Publications 2016

  1. 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., Danchin E.G.J., Maillol V., Rouached H., Samain E., Su Y-H, Thouin J., Touraine B., Puppo A., Frachisse J-M, Pauly N., Sentenac H.; 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. doi:10.3389/fpls.2016.00794; see
  2. Laurent Gentzbittel, Cécile Ben, Mélanie Mazurier, Min-Gyoung Shin, Martin Triska, Martina Rickauer, Yuri Nikolsky, Paul Marjoram, Sergey Nuzhdin, Tatiana V. Tatarinova; Whole-genome modeling accurately predicts quantitative traits, as revealed in plants; bioRxiv; doi: 10.1101/030395; see
  3. Pradiptajati Kusuma, Nicolas Brucato, Murray P. Cox, Denis Pierron, Harilanto Razafindrazaka, Alexander Adelaar, Herawati Sudoyo, Thierry Letellier & François-Xavier Ricaut; Contrasting Linguistic and Genetic Origins of the Asian Source Populations of Malagasy; Scientific Reports volume 6; doi: 10.1038/srep26066; see
  4. Nicolas Brucato, Pradiptajati Kusuma, Murray P. Cox, Denis Pierron, Gludhug A. Purnomo, Alexander Adelaar, Toomas Kivisild, Thierry Letellier Herawati Sudoyo, François-Xavier Ricaut; Malagasy Genetic Ancestry Comes from an Historical Malay Trading Post in Southeast ; Molecular Biology and Evolution, Volume 33, Issue 9, 1 September 2016, Pages 2396–2400, doi : 10.1093/molbev/msw117; see
  5. Llibertat Tusell, Hélène Gilbert, Juliette Riquet, Marie-José Mercat, Andres Legarra and Catherine Larzul; Pedigree and genomic evaluation of pigs using a terminal-cross model; Genetics Selection Evolution 2016 48:32; doi : 10.1186/s12711-016-0211-3; see
  6. Vincent Loubiere, Anna Delest, Aubin Thomas, Boyan Bonev, Bernd Schuettengruber, Satish Sati, Anne-Marie Martinez & Giacomo Cavalli; Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development; Nature Genetics ; volume 48, pages 1436–1442; doi : 10.1038/ng.3671; see
  7. Eves-van den Akker S, Laetsch DR, Thorpe P, Lilley CJ, Danchin EGJ, Da Rocha M, Rancurel C, Holroyd NE, Cotton JA, Szitenberg A, Grenier E, Montarry J, Mimee B, Duceppe MO, Boyes I, Marvin JM, Jones LM, Yusup HB, Lafond-Lapalme J, Esquibet M, Sabeh M, Rott M, Overmars H, Finkers-Tomczak A, Smant G, Koutsovoulos G, Blok V, Mantelin S, Cock PJ, Phillips W, Henrissat B, Urwin PE, Blaxter M, Jones JT. The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome Biology 17, 124. doi:10.1186/s13059-016-0985-1; see
  8. Magnanou E, Noirot C, Falcón J, Jørgensen EH. Sequencing and characterization of a multi-organ Arctic charr transcriptome: A toolbox for investigating polymorphism and seasonal life in a high Arctic fish. Mar Genomics. 2016 Oct;29:45-53. doi: 10.1016/j.margen.2016.04.006.
  9. Satgé C, Moreau S, Sallet E, Lefort G, Auriac MC, Remblière C, Cottret L, Gallardo K, Noirot C, Jardinaud MF, Gamas P. Reprogramming of DNA methylation is critical for nodule development in Medicago truncatula. Nat Plants. 2016 Oct 31;2(11):16166. doi: 10.1038/nplants.2016.166.
