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.

2017

1. Givry, S. de, and Katsirelos, G. (2017). Clique Cuts in Weighted Constraint Satisfaction. In Principles and Practice of Constraint Programming, J. C. Beck, ed. (Springer International Publishing), pp. 97–113. https://doi.org/10.1007/978-3-319-66158-2_7.

2. Ouali, A., Allouche, D., Givry, S. de, Loudni, S., Lebbah, Y., Eckhardt, F., and Loukil, L. (2017). Iterative Decomposition Guided Variable Neighborhood Search for Graphical Model Energy Minimization. In Conference on Uncertainty in Artificial Intelligence, UAI 2017.

3. 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.

4. Lippens, C., Estoup, A., Hima, M.K., Loiseau, A., Tatard, C., Dalecky, A., Bâ, K., Kane, M., Diallo, M., Sow, A., Niang, Y., Piry, S., Berthier, K., Leblois, R., Duplantier, J.-M., and Brouat, C. (2017). Genetic structure and invasion history of the house mouse (Mus musculus domesticus) in Senegal, West Africa: A legacy of colonial and contemporary times. Heredity 119, 64–75. https://doi.org/10.1038/hdy.2017.18.

5. Navascués, M., Leblois, R., and Burgarella, C. (2017). Demographic inference through approximate-Bayesian-computation skyline plots. PeerJ 5, e3530. https://doi.org/10.7717/peerj.3530.

6. Bonnet, T., Leblois, R., Rousset, F., and Crochet, P.-A. (2017). A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes. Evolution 71, 2140–2158. https://doi.org/10.1111/evo.13296.

7. Leblois, R., Gautier, M., Rohfritsch, A., Foucaud, J., Burban, C., Galan, M., Loiseau, A., Sauné, L., Branco, M., Gharbi, K., Vitalis, R., and Kerdelhué, C. (2018). Deciphering the demographic history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa. Molecular Ecology 27, 264–278. https://doi.org/10.1111/mec.14411.

8. Wereszczuk, A., Leblois, R., and Zalewski, A. (2017). Genetic diversity and structure related to expansion history and habitat isolation: Stone marten populating rural–urban habitats. BMC Ecology 17, 46. https://doi.org/10.1186/s12898-017-0156-6.

9. 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 134, 441–452. https://doi.org/10.1111/jbg.12284.

10. Roselli, S., Olry, A., Vautrin, S., Coriton, O., Ritchie, D., Galati, G., Navrot, N., Krieger, C., Vialart, G., Bergès, H., Bourgaud, F., and Hehn, A. (2017). A bacterial artificial chromosome (BAC) genomic approach reveals partial clustering of the furanocoumarin pathway genes in parsnip. The Plant Journal 89, 1119–1132. https://doi.org/10.1111/tpj.13450.

11. 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.

12. Brucato, N., Kusuma, P., Beaujard, P., Sudoyo, H., Cox, M.P., and Ricaut, F.-X. (2017). Genomic admixture tracks pulses of economic activity over 2,000 years in the Indian Ocean trading network. Scientific Reports 7, 2919. https://doi.org/10.1038/s41598-017-03204-y.

13. Tannous, J., Snini, S.P., El Khoury, R., Canlet, C., Pinton, P., Lippi, Y., Alassane-Kpembi, I., Gauthier, T., El Khoury, A., Atoui, A., Zhou, T., Lteif, R., Oswald, I.P., and Puel, O. (2017). Patulin transformation products and last intermediates in its biosynthetic pathway, E- and Z-ascladiol, are not toxic to human cells. Archives of Toxicology 91, 2455–2467. https://doi.org/10.1007/s00204-016-1900-y.

14. Heinze, K., Frank, X., Lullien-Pellerin, V., George, M., Radjai, F., and Delenne, J.-Y. (2017). Numerical modeling of the tensile strength of a biological granular aggregate: Effect of the particle size distribution. EPJ Web of Conferences 140, 08013. https://doi.org/10.1051/epjconf/201714008013.

15. Ployet, R., Soler, M., Carocha, V., Ladouce, N., Alves, A., Rodrigues, J.-C., Harvengt, L., Marque, C., Teulières, C., Grima-Pettenati, J., and Mounet, F. (2018). Long cold exposure induces transcriptional and biochemical remodelling of xylem secondary cell wall in Eucalyptus. Tree Physiology 38, 409–422. https://doi.org/10.1093/treephys/tpx062.

