Publications 2018

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. Ogiyama, Y., Schuettengruber, B., Papadopoulos, G., Chang, J.-M. & Cavalli, G. Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development. Mol Cell (2018). doi:10.1016/j.molcel.2018.05.032. see
  2. Louise Brousseau, Paul V. A. Fine, Erwin Dreyer, Giovanni G. Vendramin, Ivan Scotti, Genomics of microgeographic adaptation in the Amazonian hyperdominant tree Eperua falcata Aubl. (Fabaceae), bioRxiv, see
  3. L. Brousseau, S. Nidelet, R. Streiff, New WGS data and annotation of the heterosomal vs. autosomal localization of Ostrinia scapulalis (Lepidoptera, Crambidae) nuclear genomic scaffolds, Data in Brief, doi:10.1016/j.dib.2018.08.011i see
  4. N. Pierre Charrier, Marjorie Couton, Maarten J. Voordouw, Olivier Rais, Axelle Durand-Hermouet, Caroline Hervet, Olivier Plantard and Claude Rispe. Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus. Parasites & Vectors 2018 11:364. DOI: 10.1186/s13071-018-2932-3. see
  5. Quentin Szabo, Daniel Jost, Jia-Ming Chang, Diego I. Cattoni, Giorgio L. Papadopoulos, Boyan Bonev, Tom Sexton, Julian Gurgo, Caroline Jacquier, Marcelo Nollmann, Frédéric Bantignies, Giacomo Cavalli. TADs are 3D structural units of higher-order chromosome organization in Drosophila. Science Advances, 28 Feb 2018. DOI: 10.1126/sciadv.aar8082. see
  6. Clément Viricel Simon de Givry Thomas Schiex Sophie Barbe. UCost Function Network-based Design of Protein-Protein Interactions: predicting changes in binding affinity. Bioinformatics, 2018. doi: see
  7. Raymond O, Gouzy J, Just J, Badouin H, Verdenaud M, Lemainque A, Vergne P, Moja S, Choisne N, Pont C, Carrère S, Caissard JC, Couloux A, Cottret L, Aury JM, Szécsi J, Latrasse D, Madoui MA, François L, Fu X, Yang SH, Dubois A, Piola F, Larrieu A, Perez M, Labadie K, Perrier L, Govetto B, Labrousse Y, Villand P, Bardoux C, Boltz V, Lopez-Roques C, Heitzler P, Vernoux T, Vandenbussche M, Quesneville H, Boualem A, Bendahmane A, Liu C, Le Bris M, Salse J, Baudino S, Benhamed M, Wincker P, Bendahmane M. The Rosa genome provides new insights into the domestication of modern roses. Nat Genet. 2018 Apr 30. doi:10.1038/s41588-018-0110-3.  PubMed PMID: 29713014.see.
  8. Schroeder H, Sikora M, Gopalakrishnan S, Cassidy LM, Maisano Delser P, Sandoval Velasco M, Schraiber JG, Rasmussen S, Homburger JR, Ávila-Arcos MC, Allentoft ME, Moreno-Mayar JV, Renaud G, Gómez-Carballa A, Laffoon JE, Hopkins RJA, Higham TFG, Carr RS, Schaffer WC, Day JS, Hoogland M, Salas A, Bustamante CD, Nielsen R, Bradley DG, Hofman CL, Willerslev E. Origins and genetic legacies
    of the Caribbean Taino. Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):2341-2346. doi: 10.1073/pnas.1716839115. Epub 2018 Feb 20. PubMed PMID: 29463742; PubMed Central PMCID: PMC5877975.see.
  9. Laurent B, Palaiokostas C, Spataro C, Moinard M, Zehraoui E, Houston RD, Foulongne-Oriol M. High-resolution mapping of the recombination landscape of the phytopathogen Fusarium graminearum suggests two-speed genome evolution. Mol Plant Pathol. 2018 Feb;19(2):341-354. doi: 10.1111/mpp.12524. Epub 2017 Feb 14. PubMed PMID: 27998012.see.