  10. Mazzitelli J-Y, Bonnafe E, Klopp C, Escudier F, Geret F. De novo transcriptome sequencing and analysis of freshwater snail (Radix balthica) to discover genes and pathways affected by exposure to oxazepam. Ecotoxicology. 2016; 1–14. doi:10.1007/s10646-016-1748-1
  11. Hammoumi S, Vallaeys T, Santika A, Leleux P, Borzym E, Klopp C, et al. Targeted genomic enrichment and sequencing of CyHV-3 from carp tissues confirms low nucleotide diversity and mixed genotype infections. PeerJ. 2016;4: e2516. doi:10.7717/peerj.2516
  12. Guellerin M, Passerini D, Fontagné-Faucher C, Robert H, Gabriel V, Loux V, Klopp C, et al. Complete Genome Sequence of Lactococcus lactis subsp. lactis A12, a Strain Isolated from Wheat Sourdough. Genome Announc. 2016;4: e00692-16. doi:10.1128/genomeA.00692-16
  13. Leroy T, Roux C, Villate L, Bodénès C, Romiguier J, Paiva JAP, Dossat C, Aury JM, Plomion C, Kremer A. 2016. Extensive recent secondary contacts between four European white oak species. New Phytologist. see
  14. Jérôme Mariette, Madalina Olteanu, Nathalie Villa-Vialaneix. 2016. Efficient interpretable variants of online SOM for large dissimilarity data. Neurocomputing. doi:10.1016/j.neucom.2016.11.014. see
  15. André Pornon, Nathalie Escaravage, Monique Burrus, Hélène Holota, Aurélie Khimoun, Jérôme Mariette, Charlène Pellizzari, Amaia Iribar, Roselyne Etienne, Pierre Taberlet, Marie Vidal, Peter Winterton, Lucie Zinger & Christophe Andalo. 2016. Using metabarcoding to reveal and quantify plant-pollinator interactions. Scientific Reports 6, Article number: 27282. doi:10.1038/srep27282. see
  16. J Mariette, N Villa-Vialaneix. 2016. Aggregating Self-Organizing Maps with topology preservation. Advances in Self-Organizing Maps and Learning Vector Quantization, 27-37. see
  17. Hurley, B., O’Sullivan, B., Allouche, D., Katsirelos, G., Schiex, T., Zytnicki, M., de Givry, S.: Multi-Language Evaluation of Exact Solvers in Graphical Model Discrete Optimization. In: Proc. of CP-AI-OR’2016. Ban ff, Canada (2016)
  18. Lalis A., R. Leblois, S. Liefried, A. Ouarour, C. Reddy Beeravolu, J. Michaux, A. Hamani, C. Denys, V. Nicolas. 2016. New molecular data favor an anthropogenic introduction of the wood mouse (Apodemus sylvaticus) in North Africa. Journal of Zoological Systematics and Evolutionary Research 54 : 1-12. Doi : 10.1111/jzs.12111. see
  19. Zenboudji S., M. Cheylan, V. Arnal, A. Bertolero, R. Leblois, G. Astruc, G. Bertorelle, J. L. Pretus, M. Lo Valvo, G. Sotgiu, C. Montgelard. 2016. High genetic structure and contrasting demographic history in the endangered Mediterranean tortoise Testudo hermanni hermanni. Biological Conservation 195 : 279–291; doi:10.1016/j.biocon.2016.01.007. see
  20. Lalis A., R. Leblois, E. Stoetzel, T. Benazzou, K. Souttou, C. Denys, V. Nicolas. 2016. Integrating phylogeographic patterns of mtDNA and nDNA divergence to infer the evolutionary history of Meriones shawii (Rodentia: Muridae): a comparison of genetic and fossil data. Biological Journal of the Linean Society, In Press.
  21. Vitezica, Z. G., Varona, L., Elsen, J. M., Misztal, I., Herring, W., & Legarra, A. (2016). Genomic BLUP including additive and dominant variation in purebreds and F1 crossbreds, with an application in pigs. Genetics Selection Evolution, 48(1), 1.see.
  22. Richard, F.D., Alves, R., Kajava, A.V., 2016. Tally: a scoring tool for boundary determination between repetitive and non-repetitive protein sequences. Bioinformatics btw118. doi:10.1093/bioinformatics/btw11. see.
