Publications 2019

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

  1. Aubin Thomas, Sylvain Barriere, Lucile Broseus, Julie Brooke, Claudio Lorenzi, Jean-Philippe Villemin, Gregory Beurier, Robert Sabatier, Christelle Reynes, Alban Mancheron & William Ritchie ; GECKO is a genetic algorithm to classify and explore high throughput sequencing data ; Communications Biology, 2; 222; doi : 10.1038/s42003-019-0456-9. see
  2. Astrid Cruaud Sabine Nidelet Pierre Arnal Audrey Weber Lucian Fusu Alex Gumovsky John Huber Andrew Polaszek Jean‐Yves Rasplus; Optimised DNA extraction and library preparation for minute arthropods: application to target enrichment in chalcid wasps used for biocontrol; Molecular Ecology Resources; doi : 10.1111/1755-0998.13006. see
  3. Aude Lalis, Stefano Mona, Emmanuelle Stoetzel, François Bonhomme, Karim Souttou, Ali Ouarour, Stéphane Aulagnier, Christiane Denys & Violaine Nicolas; Out of Africa: demographic and colonization history of the Algerian mouse (Mus spretus Lataste); Heredity volume 122, pages 150–171; doi: 10.1038/s41437-018-0089-7. see
  4. Eric Pante, Vanessa Becquet, Amélia Viricel, Pascale Garcia; Investigation of the molecular signatures of selection on ATP synthase genes in the marine bivalve Limecola balthica; Aquat. Living Resour. 32 3; doi: 10.1051/alr/2019001. see
  5. Marie Vagner, Eric Pante, Amelia Viricel, Thomas Lacoue-Labarthe, Jose-Luis Zambonino-Infante, Patrick Quazuguel, Emmanuel Dubillot, Valerie Huet, Herve Le Delliou, Christel Lefrançois, Nathalie Imbert-Auvray; Ocean warming combined with lower omega-3 nutritional availability impairs the cardio-respiratory function of a marine fish; Journal of Experimental Biology; doi: 10.1242/jeb.187179. see
  6. Nagnan-Le Meillour P, Descamps A, Le Danvic C, Grandmougin M, Saliou JM, Klopp C, Milhes M, Bompard C, Chesneau D, Poissenot K, Keller M. Identification of potential chemosignals in the European water vole Arvicola terrestris. Sci Rep. 2019 Dec 5;9(1):18378. doi: 10.1038/s41598-019-54935-z. PubMed PMID: 31804568.
  7. Dalmon A, Gayral P, Decante D, Klopp C, Bigot D, Thomasson M, Herniou EA, Alaux C, Le Conte Y. Viruses in the Invasive Hornet Vespa velutina. Viruses. 2019 Nov 8;11(11). pii: E1041. doi: 10.3390/v11111041. PubMed PMID: 31717432.
  8. Kottler VA, Feron R, Nanda I, Klopp C, Du K, Kneitz S, Helmprobst F, Lamatsch DK, Lopez-Roques C, Lluch J, Journot L, Parrinello H, Guiguen Y, Schartl M. Independent Origin of XY and ZW Sex Determination Mechanisms in Mosquitofish Sister Species. Genetics. 2019 Nov 8. pii: genetics.302698.2019. doi:10.1534/genetics.119.302698. [Epub ahead of print] PubMed PMID: 31704715.
  9. Goñi-Urriza M, Klopp C, Ranchou-Peyruse M, Ranchou-Peyruse A, Monperrus M, Khalfaoui-Hassani B, Guyoneaud R. Genome insights of mercury methylation among Desulfovibrio and Pseudodesulfovibrio strains. Res Microbiol. 2019 Oct 23. pii: S0923-2508(19)30121-4. doi: 10.1016/j.resmic.2019.10.003. [Epub ahead of print] PubMed PMID: 31655199.
  10. Péden R, Poupin P, Sohm B, Flayac J, Giambérini L, Klopp C, Louis F, Pain-Devin S, Potet M, Serre RF, Devin S. Environmental transcriptomes of invasive dreissena, a model species in ecotoxicology and invasion biology. Sci Data. 2019 Oct 25;6(1):234. doi: 10.1038/s41597-019-0252-x. PubMed PMID: 31653851; PubMed Central PMCID: PMC6814772.
  11. Striberny A, Jørgensen EH, Klopp C, Magnanou E. Arctic charr brain transcriptome strongly affected by summer seasonal growth but only subtly by feed deprivation. BMC Genomics. 2019 Jun 27;20(1):529. doi: 10.1186/s12864-019-5874-z. PubMed PMID: 31248377; PubMed Central PMCID: PMC6598377.
  12. Ipoutcha T, Tsarmpopoulos I, Talenton V, Gaspin C, Moisan A, Walker CA, Brownlie J, Blanchard A, Thebault P, Sirand-Pugnet P. Multiple Origins and Specific Evolution of CRISPR/Cas9 Systems in Minimal Bacteria (Mollicutes). Front Microbiol. 2019 Nov 21;10:2701. doi: 10.3389/fmicb.2019.02701. eCollection 2019. PubMed PMID: 31824468; PubMed Central PMCID: PMC6882279.
  13. Polonais V, Niehus S, Wawrzyniak I, Franchet A, Gaspin C, Belkorchia A, Reichstadt M, Belser C, Labadie K, Couloux A, Delbac F, Peyretaillade E, Ferrandon D. Draft Genome Sequence of Tubulinosema ratisbonensis, a Microsporidian Species Infecting the Model Organism Drosophila melanogaster. Microbiol Resour Announc. 2019 Aug 1;8(31). pii: e00077-19. doi:10.1128/MRA.00077-19. PubMed PMID: 31371528; PubMed Central PMCID: PMC6675976.