  10. Segura A, Auffret P, Bibbal D, Bertoni M, Durand A, Jubelin G, Kérourédan M, Brugère H, Bertin Y, Forano E. Factors Involved in the Persistence of a Shiga Toxin-Producing Escherichia coli O157:H7 Strain in Bovine Feces and Gastro-Intestinal Content. Front Microbiol. 2018 Mar 9;9:375. doi:10.3389/fmicb.2018.00375. eCollection 2018. PubMed PMID: 29593666; PubMed Central PMCID: PMC5854682.see.
  11. Teyssier A, Rouffaer LO, Saleh Hudin N, Strubbe D, Matthysen E, Lens L, White J. Inside the guts of the city: Urban-induced alterations of the gut microbiota in a wild passerine. Sci Total Environ. 2018 Jan 15;612:1276-1286. doi:10.1016/j.scitotenv.2017.09.035. Epub 2017 Sep 8. PubMed PMID: 28898933.see.
  12. Keller J, Imperial J, Ruiz-Argüeso T, Privet K, Lima O, Michon-Coudouel S, Biget M, Salmon A, Aïnouche A, Cabello-Hurtado F. RNA sequencing and analysis of three Lupinus nodulomes provide new insights into specific host-symbiont relationships with compatible and incompatible Bradyrhizobium strains. Plant Sci. 2018 Jan;266:102-116. doi: 10.1016/j.plantsci.2017.10.015. Epub 2017 Oct 31. PubMed PMID: 29241560.see.
  13. Gaulin E, Pel MJC, Camborde L, San-Clemente H, Courbier S, Dupouy MA, Lengellé J, Veyssiere M, Le Ru A, Grandjean F, Cordaux R, Moumen B, Gilbert C, Cano LM, Aury JM, Guy J, Wincker P, Bouchez O, Klopp C, Dumas B. Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation. BMC Biol. 2018 Apr 18;16(1):43. doi: 10.1186/s12915-018-0508-5. PubMed PMID: 29669603; PubMed Central PMCID: PMC5907361.see.
  14. Szabo Q, Jost D, Chang JM, Cattoni DI, Papadopoulos GL, Bonev B, Sexton T, Gurgo J, Jacquier C, Nollmann M, Bantignies F, Cavalli G. TADs are 3D structural units of higher-order chromosome organization in Drosophila. Sci Adv. 2018 Feb 28;4(2):eaar8082. doi: 10.1126/sciadv.aar8082. eCollection 2018 Feb. PubMed PMID: 29503869; PubMed Central PMCID: PMC5829972.see.
  15. Choque E, Klopp C, Valiere S, Raynal J, Mathieu F. Whole-genome sequencing of Aspergillus tubingensis G131 and overview of its secondary metabolism potential. BMC Genomics. 2018 Mar 15;19(1):200. doi: 10.1186/s12864-018-4574-4. PubMed PMID:29703136.see.
  16. David M, Lebrun C, Duguet T, Talmont F, Beech R, Orlowski S, André F, Prichard RK, Lespine A. Structural model, functional modulation by ivermectin and tissue localization of Haemonchus contortus P-glycoprotein-13. Int J Parasitol Drugs Drug Resist. 2018 Apr;8(1):145-157. doi: 10.1016/j.ijpddr.2018.02.001. Epub 2018  Feb 15. PubMed PMID: 29571165.see.
  17. Bigot D, Atyame CM, Weill M, Justy F, Herniou EA, Gayral P. Discovery of Culex pipiens associated tunisia virus: a new ssRNA(+) virus representing a new insect associated virus family. Virus Evol. 2018 Jan 10;4(1):vex040. doi: 10.1093/ve/vex040. eCollection 2018 Jan. PubMed PMID: 29340209; PubMed Central PMCID: PMC5763275.see.
  18. Brener-Raffalli K, Clerissi C, Vidal-Dupiol J, Adjeroud M, Bonhomme F, Pratlong M, Aurelle D, Mitta G, Toulza E. Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato. Microbiome. 2018 Feb 20;6(1):39. doi:10.1186/s40168-018-0423-6. PubMed PMID: 29463295; PubMed Central PMCID: PMC5819220. see.