16. Xiang, T., Christensen, O.F., and Legarra, A. (2017). Technical note: Genomic evaluation for crossbred performance in a single-step approach with metafounders1. Journal of Animal Science 95, 1472–1480. https://doi.org/10.2527/jas.2016.1155.

17. Delrieu-Trottin, E., Mona, S., Maynard, J., Neglia, V., Veuille, M., and Planes, S. (2017). Population expansions dominate demographic histories of endemic and widespread Pacific reef fishes. Scientific Reports 7, 40519. https://doi.org/10.1038/srep40519.

18. Krasovec, M., Eyre-Walker, A., Sanchez-Ferandin, S., and Piganeau, G. (2017). Spontaneous Mutation Rate in the Smallest Photosynthetic Eukaryotes. Molecular Biology and Evolution 34, 1770–1779. https://doi.org/10.1093/molbev/msx119.

19. 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.

20. Traoré, S., Allouche, D., André, I., Schiex, T., and Barbe, S. (2017). Deterministic Search Methods for Computational Protein Design. In Computational Protein Design, I. Samish, ed. (Springer), pp. 107–123. https://doi.org/10.1007/978-1-4939-6637-0_4.

21. Blanc-Mathieu, R., Perfus-Barbeoch, L., Aury, J.-M., Rocha, M.D., Gouzy, J., Sallet, E., Martin-Jimenez, C., Bailly-Bechet, M., Castagnone-Sereno, P., Flot, J.-F., Kozlowski, D.K., Cazareth, J., Couloux, A., Silva, C.D., Guy, J., Kim-Jo, Y.-J., Rancurel, C., Schiex, T., Abad, P., Wincker, P., and Danchin, E.G.J. (2017). Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes. PLOS Genetics 13, e1006777. https://doi.org/10.1371/journal.pgen.1006777.

22. Frank, X., Delenne, J.-Y., and Radjai, F. (2017). Numerical study of the failure of materials embedding soft to hard particles. EPJ Web of Conferences 140, 02029. https://doi.org/10.1051/epjconf/201714002029.

23. Blanc, N., Frank, X., Mayer-Laigle, C., Radjaï, F., and Delenne, J.-Y. (2017). Peridynamics simulation of the comminution of particles containing microcraks. EPJ Web of Conferences 140, 07018. https://doi.org/10.1051/epjconf/201714007018.

24. Cochetel, N., Escudié, F., Cookson, S.J., Dai, Z., Vivin, P., Bert, P.-F., Muñoz, M.S., Delrot, S., Klopp, C., Ollat, N., and Lauvergeat, V. (2017). Root transcriptomic responses of grafted grapevines to heterogeneous nitrogen availability depend on rootstock genotype. Journal of Experimental Botany 68, 4339–4355. https://doi.org/10.1093/jxb/erx224.

25. Kocher, A., Thoisy, B. de, Catzeflis, F., Huguin, M., Valière, S., Zinger, L., Bañuls, A.-L., and Murienne, J. (2017). Evaluation of short mitochondrial metabarcodes for the identification of Amazonian mammals. Methods in Ecology and Evolution 8, 1276–1283. https://doi.org/10.1111/2041-210X.12729.

26. Comtet-Marre, S., Parisot, N., Lepercq, P., Chaucheyras-Durand, F., Mosoni, P., Peyretaillade, E., Bayat, A.R., Shingfield, K.J., Peyret, P., and Forano, E. (2017). Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet. Frontiers in Microbiology 8. https://doi.org/10.3389/fmicb.2017.00067.

27. Peccoud, J., Loiseau, V., Cordaux, R., and Gilbert, C. (2017). Massive horizontal transfer of transposable elements in insects. Proceedings of the National Academy of Sciences 114, 4721–4726. https://doi.org/10.1073/pnas.1621178114.

28. Rougemont, Q., Gagnaire, P.-A., Perrier, C., Genthon, C., Besnard, A.-L., Launey, S., and Evanno, G. (2017). Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes. Molecular Ecology 26, 142–162. https://doi.org/10.1111/mec.13664.

29. Laurent, B., Palaiokostas, C., Spataro, C., Moinard, M., Zehraoui, E., Houston, R.D., and Foulongne-Oriol, M. (2018). High-resolution mapping of the recombination landscape of the phytopathogen Fusarium graminearum suggests two-speed genome evolution. Molecular Plant Pathology 19, 341–354. https://doi.org/10.1111/mpp.12524.