  14. Savelli B, Li Q, Webber M, Jemmat AM, Robitaille A, Zamocky M, Mathé C, Dunand C. RedoxiBase: A database for ROS homeostasis regulated proteins. Redox Biol. 2019 Sep;26:101247. doi: 10.1016/j.redox.2019.101247. Epub 2019 Jun 6. PubMed PMID: 31228650; PubMed Central PMCID: PMC6597783.
  15. Croce S, Lesluyes T, Delespaul L, Bonhomme B, Pérot G, Velasco V, Mayeur L, Rebier F, Ben Rejeb H, Guyon F, McCluggage WG, Floquet A, Querleu D, Chakiba C, Devouassoux-Shisheboran M, Mery E, Arnould L, Averous G, Soubeyran I, Le Guellec S, Chibon F. GREB1-CTNNB1 fusion transcript detected by RNA-sequencing in a uterine tumor resembling ovarian sex cord tumor (UTROSCT): A novel CTNNB1 rearrangement. Genes Chromosomes Cancer. 2019 Mar;58(3):155-163. doi: 10.1002/gcc.22694. Epub 2019 Jan 7. PubMed PMID: 30350331.
  16. Robic A, Morisson M, Leroux S, Gourichon D, Vignal A, Thebault N, Fillon V, Minvielle F, Bed’Hom B, Zerjal T, Pitel F. Two new structural mutations in the 5′ region of the ASIP gene cause diluted feather color phenotypes in Japanese quail. Genet Sel Evol. 2019 Apr 15;51(1):12. doi: 10.1186/s12711-019-0458-6. PubMed PMID: 30987584; PubMed Central PMCID: PMC6466734.
  17. Robic A, Faraut T, Djebali S, Weikard R, Feve K, Maman S, Kuehn C. Analysis of pig transcriptomes suggests a global regulation mechanism enabling temporary bursts of circular RNAs. RNA Biol. 2019 Sep;16(9):1190-1204. doi:10.1080/15476286.2019.1621621. Epub 2019 Jun 3. PubMed PMID: 31120323; PubMed Central PMCID: PMC6693536.
  18. Milon N, Fuentes Rojas JL, Castinel A, Bigot L, Bouwmans G, Baudelle K, Boutonnet A, Gibert A, Bouchez O, Donnadieu C, Ginot F, Bancaud A. A tunable filter for high molecular weight DNA selection and linked-read sequencing. Lab Chip. 2020 Jan 7;20(1):175-184. doi: 10.1039/c9lc00965e. Epub 2019 Dec 4. PubMed PMID: 31796946.
  19. Godefroid M, Meseguer AS, Sauné L, Genson G, Streito JC, Rossi JP, Zaldívar Riverón A, Mayer F, Cruaud A, Rasplus JY. Restriction-site associated DNA markers provide new insights into the evolutionary history of the bark beetle genus Dendroctonus. Mol Phylogenet Evol. 2019 Oct;139:106528. doi:10.1016/j.ympev.2019.106528. Epub 2019 Jun 6. PubMed PMID: 31176966.
  20. Girollet N, Rubio B, Lopez-Roques C, Valière S, Ollat N, Bert PF. De novo phased assembly of the Vitis riparia grape genome. Sci Data. 2019 Jul 19;6(1):127. doi: 10.1038/s41597-019-0133-3. Erratum in: Sci Data. 2019 Oct 30;6(1):249. PubMed PMID: 31324816; PubMed Central PMCID: PMC6642119.
  21. Dardaillon J, Dauga D, Simion P, Faure E, Onuma TA, DeBiasse MB, Louis A, Nitta KR, Naville M, Besnardeau L, Reeves W, Wang K, Fagotto M, Guéroult-Bellone M, Fujiwara S, Dumollard R, Veeman M, Volff JN, Roest Crollius H, Douzery E, Ryan JF, Davidson B, Nishida H, Dantec C, Lemaire P. ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates. Nucleic Acids Res. 2019 Nov 4. pii: gkz955. doi: 10.1093/nar/gkz955. [Epub ahead of print] PubMed PMID:31680137.
  22. Dussert Y, Mazet ID, Couture C, Gouzy J, Piron MC, Kuchly C, Bouchez O, Rispe C, Mestre P, Delmotte F. A High-Quality Grapevine Downy Mildew Genome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes. Genome Biol Evol. 2019 Mar 1;11(3):954-969. doi: 10.1093/gbe/evz048. PubMed PMID:30847481; PubMed Central PMCID: PMC6660063.
  23. De Jode A, David R, Haguenauer A, Cahill AE, Erga Z, Guillemain D, Sartoretto S, Rocher C, Selva M, Le Gall L, Féral JP, Chenuil A. From seascape ecology to population genomics and back. Spatial and ecological differentiation among cryptic species of the red algae Lithophyllum stictiforme/L. cabiochiae, main bioconstructors of coralligenous habitats. Mol Phylogenet Evol. 2019 Aug;137:104-113. doi: 10.1016/j.ympev.2019.04.005. Epub 2019 Apr 2. PubMed PMID:30951921.