  19. Leblois R, Gautier M, Rohfritsch A, Foucaud J, Burban C, Galan M, Loiseau A, Sauné L, Branco M, Gharbi K, Vitalis R, Kerdelhué C. Deciphering the demographic  history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa. Mol Ecol. 2018 Jan;27(1):264-278. doi:10.1111/mec.14411. Epub 2017 Nov 29. PubMed PMID: 29113013.see.
  20. Clemente F, Gautier M, Vitalis R. Inferring sex-specific demographic history from SNP data. PLoS Genet. 2018 Jan 31;14(1):e1007191. doi:10.1371/journal.pgen.1007191. eCollection 2018 Jan. PubMed PMID: 29385127; PubMed Central PMCID: PMC5809101.see.
  21. De Cocker P, Bessiere Y, Hernandez-Raquet G, Dubos S, Mozo I, Gaval G, Caligaris M, Barillon B, Vlaeminck SE, Sperandio M. Enrichment and adaptation yield high anammox conversion rates under low temperatures. Bioresour Technol. 2018 Feb;250:505-512. doi: 10.1016/j.biortech.2017.11.079. Epub 2017 Nov 24. PubMed PMID: 29197773.see.
  22. Gauthier J, Gayral P, Le Ru BP, Jancek S, Dupas S, Kaiser L, Gyapay G, Herniou EA. Genetic footprints of adaptive divergence in the bracovirus of Cotesia sesamiae identified by targeted resequencing. Mol Ecol. 2018 Mar 30. doi:10.1111/mec.14574. [Epub ahead of print] PubMed PMID: 29603484.see.
  23. Brucato N, Fernandes V, Mazières S, Kusuma P, Cox MP, Ng’ang’a JW, Omar M, Simeone-Senelle MC, Frassati C, Alshamali F, Fin B, Boland A, Deleuze JF, Stoneking M, Adelaar A, Crowther A, Boivin N, Pereira L, Bailly P, Chiaroni J, Ricaut FX. The Comoros Show the Earliest Austronesian Gene Flow into the Swahili  Corridor. Am J Hum Genet. 2018 Jan 4;102(1):58-68. doi:10.1016/j.ajhg.2017.11.011. PubMed PMID: 29304377; PubMed Central PMCID:PMC5777450.see.
  24. Bruxaux J, Gabrielli M, Ashari H, Prŷs-Jones R, Joseph L, Milá B, Besnard G, Thébaud C. Recovering the evolutionary history of crowned pigeons (Columbidae: Goura): Implications for the biogeography and conservation of New Guinean lowland birds. Mol Phylogenet Evol. 2018 Mar;120:248-258. doi:10.1016/j.ympev.2017.11.022. Epub 2017 Dec 1. PubMed PMID: 29199106.see.
  25. Vannier N, Mony C, Bittebiere AK, Michon-Coudouel S, Biget M, Vandenkoornhuyse P. A microorganisms’ journey between plant generations. Microbiome. 2018 Apr 26;6(1):79. doi: 10.1186/s40168-018-0459-7. PubMed PMID: 29695286; PubMed Central PMCID: PMC5918900.see.
  26. Rahimova R, Fontanel S, Lionne C, Jordheim LP, Peyrottes S, Chaloin L. Identification of allosteric inhibitors of the ecto-5′-nucleotidase (CD73) targeting the dimer interface. PLoS Comput Biol. 2018 Jan 29;14(1):e1005943. doi:10.1371/journal.pcbi.1005943. eCollection 2018 Jan. PubMed PMID: 29377887; PubMedCentral PMCID: PMC5805337.see.
  27. Coleman RA, Gauffre B, Pavlova A, Beheregaray LB, Kearns J, Lyon J, Sasaki M,  Leblois R, Sgro C, Sunnucks P. Artificial barriers prevent genetic recovery of small isolated populations of a low-mobility freshwater fish. Heredity (Edinb). 2018 Jan 12. doi: 10.1038/s41437-017-0008-3. [Epub ahead of print] PubMed PMID:29326479. see.