30. Simoncini, D., Schiex, T., and Zhang, K.Y.J. (2017). Balancing exploration and exploitation in population-based sampling improves fragment-based de novo protein structure prediction. Proteins: Structure, Function, and Bioinformatics 85, 852–858. https://doi.org/10.1002/prot.25244.

31. Mallet, L., Bitard-Feildel, T., Cerutti, F., and Chiapello, H. (2017). PhylOligo: A package to identify contaminant or untargeted organism sequences in genome assemblies. Bioinformatics 33, 3283–3285. https://doi.org/10.1093/bioinformatics/btx396.

32. Kocher, A., Gantier, J.-C., Gaborit, P., Zinger, L., Holota, H., Valiere, S., Dusfour, I., Girod, R., Bañuls, A.-L., and Murienne, J. (2017). Vector soup: High-throughput identification of Neotropical phlebotomine sand flies using metabarcoding. Molecular Ecology Resources 17, 172–182. https://doi.org/10.1111/1755-0998.12556.

33. Payton, L., Perrigault, M., Hoede, C., Massabuau, J.-C., Sow, M., Huvet, A., Boullot, F., Fabioux, C., Hegaret, H., and Tran, D. (2017). Remodeling of the cycling transcriptome of the oyster Crassostrea gigas by the harmful algae Alexandrium minutum. Scientific Reports 7, 3480. https://doi.org/10.1038/s41598-017-03797-4.

34. Badouin, H., Gouzy, J., Grassa, C.J., Murat, F., Staton, S.E., Cottret, L., Lelandais-Brière, C., Owens, G.L., Carrère, S., Mayjonade, B., Legrand, L., Gill, N., Kane, N.C., Bowers, J.E., Hubner, S., Bellec, A., Bérard, A., Bergès, H., Blanchet, N., Boniface, M.-C., Brunel, D., Catrice, O., Chaidir, N., Claudel, C., Donnadieu, C., Faraut, T., Fievet, G., Helmstetter, N., King, M., Knapp, S.J., Lai, Z., Le Paslier, M.-C., Lippi, Y., Lorenzon, L., Mandel, J.R., Marage, G., Marchand, G., Marquand, E., Bret-Mestries, E., Morien, E., Nambeesan, S., Nguyen, T., Pegot-Espagnet, P., Pouilly, N., Raftis, F., Sallet, E., Schiex, T., Thomas, J., Vandecasteele, C., Varès, D., Vear, F., Vautrin, S., Crespi, M., Mangin, B., Burke, J.M., Salse, J., Muños, S., Vincourt, P., Rieseberg, L.H., and Langlade, N.B. (2017). The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution. Nature 546, 148–152. https://doi.org/10.1038/nature22380.

35. Freitas Castro, F., Ruy, P.C., Nogueira Zeviani, K., Freitas Santos, R., Simões Toledo, J., and Kaysel Cruz, A. (2017). Evidence of putative non-coding RNAs from leishmania untranslated regions. Molecular and Biochemical Parasitology 214, 69–74. https://doi.org/10.1016/j.molbiopara.2017.04.002.

36. García-Baccino, C.a., Munilla, S., Legarra, A., Vitezica, Z.g., Forneris, N.s., Bates, R.o., Ernst, C.w., Raney, N.e., Steibel, J.p., and Cantet, R.j.c. (2017). Estimates of the actual relationship between half-sibs in a pig population. Journal of Animal Breeding and Genetics 134, 109–118. https://doi.org/10.1111/jbg.12236.

37. Garcia-Baccino, C.A., Legarra, A., Christensen, O.F., Misztal, I., Pocrnic, I., Vitezica, Z.G., and Cantet, R.J.C. (2017). Metafounders are related to Fst fixation indices and reduce bias in single-step genomic evaluations. Genetics Selection Evolution 49, 34. https://doi.org/10.1186/s12711-017-0309-2.

38. Bécavin, C., Koutero, M., Tchitchek, N., Cerutti, F., Lechat, P., Maillet, N., Hoede, C., Chiapello, H., Gaspin, C., and Cossart, P. (2017). Listeriomics: An Interactive Web Platform for Systems Biology of Listeria. mSystems 2, 10.1128/msystems.00186–16. https://doi.org/10.1128/msystems.00186-16.

39. Rzeznik-Orignac, J., Kalenitchenko, D., Mariette, J., Bodiou, J.-Y., Le Bris, N., and Derelle, E. (2017). Comparison of meiofaunal diversity by combined morphological and molecular approaches in a shallow Mediterranean sediment. Marine Biology 164, 40. https://doi.org/10.1007/s00227-017-3074-4.