  24. Maisano Delser P, Corrigan S, Duckett D, Suwalski A, Veuille M, Planes S, Naylor GJP, Mona S. Demographic inferences after a range expansion can be biased: the test case of the blacktip reef shark (Carcharhinus melanopterus). Heredity (Edinb). 2019 Jun;122(6):759-769. doi: 10.1038/s41437-018-0164-0. Epub 2018 Nov 21. PubMed PMID: 30459340; PubMed Central PMCID: PMC6781168.
  25. Cruaud A, Nidelet S, Arnal P, Weber A, Fusu L, Gumovsky A, Huber J, Polaszek A, Rasplus JY. Optimized DNA extraction and library preparation for minute arthropods: Application to target enrichment in chalcid wasps used for biocontrol. Mol Ecol Resour. 2019 May;19(3):702-710. doi:10.1111/1755-0998.13006. PubMed PMID: 30758892.
  26. Bouteiller XP, Verdu CF, Aikio E, Bloese P, Dainou K, Delcamp A, De Thier O, Guichoux E, Mengal C, Monty A, Pucheu M, van Loo M, Josée Porté A, Lassois L, Mariette S. A few north Appalachian populations are the source of European black locust. Ecol Evol. 2019 Feb 16;9(5):2398-2414. doi: 10.1002/ece3.4776. eCollection 2019 Mar. PubMed PMID: 30891188; PubMed Central PMCID: PMC6405530.
  27. Le Boulch M, Déhais P, Combes S, Pascal G. The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups. Database (Oxford). 2019 Jan 1;2019. pii: baz049. doi: 10.1093/database/baz049. PubMed PMID: 31032842; PubMed Central PMCID: PMC6487390.
  28. Vignal A, Boitard S, Thébault N, Dayo GK, Yapi-Gnaore V, Youssao Abdou Karim I, Berthouly-Salazar C, Pálinkás-Bodzsár N, Guémené D, Thibaud-Nissen F, Warren WC, Tixier-Boichard M, Rognon X. A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes. Mol Ecol Resour. 2019 Jul;19(4):997-1014. doi: 10.1111/1755-0998.13017. Epub 2019 May 5. PubMed PMID: 30945415; PubMed Central PMCID: PMC6579635.
  29. Dordet-Frisoni E, Faucher M, Sagné E, Baranowski E, Tardy F, Nouvel LX, Citti C. Mycoplasma Chromosomal Transfer: A Distributive, Conjugative Process Creating an Infinite Variety of Mosaic Genomes. Front Microbiol. 2019 Oct 23;10:2441. doi: 10.3389/fmicb.2019.02441. eCollection 2019. PubMed PMID: 31708906; PubMed Central PMCID: PMC6819513.
  30.  Ambroise C, Dehman A, Neuvial P, Rigaill G, Vialaneix N. Adjacency-constrained hierarchical clustering of a band similarity matrix with application to genomics. Algorithms Mol Biol. 2019 Nov 15;14:22. doi: 10.1186/s13015-019-0157-4. eCollection 2019. PubMed PMID: 31807137; PubMed Central PMCID: PMC6857244.
  31. Hérault F, Houée-Bigot M, Baéza E, Bouchez O, Esquerré D, Klopp C, Diot C. RNA-seq analysis of hepatic gene expression of common Pekin, Muscovy, mule and hinny ducks fed ad libitum or overfed. BMC Genomics. 2019 Jan 7;20(1):13. doi: 10.1186/s12864-018-5415-1. PubMed PMID: 30616512; PubMed Central PMCID:PMC6323773.
  32. Fusade-Boyer M, Pato PS, Komlan M, Dogno K, Jeevan T, Rubrum A, Kouakou CK, Couacy-Hymann E, Batawui D, Go-Maro E, McKenzie P, Webby RJ, Ducatez MF. Evolution of Highly Pathogenic Avian Influenza A(H5N1) Virus in Poultry, Togo, 2018. Emerg Infect Dis. 2019 Dec;25(12):2287-2289. doi: 10.3201/eid2512.190054. PubMed PMID: 31742528; PubMed Central PMCID: PMC6874233.
  33. Willemsen A, Bravo IG. Origin and evolution of papillomavirus (onco)genes and genomes. Philos Trans R Soc Lond B Biol Sci. 2019 May 27;374(1773):20180303. doi: 10.1098/rstb.2018.0303. PubMed PMID: 30955499; PubMed Central PMCID: PMC6501903.
  34. Pan Q, Feron R, Yano A, Guyomard R, Jouanno E, Vigouroux E, Wen M, Busnel JM, Bobe J, Concordet JP, Parrinello H, Journot L, Klopp C, Lluch J, Roques C, Postlethwait J, Schartl M, Herpin A, Guiguen Y. Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation. PLoS Genet. 2019 Aug 22;15(8):e1008013. doi: 10.1371/journal.pgen.1008013. eCollection 2019 Aug. PubMed PMID: 31437150; PubMed Central PMCID: PMC6726246.
  35. Pampouille E, Hennequet-Antier C, Praud C, Juanchich A, Brionne A, Godet E, Bordeau T, Fagnoul F, Le Bihan-Duval E, Berri C. Differential expression and co-expression gene network analyses reveal molecular mechanisms and candidate biomarkers involved in breast muscle myopathies in chicken. Sci Rep. 2019 Oct 17;9(1):14905. doi: 10.1038/s41598-019-51521-1. PubMed PMID: 31624339; PubMed Central PMCID: PMC6797748.
