cells Expanded Under Ambient Oxygen Concentration Accumulate Oxidative DNA Lesions and Experience Procarcinogenic DNA Replication Stress. Stem Cells Translational Medicine 6, 68–76. https://doi.org/10.5966/sctm.2015-0401.

11. Sierra, R., Cañas-Duarte, S.J., Burki, F., Schwelm, A., Fogelqvist, J., Dixelius, C., González-García, L.N., Gile, G.H., Slamovits, C.H., Klopp, C., Restrepo, S., Arzul, I., and Pawlowski, J. (2016). Evolutionary Origins of Rhizarian Parasites. Molecular Biology and Evolution 33, 980–983. https://doi.org/10.1093/molbev/msv340.

12. Cabau, C., Escudié, F., Djari, A., Guiguen, Y., Bobe, J., and Klopp, C. (2017). Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies. PeerJ 5, e2988. https://doi.org/10.7717/peerj.2988.

13. Aubé, J., Senin, P., Pringault, O., Bonin, P., Deflandre, B., Bouchez, O., Bru, N., Biritxinaga-Etchart, E., Klopp, C., Guyoneaud, R., and Goñi-Urriza, M. (2016). The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats. Marine Pollution Bulletin 111, 115–125. https://doi.org/10.1016/j.marpolbul.2016.07.023.

14. Chaintreuil, C., Rivallan, R., Bertioli, D.J., Klopp, C., Gouzy, J., Courtois, B., Leleux, P., Martin, G., Rami, J.-F., Gully, D., Parrinello, H., Séverac, D., Patrel, D., Fardoux, J., Ribière, W., Boursot, M., Cartieaux, F., Czernic, P., Ratet, P., Mournet, P., Giraud, E., and Arrighi, J.-F. (2016). A gene-based map of the Nod factor-independent Aeschynomene evenia sheds new light on the evolution of nodulation and legume genomes. DNA Research 23, 365–376. https://doi.org/10.1093/dnares/dsw020.

15. Boitard, S., Rodríguez, W., Jay, F., Mona, S., and Austerlitz, F. (2016). Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach. PLOS Genetics 12, e1005877. https://doi.org/10.1371/journal.pgen.1005877.

16. Boitard, S., Boussaha, M., Capitan, A., Rocha, D., and Servin, B. (2016). Uncovering Adaptation from Sequence Data: Lessons from Genome Resequencing of Four Cattle Breeds. Genetics 203, 433–450. https://doi.org/10.1534/genetics.115.181594.

17. Feugeas, J.-P., Tourret, J., Launay, A., Bouvet, O., Hoede, C., Denamur, E., and Tenaillon, O. (2016). Links between Transcription, Environmental Adaptation and Gene Variability in Escherichia coli: Correlations between Gene Expression and Gene Variability Reflect Growth Efficiencies. Molecular Biology and Evolution 33, 2515–2529. https://doi.org/10.1093/molbev/msw105.

18. Juanchich, A., Bardou, P., Rué, O., Gabillard, J.-C., Gaspin, C., Bobe, J., and Guiguen, Y. (2016). Characterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing. BMC Genomics 17, 164. https://doi.org/10.1186/s12864-016-2505-9.

19. Richard, F.D., Alves, R., and Kajava, A.V. (2016). Tally: A scoring tool for boundary determination between repetitive and non-repetitive protein sequences. Bioinformatics 32, 1952–1958. https://doi.org/10.1093/bioinformatics/btw118.

20. Vitezica, Z.G., Varona, L., Elsen, J.-M., Misztal, I., Herring, W., and Legarra, A. (2016). Genomic BLUP including additive and dominant variation in purebreds and F1 crossbreds, with an application in pigs. Genetics Selection Evolution 48, 6. https://doi.org/10.1186/s12711-016-0185-1.

21. Zenboudji, S., Cheylan, M., Arnal, V., Bertolero, A., Leblois, R., Astruc, G., Bertorelle, G., Pretus, J.Ll., Lo Valvo, M., Sotgiu, G., and Montgelard, C. (2016). Conservation of the endangered Mediterranean tortoise Testudo hermanni hermanni: The contribution of population genetics and historical demography. Biological Conservation 195, 279–291. https://doi.org/10.1016/j.biocon.2016.01.007.

22. Mariette, J., and Villa-Vialaneix, N. (2016). Aggregating Self-Organizing Maps with Topology Preservation. In Advances in Self-Organizing Maps and Learning Vector Quantization, E. Merényi, M. J. Mendenhall, and P. O’Driscoll, eds. (Springer International Publishing), pp. 27–37. https://doi.org/10.1007/978-3-319-28518-4_2.