  23. Juanchich A. Bardou P., Rué O., Gabillard JC, Gaspin C., Bobe J., Guigen Y., Chacacterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing. BMC Genomics. 2016 Mar 1;17:164. see.
  24. Feugeas JP, Tourret J, Launay A, Bouvet O, Hoede C, Denamur E, and Tenaillon O. Links between Transcription, Environmental Adaptation and Gene Variability in Escherichia coli: Correlations between Gene Expression and Gene Variability Reflect Growth Efficiencies. Mol Biol Evol first published online June 28, 2016 doi:10.1093/molbev/msw105. see
  25. Boitard, S., Boussaha, M., Capitan, A., Rocha, D., Servin, B. (2016). Uncovering Adaptation from Sequence Data : Lessons from Genome Resequencing of Four Cattle Breeds. Genetics, 203 (1), 433-450. see.
  26. Boitard, S., Rodriguez, W., Jay, F., Mona, S., Austerlitz, F. (2016). Inferring population size history from large samples of genome-wide molecular data – an approximate bayesian computation approach. PLOS Genetics, 12 (3), 1-36. see.
  27. Clémence Chaintreuil, Ronan Rivallan, David J. Bertioli, Christophe Klopp, Jérôme Gouzy, Brigitte Courtois, Philippe Leleux, Guillaume Martin, Jean-François Rami, Djamel Gully, Hugues Parrinello, Dany Séverac, Delphine Patrel, Joël Fardoux, William Ribière, Marc Boursot, Fabienne Cartieaux, Pierre Czernic, Pascal Ratet, Pierre Mournet, Eric Giraud, and Jean-François Arrighi. A gene-based map of the Nod factor-independent Aeschynomene evenia sheds new light on the evolution of nodulation and legume genomes. DNA Res (2016) 23 (4): 365-376. doi:10.1093/dnares/dsw020. see.
  28. Johanne Aubé, Pavel Senin, Olivier ringault, Patricia Bonin, Bruno Deflandre, Olivier Bouchez, Noëlle Bru, Edurne Biritxinaga-Etchart, Christophe Klopp, Rémy Guyoneau, Marisol Goñi-Urriza. The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats. doi:10.1016/j.marpolbul.2016.07.023. see.
  29. Cabau C, Escudié F, Djari A, Guiguen Y, Bobe J, Klopp C. (2016) Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies. PeerJ Preprints 4:e2284v1 see.
  30. Roberto Sierra, Silvia J. Cañas-Duarte, Fabien Burki, Arne Schwelm, Johan Fogelqvist, Christina Dixelius, Laura N. González-García, Gillian H. Gile, Claudio H. Slamovits, Christophe Klopp, Silvia Restrepo, Isabelle Arzul, and Jan Pawlowski. Evolutionary Origins of Rhizarian Parasites. Mol Biol Evol (2016) 33 (4): 980-983. doi:10.1093/molbev/msv340. see.
  31. Bétous R, Renoud ML, Hoede C, Gonzalez I, Jones N, Longy M, Sensebé L, Cazaux C, Hoffmann JS. Human Adipose-Derived Stem Cells Expanded Under Ambient Oxygen Concentration Accumulate Oxidative DNA Lesions and Experience Procarcinogenic DNA Replication Stress. Stem Cells Transl Med. 2016 Aug 24. DOI:10.5966/sctm.2015-0401; see.
  32. Merle C, Leblois R, Rousset F, Pudlo P. Resampling: An improvement of importance sampling in varying population size models. Theor Popul Biol. 2016 Oct 3. doi: 10.1016/j.tpb.2016.09.002; see.
  33. Berthier K., M. Garba, R. Leblois, M. Navascues, C. Tatard, P. Gauthier, S Gagaré, S. Piry, A. Dalecky, A. Loiseau , G. Dobigny. 2016. Black rat invasion of inland Sahel: insights from interviews and population genetics in South Western Niger. Biological Journal of the Linean Society 119:748–765. see.