  28. Darnaud M, Dos Santos A, Gonzalez P, Augui S, Lacoste C, Desterke C, De Hertogh G, Valentino E, Braun E, Zheng J, Boisgard R, Neut C, Dubuquoy L, Chiappini F, Samuel D, Lepage P, Guerrieri F, Doré J, Bréchot C, Moniaux N, Faivre J. Enteric Delivery of Regenerating Family Member 3 alpha Alters the Intestinal Microbiota and Controls Inflammation in Mice With Colitis. Gastroenterology. 2018 Mar;154(4):1009-1023.e14. doi: 10.1053/j.gastro.2017.11.003. Epub 2017 Nov 11. PubMed PMID: 29133078.see.
  29. Lopez D, Ribeiro S, Label P, Fumanal B, Venisse JS, Kohler A, de Oliveira RR,  Labutti K, Lipzen A, Lail K, Bauer D, Ohm RA, Barry KW, Spatafora J, Grigoriev IV, Martin FM, Pujade-Renaud V. Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors. Front Microbiol. 2018 Mar 2;9:276. doi:10.3389/fmicb.2018.00276. eCollection 2018. PubMed PMID: 29551995; PubMed Central PMCID: PMC5840194.see.
  30. Derelle E, Yau S, Moreau H, Grimsley NH. Prasinovirus Attack of Ostreococcus Is Furtive by Day but Savage by Night. J Virol. 2018 Jan 30;92(4). pii: e01703-17. doi: 10.1128/JVI.01703-17. Print 2018 Feb 15. PubMed PMID: 29187539; PubMed Central PMCID: PMC5790953.see.
  31. Chikhi L, Rodríguez W, Grusea S, Santos P, Boitard S, Mazet O. The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice. Heredity (Edinb). 2018 Jan;120(1):13-24. doi: 10.1038/s41437-017-0005-6. Epub 2017 Nov 8. PubMed PMID:29234166; PubMed Central PMCID: PMC5837117.see.
  32. Boher P, Soler M, Sánchez A, Hoede C, Noirot C, Paiva JAP, Serra O, Figueras M. A comparative transcriptomic approach to understanding the formation of cork. Plant Mol Biol. 2018 Jan;96(1-2):103-118. doi: 10.1007/s11103-017-0682-9. Epub 2017 Nov 15. PubMed PMID: 29143299.see.
  33. Fumey J, Hinaux H, Noirot C, Thermes C, Rétaux S, Casane D. Evidence for late Pleistocene origin of Astyanax mexicanus cavefish. BMC Evol Biol. 2018 Apr 18;18(1):43. doi: 10.1186/s12862-018-1156-7. PubMed PMID: 29665771; PubMed Central PMCID: PMC5905186.see.
  34. Plomion C, Aury JM, Amselem J, Leroy T, Murat F, Duplessis S, Faye S, Francillonne N, Labadie K, Le Provost G, Lesur I, Bartholomé J, Faivre-Rampant P, Kohler A, Leplé JC, Chantret N, Chen J, Diévart A, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Bogeat-Triboulot MB, Bouffaud ML, Brachi B, Chancerel E, Cohen D, Couloux A, Da Silva C, Dossat C, Ehrenmann F, Gaspin C, Grima-Pettenati J, Guichoux E, Hecker A, Herrmann S, Hugueney P, Hummel I, Klopp C, Lalanne C, Lascoux M, Lasserre E, Lemainque A, Desprez-Loustau ML, Luyten I, Madoui MA, Mangenot S, Marchal C, Maumus F, Mercier J, Michotey C, Panaud O, Picault N, Rouhier N, Rué O, Rustenholz C, Salin F, Soler M, Tarkka M, Velt A, Zanne AE, Martin F, Wincker P, Quesneville H, Kremer A, Salse J. Oak genome reveals facets of long lifespan. Nat Plants. 2018 Jun 18. doi: 10.1038/s41477-018-0172-3. PubMed PMID: 29915331.see.
  35. Escudié F, Auer L, Bernard M, Mariadassou M, Cauquil L, Vidal K, Maman S, Hernandez-Raquet G, Combes S, Pascal G. FROGS: Find, Rapidly, OTUs with Galaxy Solution. Bioinformatics. 2018 Apr 15;34(8):1287-1294. doi: 10.1093/bioinformatics/btx791. PubMed PMID: 29228191.see.