  36. Le Roy N, Combes-Soia L, Brionne A, Labas V, Rodriguez-Navarro AB, Hincke MT, Nys Y, Gautron J. Guinea fowl eggshell quantitative proteomics yield new findings related to its unique structural characteristics and superior mechanical properties. J Proteomics. 2019 Oct 30;209:103511. doi:10.1016/j.jprot.2019.103511. Epub 2019 Sep 5. PubMed PMID: 31493547.
  37. Charrier NP, Hermouet A, Hervet C, Agoulon A, Barker SC, Heylen D, Toty C, McCoy KD, Plantard O, Rispe C. A transcriptome-based phylogenetic study of hard ticks (Ixodidae). Sci Rep. 2019 Sep 9;9(1):12923. doi:10.1038/s41598-019-49641-9. PubMed PMID: 31501478; PubMed Central PMCID:PMC6733903.
  38. Mesbah-Uddin M, Guldbrandtsen B, Lund MS, Boichard D, Sahana G. Joint imputation of whole-genome sequence variants and large chromosomal deletions in cattle. J Dairy Sci. 2019 Dec;102(12):11193-11206. doi: 10.3168/jds.2019-16946. Epub 2019 Oct 9. PubMed PMID: 31606212.
  39. Faucher M, Nouvel LX, Dordet-Frisoni E, Sagné E, Baranowski E, Hygonenq MC, Marenda MS, Tardy F, Citti C. Mycoplasmas under experimental antimicrobial selection: The unpredicted contribution of horizontal chromosomal transfer. PLoS Genet. 2019 Jan 22;15(1):e1007910. doi: 10.1371/journal.pgen.1007910. eCollection 2019 Jan. PubMed PMID: 30668569; PubMed Central PMCID: PMC6358093. Yu X, Martin PGP, Michaels SD. BORDER proteins protect expression of neighboring genes by promoting 3′ Pol II pausing in plants. Nat Commun. 2019 Sep 25;10(1):4359. doi: 10.1038/s41467-019-12328-w. PubMed PMID: 31554790; PubMed Central PMCID: PMC6761125.
  40. Milon N, Chantry-Darmon C, Satge C, Fustier MA, Cauet S, Moreau S, Callot C, Bellec A, Gabrieli T, Saïas L, Boutonnet A, Ginot F, Bergès H, Bancaud A. μLAS technology for DNA isolation coupled to Cas9-assisted targeting for sequencing and assembly of a 30 kb region in plant genome. Nucleic Acids Res. 2019 Sep 5;47(15):8050-8060. doi: 10.1093/nar/gkz632. PubMed PMID: 31505675; PubMed Central PMCID: PMC6736094.
  41. Boutigny AL, Gautier A, Basler R, Dauthieux F, Leite S, Valade R, Aguayo J, Ioos R, Laval V. Metabarcoding targeting the EF1 alpha region to assess Fusarium diversity on cereals. PLoS One. 2019 Jan 11;14(1):e0207988. doi:10.1371/journal.pone.0207988. eCollection 2019. PubMed PMID: 30633747; PubMed Central PMCID: PMC6329491.
  42. Zinger L, Taberlet P, Schimann H, Bonin A, Boyer F, De Barba M, Gaucher P, Gielly L, Giguet-Covex C, Iribar A, Réjou-Méchain M, Rayé G, Rioux D, Schilling V, Tymen B, Viers J, Zouiten C, Thuiller W, Coissac E, Chave J. Body size determines soil community assembly in a tropical forest. Mol Ecol. 2019 Feb;28(3):528-543. doi: 10.1111/mec.14919. Epub 2018 Nov 22. PubMed PMID:30375061.
  43. Burz SD, Abraham AL, Fonseca F, David O, Chapron A, Béguet-Crespel F, Cénard S, Le Roux K, Patrascu O, Levenez F, Schwintner C, Blottière HM, Béra-Maillet C,  Lepage P, Doré J, Juste C. A Guide for Ex Vivo Handling and Storage of Stool Samples Intended for Fecal Microbiota Transplantation. Sci Rep. 2019 Jun 20;9(1):8897. doi: 10.1038/s41598-019-45173-4. PubMed PMID: 31222022; PubMed Central PMCID: PMC6586871.
  44. Read T, Fortun-Lamothe L, Pascal G, Le Boulch M, Cauquil L, Gabinaud B, Bannelier C, Balmisse E, Destombes N, Bouchez O, Gidenne T, Combes S. Diversity and Co-occurrence Pattern Analysis of Cecal Microbiota Establishment at the Onset of Solid Feeding in Young Rabbits. Front Microbiol. 2019 May 10;10:973. doi:10.3389/fmicb.2019.00973. eCollection 2019. PubMed PMID: 31134019; PubMed Central PMCID: PMC6524096.
  45. Debray K, Marie-Magdelaine J, Ruttink T, Clotault J, Foucher F, Malécot V. Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae). BMC Evol Biol. 2019 Jul 24;19(1):152. doi: 10.1186/s12862-019-1479-z. PubMed PMID:31340752; PubMed Central PMCID: PMC6657147.
  46. Martínez de Paz A, Khajavi L, Martin H, Claveria-Gimeno R, Tom Dieck S, Cheema MS, Sanchez-Mut JV, Moksa MM, Carles A, Brodie NI, Sheikh TI, Freeman ME, Petrotchenko EV, Borchers CH, Schuman EM, Zytnicki M, Velazquez-Campoy A, Abian O, Hirst M, Esteller M, Vincent JB, Malnou CE, Ausió J. MeCP2-E1 isoform is a dynamically expressed, weakly DNA-bound protein with different protein and DNA interactions compared to MeCP2-E2. Epigenetics Chromatin. 2019 Oct 10;12(1):63. doi: 10.1186/s13072-019-0298-1. PubMed PMID: 31601272; PubMed Central PMCID:PMC6786283.
