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Items: 18

1.

Transcriptome profiling of sorted endoreduplicated nuclei from tomato fruits: how the global shift in expression ascribed to DNA ploidy influences RNA-Seq data normalization and interpretation.

Pirrello J, Deluche C, Frangne N, Gévaudant F, Maza E, Djari A, Bourge M, Renaudin JP, Brown S, Bowler C, Zouine M, Chevalier C, Gonzalez N.

Plant J. 2018 Jan;93(2):387-398. doi: 10.1111/tpj.13783. Erratum in: Plant J. 2018 Dec;96(6):1317.

2.

TomExpress, a unified tomato RNA-Seq platform for visualization of expression data, clustering and correlation networks.

Zouine M, Maza E, Djari A, Lauvernier M, Frasse P, Smouni A, Pirrello J, Bouzayen M.

Plant J. 2017 Nov;92(4):727-735. doi: 10.1111/tpj.13711. Epub 2017 Oct 25.

3.

Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle.

Meersseman C, Letaief R, Léjard V, Rebours E, Guillocheau G, Esquerré D, Djari A, Chamberlain A, Vander Jagt C, Klopp C, Boussaha M, Renand G, Maftah A, Petit D, Rocha D.

DNA Res. 2017 Jun 1;24(3):221-233. doi: 10.1093/dnares/dsx004.

4.

Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies.

Cabau C, Escudié F, Djari A, Guiguen Y, Bobe J, Klopp C.

PeerJ. 2017 Feb 16;5:e2988. doi: 10.7717/peerj.2988. eCollection 2017.

5.

The Extent of mRNA Editing Is Limited in Chicken Liver and Adipose, but Impacted by Tissular Context, Genotype, Age, and Feeding as Exemplified with a Conserved Edited Site in COG3.

Roux PF, Frésard L, Boutin M, Leroux S, Klopp C, Djari A, Esquerré D, Martin PG, Zerjal T, Gourichon D, Pitel F, Lagarrigue S.

G3 (Bethesda). 2015 Dec 4;6(2):321-35. doi: 10.1534/g3.115.022251.

6.

Genome-Wide Study of Structural Variants in Bovine Holstein, Montbéliarde and Normande Dairy Breeds.

Boussaha M, Esquerré D, Barbieri J, Djari A, Pinton A, Letaief R, Salin G, Escudié F, Roulet A, Fritz S, Samson F, Grohs C, Bernard M, Klopp C, Boichard D, Rocha D.

PLoS One. 2015 Aug 28;10(8):e0135931. doi: 10.1371/journal.pone.0135931. eCollection 2015.

7.

Genome-Wide Characterization of RNA Editing in Chicken Embryos Reveals Common Features among Vertebrates.

Frésard L, Leroux S, Roux PF, Klopp C, Fabre S, Esquerré D, Dehais P, Djari A, Gourichon D, Lagarrigue S, Pitel F.

PLoS One. 2015 May 29;10(5):e0126776. doi: 10.1371/journal.pone.0126776. eCollection 2015.

8.

Expanding Duplication of Free Fatty Acid Receptor-2 (GPR43) Genes in the Chicken Genome.

Meslin C, Desert C, Callebaut I, Djari A, Klopp C, Pitel F, Leroux S, Martin P, Froment P, Guilbert E, Gondret F, Lagarrigue S, Monget P.

Genome Biol Evol. 2015 Apr 24;7(5):1332-48. doi: 10.1093/gbe/evv072.

9.

The BioMart community portal: an innovative alternative to large, centralized data repositories.

Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G, Bardou P, Beck T, Blake A, Bonierbale M, Brookes AJ, Bucci G, Buetti I, Burge S, Cabau C, Carlson JW, Chelala C, Chrysostomou C, Cittaro D, Collin O, Cordova R, Cutts RJ, Dassi E, Di Genova A, Djari A, Esposito A, Estrella H, Eyras E, Fernandez-Banet J, Forbes S, Free RC, Fujisawa T, Gadaleta E, Garcia-Manteiga JM, Goodstein D, Gray K, Guerra-Assunção JA, Haggarty B, Han DJ, Han BW, Harris T, Harshbarger J, Hastings RK, Hayes RD, Hoede C, Hu S, Hu ZL, Hutchins L, Kan Z, Kawaji H, Keliet A, Kerhornou A, Kim S, Kinsella R, Klopp C, Kong L, Lawson D, Lazarevic D, Lee JH, Letellier T, Li CY, Lio P, Liu CJ, Luo J, Maass A, Mariette J, Maurel T, Merella S, Mohamed AM, Moreews F, Nabihoudine I, Ndegwa N, Noirot C, Perez-Llamas C, Primig M, Quattrone A, Quesneville H, Rambaldi D, Reecy J, Riba M, Rosanoff S, Saddiq AA, Salas E, Sallou O, Shepherd R, Simon R, Sperling L, Spooner W, Staines DM, Steinbach D, Stone K, Stupka E, Teague JW, Dayem Ullah AZ, Wang J, Ware D, Wong-Erasmus M, Youens-Clark K, Zadissa A, Zhang SJ, Kasprzyk A.