40. 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.

41. Ciabrelli, F., Comoglio, F., Fellous, S., Bonev, B., Ninova, M., Szabo, Q., Xuéreb, A., Klopp, C., Aravin, A., Paro, R., Bantignies, F., and Cavalli, G. (2017). Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila. Nature Genetics 49, 876–886. https://doi.org/10.1038/ng.3848.

42. 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.

43. Mercière, M., Boulord, R., Carasco-Lacombe, C., Klopp, C., Lee, Y.-P., Tan, J.-S., Syed Alwee, S.S.R., Zaremski, A., De Franqueville, H., Breton, F., and Camus-Kulandaivelu, L. (2017). 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 121, 529–540. https://doi.org/10.1016/j.funbio.2017.01.001.

44. Murat, F., Armero, A., Pont, C., Klopp, C., and Salse, J. (2017). Reconstructing the genome of the most recent common ancestor of flowering plants. Nature Genetics 49, 490–496. https://doi.org/10.1038/ng.3813.

45. Nouwen, N., Arrighi, J.-F., Cartieaux, F., Chaintreuil, C., Gully, D., Klopp, C., and Giraud, E. (2017). The role of rhizobial (NifV) and plant (FEN1) homocitrate synthases in Aeschynomene/photosynthetic Bradyrhizobium symbiosis. Scientific Reports 7, 448. https://doi.org/10.1038/s41598-017-00559-0.

46. Panicz, R., Klopp, C., Igielski, R., Hofsoe, P., Sadowski, J., and Coller, J.A. (2017). Tench (tinca tinca) high-throughput transcriptomics reveal feed dependent gut profiles. Aquaculture 479, 200–207. https://doi.org/10.1016/j.aquaculture.2017.05.047.

47. Patrascu, O., Béguet-Crespel, F., Marinelli, L., Le Chatelier, E., Abraham, A.-L., Leclerc, M., Klopp, C., Terrapon, N., Henrissat, B., Blottière, H.M., Doré, J., and Béra-Maillet, C. (2017). A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic. Scientific Reports 7, 40248. https://doi.org/10.1038/srep40248.

48. Goñi Urriza, M., Gassie, C., Bouchez, O., Klopp, C., and Guyoneaud, R. (2017). Draft Genome Sequence of Desulfovibrio BerOc1, a Mercury-Methylating Strain. Genome Announcements 5, 10.1128/genomea.01483–16. https://doi.org/10.1128/genomea.01483-16.

49. Belkorchia, A., Pombert, J.-F., Polonais, V., Parisot, N., Delbac, F., Brugère, J.-F., Peyret, P., Gaspin, C., and Peyretaillade, E. (2017). Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes. DNA Research 24, 251–260. https://doi.org/10.1093/dnares/dsx002.

50. Auer, L., Mariadassou, M., O’Donohue, M., Klopp, C., and Hernandez-Raquet, G. (2017). Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description. Molecular Ecology Resources 17, e122–e132. https://doi.org/10.1111/1755-0998.12700.

51. Durrens, P., Klopp, C., Biteau, N., Fitton-Ouhabi, V., Dementhon, K., Accoceberry, I., Sherman, D.J., and Noël, T. (2017). Genome Sequence of the Yeast Clavispora lusitaniae Type Strain CBS 6936. Genome Announcements 5, 10.1128/genomea.00724–17. https://doi.org/10.1128/genomea.00724-17.

52. Caldelari, I., Chane-Woon-Ming, B., Noirot, C., Moreau, K., Romby, P., Gaspin, C., and Marzi, S. (2017). Complete Genome Sequence and Annotation of the Staphylococcus aureus Strain HG001. Genome Announcements 5, 10.1128/genomea.00783–17. https://doi.org/10.1128/genomea.00783-17.

53. Pérez-Pascual, D., Lunazzi, A., Magdelenat, G., Rouy, Z., Roulet, A., Lopez-Roques, C., Larocque, R., Barbeyron, T., Gobet, A., Michel, G., Bernardet, J.-F., and Duchaud, E. (2017). The Complete Genome Sequence of the Fish Pathogen Tenacibaculum maritimum Provides Insights into Virulence Mechanisms. Frontiers in Microbiology 8. https://doi.org/10.3389/fmicb.2017.01542.