  47. Gervais L, Perrier C, Bernard M, Merlet J, Pemberton JM, Pujol B, Quéméré E. RAD-sequencing for estimating genomic relatedness matrix-based heritability in the wild: A case study in roe deer. Mol Ecol Resour. 2019 Sep;19(5):1205-1217. doi: 10.1111/1755-0998.13031. Epub 2019 Jun 12. PubMed PMID: 31058463.
  48. Macedo FL, Reverter A, Legarra A. Behavior of the Linear Regression method to estimate bias and accuracies with correct and incorrect genetic evaluation models. J Dairy Sci. 2020 Jan;103(1):529-544. doi: 10.3168/jds.2019-16603. Epub 2019 Nov 6. PubMed PMID: 31704008.
  49. Navelsaker S, Magadan S, Jouneau L, Quillet E, Olesen NJ, Munang’andu HM, Boudinot P, Evensen Ø. Sequential Immunization With Heterologous Viruses Does Not Result in Attrition of the B Cell Memory in Rainbow Trout. Front Immunol. 2019 Nov 19;10:2687. doi: 10.3389/fimmu.2019.02687. eCollection 2019. PubMed PMID:31824488; PubMed Central PMCID: PMC6882293.
  50. Meola M, Rifa E, Shani N, Delbès C, Berthoud H, Chassard C. DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products. BMC Genomics. 2019 Jul 8;20(1):560. doi: 10.1186/s12864-019-5914-8. PubMed PMID: 31286860; PubMed Central PMCID:PMC6615214.
  51. Nay K, Jollet M, Goustard B, Baati N, Vernus B, Pontones M, Lefeuvre-Orfila L, Bendavid C, Rué O, Mariadassou M, Bonnieu A, Ollendorff V, Lepage P, Derbré F, Koechlin-Ramonatxo C. Gut bacteria are critical for optimal muscle function: a potential link with glucose homeostasis. Am J Physiol Endocrinol Metab. 2019 Jul 1;317(1):E158-E171. doi: 10.1152/ajpendo.00521.2018. Epub 2019
  52. Milet J, Boland A, Luisi P, Sabbagh A, Sadissou I, Sonon P, Domingo N, Palstra F, Gineau L, Courtin D, Massougbodji A, Garcia A, Deleuze JF, Perdry H. First genome-wide association study of non-severe malaria in two birth cohorts in Benin. Hum Genet. 2019 Dec;138(11-12):1341-1357. doi: 10.1007/s00439-019-02079-5. Epub 2019 Oct 30. PubMed PMID: 31667592.Apr 30. PubMed PMID: 31039010.
  53. Manzano-Marı N A, Coeur d’acier A, Clamens AL, Orvain C, Cruaud C, Barbe V, Jousselin E. Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids’ di-symbiotic systems. ISME J. 2020 Jan;14(1):259-273. doi: 10.1038/s41396-019-0533-6. Epub 2019 Oct 17. PubMed PMID: 31624345.
  54. Mesbah-Uddin M, Hoze C, Michot P, Barbat A, Lefebvre R, Boussaha M, Sahana G, Fritz S, Boichard D, Capitan A. A missense mutation (p.Tyr452Cys) in the CAD gene compromises reproductive success in French Normande cattle. J Dairy Sci. 2019 Jul;102(7):6340-6356. doi: 10.3168/jds.2018-16100. Epub 2019 May 2. PubMed PMID:31056337.
  55. Lalis A, Mona S, Stoetzel E, Bonhomme F, Souttou K, Ouarour A, Aulagnier S, Denys C, Nicolas V. Out of Africa: demographic and colonization history of the Algerian mouse (Mus spretus Lataste). Heredity (Edinb). 2019 Feb;122(2):150-171. doi: 10.1038/s41437-018-0089-7. Epub 2018 May 23. PubMed PMID: 29795180; PubMed Central PMCID: PMC6327062.
  56. Gresse R, Chaucheyras Durand F, Dunière L, Blanquet-Diot S, Forano E. Microbiota Composition and Functional Profiling Throughout the Gastrointestinal Tract of Commercial Weaning Piglets. Microorganisms. 2019 Sep 12;7(9). pii: E343. doi: 10.3390/microorganisms7090343. PubMed PMID: 31547478; PubMed Central PMCID:PMC6780805.
  57. Paris C, Servin B, Boitard S. Inference of Selection from Genetic Time Series Using Various Parametric Approximations to the Wright-Fisher Model. G3 (Bethesda). 2019 Dec 3;9(12):4073-4086. doi: 10.1534/g3.119.400778. PubMed PMID: 31597676; PubMed Central PMCID: PMC6893182.
  58. Krasovec M, Sanchez-Brosseau S, Piganeau G. First Estimation of the Spontaneous Mutation Rate in Diatoms. Genome Biol Evol. 2019 Jul 1;11(7):1829-1837. doi: 10.1093/gbe/evz130. PubMed PMID: 31218358; PubMed Central PMCID: PMC6604790.
  59. Sommeria-Klein G, Zinger L, Coissac E, Iribar A, Schimann H, Taberlet P, Chave J. Latent Dirichlet Allocation reveals spatial and taxonomic structure in a DNA-based census of soil biodiversity from a tropical forest. Mol Ecol Resour. 2019 Oct 24. doi: 10.1111/1755-0998.13109. [Epub ahead of print] PubMed PMID:31650682.