23. Pornon, A., Escaravage, N., Burrus, M., Holota, H., Khimoun, A., Mariette, J., Pellizzari, C., Iribar, A., Etienne, R., Taberlet, P., Vidal, M., Winterton, P., Zinger, L., and Andalo, C. (2016). Using metabarcoding to reveal and quantify plant-pollinator interactions. Scientific Reports 6, 27282. https://doi.org/10.1038/srep27282.

24. Mariette, J., Olteanu, M., and Villa-Vialaneix, N. (2017). Efficient interpretable variants of online SOM for large dissimilarity data. Neurocomputing 225, 31–48. https://doi.org/10.1016/j.neucom.2016.11.014.

25. Leroy, T., Roux, C., Villate, L., Bodénès, C., Romiguier, J., Paiva, J.A.P., Dossat, C., Aury, J.-M., Plomion, C., and Kremer, A. (2017). Extensive recent secondary contacts between four European white oak species. New Phytologist 214, 865–878. https://doi.org/10.1111/nph.14413.

26. Eves-van den Akker, S., Laetsch, D.R., Thorpe, P., Lilley, C.J., Danchin, E.G.J., Da Rocha, M., Rancurel, C., Holroyd, N.E., Cotton, J.A., Szitenberg, A., Grenier, E., Montarry, J., Mimee, B., Duceppe, M.-O., Boyes, I., Marvin, J.M.C., Jones, L.M., Yusup, H.B., Lafond-Lapalme, J., Esquibet, M., Sabeh, M., Rott, M., Overmars, H., Finkers-Tomczak, A., Smant, G., Koutsovoulos, G., Blok, V., Mantelin, S., Cock, P.J.A., Phillips, W., Henrissat, B., Urwin, P.E., Blaxter, M., and Jones, J.T. (2016). The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome Biology 17, 124. https://doi.org/10.1186/s13059-016-0985-1.

27. Tusell, L., Gilbert, H., Riquet, J., Mercat, M.-J., Legarra, A., and Larzul, C. (2016). Pedigree and genomic evaluation of pigs using a terminal-cross model. Genetics Selection Evolution 48, 32. https://doi.org/10.1186/s12711-016-0211-3.

28. Brucato, N., Kusuma, P., Cox, M.P., Pierron, D., Purnomo, G.A., Adelaar, A., Kivisild, T., Letellier, T., Sudoyo, H., and Ricaut, F.-X. (2016). Malagasy Genetic Ancestry Comes from an Historical Malay Trading Post in Southeast Borneo. Molecular Biology and Evolution 33, 2396–2400. https://doi.org/10.1093/molbev/msw117.

29. Kusuma, P., Brucato, N., Cox, M.P., Pierron, D., Razafindrazaka, H., Adelaar, A., Sudoyo, H., Letellier, T., and Ricaut, F.-X. (2016). Contrasting Linguistic and Genetic Origins of the Asian Source Populations of Malagasy. Scientific Reports 6, 26066. https://doi.org/10.1038/srep26066.

30. Gentzbittel, L., Ben, C., Mazurier, M., Shin, M.-G., Triska, M., Rickauer, M., Nikolsky, Y., Marjoram, P., Nuzhdin, S., and Tatarinova, T.V. (2016). Whole-genome modeling accurately predicts quantitative traits, as revealed in plants. https://doi.org/10.1101/030395.

31. Damiani, I., Drain, A., Guichard, M., Balzergue, S., Boscari, A., Boyer, J.-C., Brunaud, V., Cottaz, S., Rancurel, C., Da Rocha, M., Fizames, C., Fort, S., Gaillard, I., Maillol, V., Danchin, E.G.J., Rouached, H., Samain, E., Su, Y.-H., Thouin, J., Touraine, B., Puppo, A., Frachisse, J.-M., Pauly, N., and Sentenac, H. (2016). Nod Factor Effects on Root Hair-Specific Transcriptome of Medicago truncatula: Focus on Plasma Membrane Transport Systems and Reactive Oxygen Species Networks. Frontiers in Plant Science 7. https://doi.org/10.3389/fpls.2016.00794.

32. Loubiere, V., Delest, A., Thomas, A., Bonev, B., Schuettengruber, B., Sati, S., Martinez, A.-M., and Cavalli, G. (2016). Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development. Nature Genetics 48, 1436–1442. https://doi.org/10.1038/ng.3671.

33. Lalis, A., Leblois, R., Liefried, S., Ouarour, A., Reddy Beeravolu, C., Michaux, J., Hamani, A., Denys, C., and Nicolas, V. (2016). New molecular data favour an anthropogenic introduction of the wood mouse (Apodemus sylvaticus) in North Africa. Journal of Zoological Systematics and Evolutionary Research 54, 1–12. https://doi.org/10.1111/jzs.12111.