54. Mariette, J., and Villa-Vialaneix, N. (2018). Unsupervised multiple kernel learning for heterogeneous data integration. Bioinformatics 34, 1009–1015. https://doi.org/10.1093/bioinformatics/btx682.

55. Urrestarazu, J., Muranty, H., Denancé, C., Leforestier, D., Ravon, E., Guyader, A., Guisnel, R., Feugey, L., Aubourg, S., Celton, J.-M., Daccord, N., Dondini, L., Gregori, R., Lateur, M., Houben, P., Ordidge, M., Paprstein, F., Sedlak, J., Nybom, H., Garkava-Gustavsson, L., Troggio, M., Bianco, L., Velasco, R., Poncet, C., Théron, A., Moriya, S., Bink, M.C.A.M., Laurens, F., Tartarini, S., and Durel, C.-E. (2017). Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple. Frontiers in Plant Science 8. https://doi.org/10.3389/fpls.2017.01923.

56. Boher, P., Soler, M., Sánchez, A., Hoede, C., Noirot, C., Paiva, J.A.P., Serra, O., and Figueras, M. (2018). A comparative transcriptomic approach to understanding the formation of cork. Plant Molecular Biology 96, 103–118. https://doi.org/10.1007/s11103-017-0682-9.

57. Bestion, E., Jacob, S., Zinger, L., Di Gesu, L., Richard, M., White, J., and Cote, J. (2017). Climate warming reduces gut microbiota diversity in a vertebrate ectotherm. Nature Ecology & Evolution 1, 0161. https://doi.org/10.1038/s41559-017-0161.

58. Cerutti, F., Mallet, L., Painset, A., Hoede, C., Moisan, A., Bécavin, C., Duval, M., Dussurget, O., Cossart, P., Gaspin, C., and Chiapello, H. (2017). Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria. BMC Genomics 18, 882. https://doi.org/10.1186/s12864-017-4242-0.

59. Rancurel, C., Legrand, L., and Danchin, E.G.J. (2017). Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life. Genes 8, 248. https://doi.org/10.3390/genes8100248.

60. Danchin, E.G.J., Perfus-Barbeoch, L., Rancurel, C., Thorpe, P., Da Rocha, M., Bajew, S., Neilson, R., (Guzeeva), E.S., Da Silva, C., Guy, J., Labadie, K., Esmenjaud, D., Helder, J., Jones, J.T., and Den Akker, S.E. (2017). The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes. Genes 8, 287. https://doi.org/10.3390/genes8100287.

61. Mona, S. (2017). On the role played by the carrying capacity and the ancestral population size during a range expansion. Heredity 118, 143–153. https://doi.org/10.1038/hdy.2016.73.

62. Kusuma, P., Brucato, N., Cox, M.P., Letellier, T., Manan, A., Nuraini, C., Grangé, P., Sudoyo, H., and Ricaut, F.-X. (2017). The last sea nomads of the Indonesian archipelago: Genomic origins and dispersal. European Journal of Human Genetics 25, 1004–1010. https://doi.org/10.1038/ejhg.2017.88.

63. Benazzo, A., Trucchi, E., Cahill, J.A., Maisano Delser, P., Mona, S., Fumagalli, M., Bunnefeld, L., Cornetti, L., Ghirotto, S., Girardi, M., Ometto, L., Panziera, A., Rota-Stabelli, O., Zanetti, E., Karamanlidis, A., Groff, C., Paule, L., Gentile, L., Vilà, C., Vicario, S., Boitani, L., Orlando, L., Fuselli, S., Vernesi, C., Shapiro, B., Ciucci, P., and Bertorelle, G. (2017). Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers. Proceedings of the National Academy of Sciences 114, E9589–E9597. https://doi.org/10.1073/pnas.1707279114.

64. Thouzeau, V., Mennecier, P., Verdu, P., and Austerlitz, F. (2017). Genetic and linguistic histories in Central Asia inferred using approximate Bayesian computations. Proceedings of the Royal Society B: Biological Sciences 284, 20170706. https://doi.org/10.1098/rspb.2017.0706.

65. Teyssier, A., Rouffaer, L.O., Saleh Hudin, N., Strubbe, D., Matthysen, E., Lens, L., and White, J. (2018). Inside the guts of the city: Urban-induced alterations of the gut microbiota in a wild passerine. Science of The Total Environment 612, 1276–1286. https://doi.org/10.1016/j.scitotenv.2017.09.035.