  60. Jay F, Boitard S, Austerlitz F. An ABC Method for Whole-Genome Sequence Data: Inferring Paleolithic and Neolithic Human Expansions. Mol Biol Evol. 2019 Jul 1;36(7):1565-1579. doi: 10.1093/molbev/msz038. PubMed PMID: 30785202.
  61. Willemsen A, Félez-Sánchez M, Bravo IG. Genome Plasticity in Papillomaviruses and De Novo Emergence of E5 Oncogenes. Genome Biol Evol. 2019 Jun 1;11(6):1602-1617. doi: 10.1093/gbe/evz095. PubMed PMID: 31076746; PubMed Central PMCID: PMC6557308.
  62. Pont C, Leroy T, Seidel M, Tondelli A, Duchemin W, Armisen D, Lang D, Bustos-Korts D, Goué N, Balfourier F, Molnár-Láng M, Lage J, Kilian B, Özkan H, Waite D, Dyer S, Letellier T, Alaux M; Wheat and Barley Legacy for Breeding Improvement (WHEALBI) consortium, Russell J, Keller B, van Eeuwijk F, Spannagl M, Mayer KFX, Waugh R, Stein N, Cattivelli L, Haberer G, Charmet G, Salse J. Tracing the ancestry of modern bread wheats. Nat Genet. 2019 May;51(5):905-911. doi:10.1038/s41588-019-0393-z. Epub 2019 May 1. PubMed PMID: 31043760.
  63. Brucato N, Fernandes V, Kusuma P, Černý V, Mulligan CJ, Soares P, Rito T, Besse C, Boland A, Deleuze JF, Cox MP, Sudoyo H, Stoneking M, Pereira L, Ricaut FX. Evidence of Austronesian Genetic Lineages in East Africa and South Arabia:Complex Dispersal from Madagascar and Southeast Asia. Genome Biol Evol. 2019 Mar 1;11(3):748-758. doi: 10.1093/gbe/evz028. PubMed PMID: 30715341; PubMed Central PMCID: PMC6423374.
  64. Bellec L, Bonavita MC, Hourdez S, Jebbar M, Tasiemski A, Durand L, Gayet N, Zeppilli D. Chemosynthetic ectosymbionts associated with a shallow-water marine nematode. Sci Rep. 2019 May 7;9(1):7019. doi: 10.1038/s41598-019-43517-8. PubMed PMID: 31065037; PubMed Central PMCID: PMC6505526.
  65. Zhang X, Grosfeld A, Williams E, Vasiliauskas D, Barretto S, Smith L, Mariadassou M, Philippe C, Devime F, Melchior C, Gourcerol G, Dourmap N, Lapaque N, Larraufie P, Blottière HM, Herberden C, Gerard P, Rehfeld JF, Ferraris RP, Fritton JC, Ellero-Simatos S, Douard V. Fructose malabsorption induces cholecystokinin expression in the ileum and cecum by changing microbiota composition and metabolism. FASEB J. 2019 Jun;33(6):7126-7142. doi:10.1096/fj.201801526RR. Epub 2019 Apr 2. PubMed PMID: 30939042.
  66. Martin OCB, Olier M, Ellero-Simatos S, Naud N, Dupuy J, Huc L, Taché S, Graillot V, Levêque M, Bézirard V, Héliès-Toussaint C, Estrada FBY, Tondereau V, Lippi Y, Naylies C, Peyriga L, Canlet C, Davila AM, Blachier F, Ferrier L, Boutet-Robinet E, Guéraud F, Théodorou V, Pierre FHF. Haem iron reshapes colonic luminal environment: impact on mucosal homeostasis and microbiome through aldehyde formation. Microbiome. 2019 May 6;7(1):72. doi:10.1186/s40168-019-0685-7. PubMed PMID: 31060614; PubMed Central PMCID:PMC6503375.
  67. Grimm P, Combes S, Pascal G, Cauquil L, Julliand V. Dietary composition and yeast/microalgae combination supplementation modulate the microbial ecosystem in the caecum, colon and faeces of horses. Br J Nutr. 2019 Nov 6:1-27. doi:10.1017/S0007114519002824. [Epub ahead of print] PubMed PMID: 31690358.
  68. Schiffer PH, Danchin EGJ, Burnell AM, Creevey CJ, Wong S, Dix I, O’Mahony G, Culleton BA, Rancurel C, Stier G, Martínez-Salazar EA, Marconi A, Trivedi U, Kroiher M, Thorne MAS, Schierenberg E, Wiehe T, Blaxter M. Signatures of the Evolution of Parthenogenesis and Cryptobiosis in the Genomes of Panagrolaimid Nematodes. iScience. 2019 Nov 22;21:587-602. doi: 10.1016/j.isci.2019.10.039. Epub 2019 Oct 24. PubMed PMID: 31759330.
  69. Prorok P, Artufel M, Aze A, Coulombe P, Peiffer I, Lacroix L, Guédin A, Mergny JL, Damaschke J, Schepers A, Ballester B, Méchali M. Involvement of G-quadruplex regions in mammalian replication origin activity. Nat Commun. 2019 Jul 22;10(1):3274. doi: 10.1038/s41467-019-11104-0. PubMed PMID: 31332171; PubMed Central PMCID: PMC6646384.
