Publications 2016

  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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)
  • 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
  • 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
  • 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.
  • 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.
  • 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.
  • 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.
  • 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
  • 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.
  • 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.
  • 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.
  • 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.
  • 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 https://doi.org/10.7287/peerj.preprints.2284v1. see.
  • 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.
  • 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.
  • 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.