  70. Achard CS, Dupouy V, Siviglia S, Arpaillange N, Cauquil L, Bousquet-Mélou A, Zemb O. Variability of the Ability of Complex Microbial Communities to Exclude Microbes Carrying Antibiotic Resistance Genes in Rabbits. Front Microbiol. 2019 Jul 2;10:1503. doi: 10.3389/fmicb.2019.01503. eCollection 2019. PubMed PMID: 31333614; PubMed Central PMCID: PMC6615258.
  71. Gautier F, Label P, Eliášová K, Leplé JC, Motyka V, Boizot N, Vondráková Z, Malbeck J, Trávníčková A, Le Metté C, Lesage-Descauses MC, Lomenech AM, Trontin JF, Costa G, Lelu-Walter MA, Teyssier C. Cytological, Biochemical and Molecular Events of the Embryogenic State in Douglas-fir (Pseudotsuga menziesii [Mirb.]). Front Plant Sci. 2019 Feb 28;10:118. doi: 10.3389/fpls.2019.00118. eCollection 2019. PubMed PMID: 30873184; PubMed Central PMCID: PMC6403139.
  72. Coufal S, Galanova N, Bajer L, Gajdarova Z, Schierova D, Jiraskova Zakostelska Z, Kostovcikova K, Jackova Z, Stehlikova Z, Drastich P, Tlaskalova-Hogenova H, Kverka M. Inflammatory Bowel Disease Types Differ in Markers of Inflammation, Gut Barrier and in Specific Anti-Bacterial Response. Cells. 2019 Jul 13;8(7). pii:E719. doi: 10.3390/cells8070719. PubMed PMID: 31337064; PubMed Central PMCID:PMC6678638.
  73. Luis P, Saint-Genis G, Vallon L, Bourgeois C, Bruto M, Marchand C, Record E, Hugoni M. Contrasted ecological niches shape fungal and prokaryotic community structure in mangroves sediments. Environ Microbiol. 2019 Apr;21(4):1407-1424. doi: 10.1111/1462-2920.14571. Epub 2019 Mar 19. PubMed PMID: 30807675.
  74. Dupouy V, Abdelli M, Moyano G, Arpaillange N, Bibbal D, Cadiergues MC, Lopez-Pulin D, Sayah-Jeanne S, de Gunzburg J, Saint-Lu N, Gonzalez-Zorn B, Andremont A, Bousquet-Mélou A. Prevalence of Beta-Lactam and Quinolone/Fluoroquinolone Resistance in Enterobacteriaceae From Dogs in France and Spain-Characterization of ESBL/pAmpC Isolates, Genes, and Conjugative Plasmids. Front Vet Sci. 2019 Aug 30;6:279. doi: 10.3389/fvets.2019.00279. eCollection 2019. PubMed PMID: 31544108; PubMed Central PMCID: PMC6730528.
  75. Rodríguez-Ramilo ST, Elsen JM, Legarra A. Inbreeding and effective population size in French dairy sheep: Comparison between genomic and pedigree estimates. J Dairy Sci. 2019 May;102(5):4227-4237. doi: 10.3168/jds.2018-15405. Epub 2019 Mar 1. PubMed PMID: 30827541.
  76. Benites LF, Poulton N, Labadie K, Sieracki ME, Grimsley N, Piganeau G. Single cell ecogenomics reveals mating types of individual cells and ssDNA viral infections in the smallest photosynthetic eukaryotes. Philos Trans R Soc Lond B Biol Sci. 2019 Nov 25;374(1786):20190089. doi: 10.1098/rstb.2019.0089. Epub 2019 Oct 7. PubMed PMID: 31587637; PubMed Central PMCID: PMC6792451.
  77. Torres L, Welch AJ, Zanchetta C, Chesser RT, Manno M, Donnadieu C, Bretagnolle V, Pante E. Evidence for a duplicated mitochondrial region in Audubon’s shearwater based on MinION sequencing. Mitochondrial DNA A DNA Mapp Seq Anal. 2019 Mar;30(2):256-263. doi: 10.1080/24701394.2018.1484116. Epub 2018 Jul 25. PubMed PMID: 30043666.
  78. Rincel M, Olier M, Minni A, Monchaux de Oliveira C, Matime Y, Gaultier E, Grit I, Helbling JC, Costa AM, Lépinay A, Moisan MP, Layé S, Ferrier L, Parnet P, Theodorou V, Darnaudéry M. Pharmacological restoration of gut barrier function in stressed neonates partially reverses long-term alterations associated with maternal separation. Psychopharmacology (Berl). 2019 May;236(5):1583-1596. doi:10.1007/s00213-019-05252-w. Epub 2019 May 23. PubMed PMID: 31147734.
  79. Veerman K, Tardiveau C, Martins F, Coudert J, Girard JP. Single-Cell Analysis Reveals Heterogeneity of High Endothelial Venules and Different Regulation of Genes Controlling Lymphocyte Entry to Lymph Nodes. Cell Rep. 2019 Mar 12;26(11):3116-3131.e5. doi: 10.1016/j.celrep.2019.02.042. PubMed PMID: 30865898.
  80. Vagner M, Pante E, Viricel A, Lacoue-Labarthe T, Zambonino-Infante JL, Quazuguel P, Dubillot E, Huet V, Le Delliou H, Lefrançois C, Imbert-Auvray N. Ocean warming combined with lower omega-3 nutritional availability impairs the cardio-respiratory function of a marine fish. J Exp Biol. 2019 Apr 15;222(Pt 8).pii: jeb187179. doi: 10.1242/jeb.187179. PubMed PMID: 30630962.
  81. Ruppé E, Ghozlane A, Tap J, Pons N, Alvarez AS, Maziers N, Cuesta T, Hernando-Amado S, Clares I, Martínez JL, Coque TM, Baquero F, Lanza VF, Máiz L, Goulenok T, de Lastours V, Amor N, Fantin B, Wieder I, Andremont A, van Schaik W, Rogers M, Zhang X, Willems RJL, de Brevern AG, Batto JM, Blottière HM, Léonard P, Léjard V, Letur A, Levenez F, Weiszer K, Haimet F, Doré J, Kennedy SP, Ehrlich SD. Prediction of the intestinal resistome by a three-dimensional structure-based method. Nat Microbiol. 2019 Jan;4(1):112-123. doi: 10.1038/s41564-018-0292-6. Epub 2018 Nov 26. PubMed PMID: 30478291.
  82. Mangin B, Rincent R, Rabier CE, Moreau L, Goudemand-Dugue E. Training set optimization of genomic prediction by means of EthAcc. PLoS One. 2019 Feb 19;14(2):e0205629. doi: 10.1371/journal.pone.0205629. eCollection 2019. PubMed PMID: 30779753; PubMed Central PMCID: PMC6380617.
  83. Juhel AS, Barbu CM, Valantin-Morison M, Gauffre B, Leblois R, Olivares J, Franck P. Limited genetic structure and demographic expansion of the Brassicogethes aeneus populations in France and in Europe. Pest Manag Sci. 2019 Mar;75(3):667-675. doi: 10.1002/ps.5162. PubMed PMID: 30105772.
  84. Thomas A, Barriere S, Broseus L, Brooke J, Lorenzi C, Villemin JP, Beurier G, Sabatier R, Reynes C, Mancheron A, Ritchie W. GECKO is a genetic algorithm to classify and explore high throughput sequencing data. Commun Biol. 2019 Jun 20;2:222. doi: 10.1038/s42003-019-0456-9. eCollection 2019. PubMed PMID:31240260; PubMed Central PMCID: PMC6586863.
  85. Macedo D, Caballero I, Mateos M, Leblois R, McCay S, Hurtado LA. Population genetics and historical demographic inferences of the blue crab Callinectes sapidus in the US based on microsatellites. PeerJ. 2019 Oct 14;7:e7780. doi: 10.7717/peerj.7780. eCollection 2019. PubMed PMID: 31632846; PubMed Central PMCID: PMC6796965.
  86. Bonhomme M, Fariello MI, Navier H, Hajri A, Badis Y, Miteul H, Samac DA, Dumas B, Baranger A, Jacquet C, Pilet-Nayel ML. A local score approach improves GWAS resolution and detects minor QTL: application to Medicago truncatula quantitative disease resistance to multiple Aphanomyces euteiches isolates. Heredity (Edinb). 2019 Oct;123(4):517-531. doi: 10.1038/s41437-019-0235-x. Epub 2019 May 28. PubMed PMID: 31138867; PubMed Central PMCID: PMC6781128.
  87. Adoue V, Binet B, Malbec A, Fourquet J, Romagnoli P, van Meerwijk JPM, Amigorena S, Joffre OP. The Histone Methyltransferase SETDB1 Controls T Helper Cell Lineage Integrity by Repressing Endogenous Retroviruses. Immunity. 2019 Mar 19;50(3):629-644.e8. doi: 10.1016/j.immuni.2019.01.003. Epub 2019 Feb 5. PubMed PMID: 30737147.
  88. Araujo Furlan CL, Tosello Boari J, Rodriguez C, Canale FP, Fiocca Vernengo F, Boccardo S, Beccaria CG, Adoue V, Joffre O, Gruppi A, Montes CL, Acosta Rodriguez EV. Limited Foxp3(+) Regulatory T Cells Response During Acute Trypanosoma cruzi Infection Is Required to Allow the Emergence of Robust Parasite-Specific CD8(+) T Cell Immunity. Front Immunol. 2018 Nov 5;9:2555. doi: 10.3389/fimmu.2018.02555. eCollection 2018. PubMed PMID: 30455700; PubMed Central PMCID: PMC6230662.
  89. Pont F, Tosolini M, Fournié JJ. Single-Cell Signature Explorer for comprehensive visualization of single cell signatures across scRNA-seq datasets. Nucleic Acids Res. 2019 Dec 2;47(21):e133. doi: 10.1093/nar/gkz601. PubMed PMID:31294801; PubMed Central PMCID: PMC6868346.
  90. Leroy T, Louvet JM, Lalanne C, Le Provost G, Labadie K, Aury JM, Delzon S, Plomion C, Kremer A. Adaptive introgression as a driver of local adaptation to climate in European white oaks. New Phytol. 2019 Aug 8. doi: 10.1111/nph.16095.[Epub ahead of print] PubMed PMID: 31394003.
  91. Guillocheau GM, El Hou A, Meersseman C, Esquerré D, Rebours E, Letaief R, Simao M, Hypolite N, Bourneuf E, Bruneau N, Vaiman A, Vander Jagt CJ, Chamberlain  AJ, Rocha D. Survey of allele specific expression in bovine muscle. Sci Rep. 2019 Mar 12;9(1):4297. doi: 10.1038/s41598-019-40781-6. PubMed PMID: 30862965; PubMed Central PMCID: PMC6414783.