Nucleic Acids Res. 2015 Jul 1;43(W1):W589-98. doi: 10.1093/nar/gkv350. Epub 2015 Apr 20.

10.

Combined QTL and selective sweep mappings with coding SNP annotation and cis-eQTL analysis revealed PARK2 and JAG2 as new candidate genes for adiposity regulation.

Roux PF, Boitard S, Blum Y, Parks B, Montagner A, Mouisel E, Djari A, Esquerré D, Désert C, Boutin M, Leroux S, Lecerf F, Le Bihan-Duval E, Klopp C, Servin B, Pitel F, Duclos MJ, Guillou H, Lusis AJ, Demeure O, Lagarrigue S.

G3 (Bethesda). 2015 Feb 3;5(4):517-29. doi: 10.1534/g3.115.016865.

11.

Comparison of whole-genome (13X) and capture (87X) resequencing methods for SNP and genotype callings.

Roux PF, Marthey S, Djari A, Moroldo M, Esquerré D, Estellé J, Klopp C, Lagarrigue S, Demeure O.

Anim Genet. 2015 Feb;46(1):82-6. doi: 10.1111/age.12248. Epub 2014 Dec 16.

PMID:
25515399
12.

Re-sequencing data for refining candidate genes and polymorphisms in QTL regions affecting adiposity in chicken.

Roux PF, Boutin M, Désert C, Djari A, Esquerré D, Klopp C, Lagarrigue S, Demeure O.

PLoS One. 2014 Oct 21;9(10):e111299. doi: 10.1371/journal.pone.0111299. eCollection 2014.

13.

Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle.

Daetwyler HD, Capitan A, Pausch H, Stothard P, van Binsbergen R, Brøndum RF, Liao X, Djari A, Rodriguez SC, Grohs C, Esquerré D, Bouchez O, Rossignol MN, Klopp C, Rocha D, Fritz S, Eggen A, Bowman PJ, Coote D, Chamberlain AJ, Anderson C, VanTassell CP, Hulsegge I, Goddard ME, Guldbrandtsen B, Lund MS, Veerkamp RF, Boichard DA, Fries R, Hayes BJ.

Nat Genet. 2014 Aug;46(8):858-65. doi: 10.1038/ng.3034. Epub 2014 Jul 13.

PMID:
25017103
14.

Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing.

Billerey C, Boussaha M, Esquerré D, Rebours E, Djari A, Meersseman C, Klopp C, Gautheret D, Rocha D.

BMC Genomics. 2014 Jun 19;15:499. doi: 10.1186/1471-2164-15-499.

15.

RNAbrowse: RNA-Seq de novo assembly results browser.

Mariette J, Noirot C, Nabihoudine I, Bardou P, Hoede C, Djari A, Cabau C, Klopp C.

PLoS One. 2014 May 13;9(5):e96821. doi: 10.1371/journal.pone.0096821. eCollection 2014. Erratum in: PLoS One. 2014;9(8):e106187.

16.

Detection of haplotypes associated with prenatal death in dairy cattle and identification of deleterious mutations in GART, SHBG and SLC37A2.

Fritz S, Capitan A, Djari A, Rodriguez SC, Barbat A, Baur A, Grohs C, Weiss B, Boussaha M, Esquerré D, Klopp C, Rocha D, Boichard D.

PLoS One. 2013 Jun 7;8(6):e65550. doi: 10.1371/journal.pone.0065550. Print 2013.

17.

Novel insights into the bovine polled phenotype and horn ontogenesis in Bovidae.

Allais-Bonnet A, Grohs C, Medugorac I, Krebs S, Djari A, Graf A, Fritz S, Seichter D, Baur A, Russ I, Bouet S, Rothammer S, Wahlberg P, Esquerré D, Hoze C, Boussaha M, Weiss B, Thépot D, Fouilloux MN, Rossignol MN, van Marle-Köster E, Hreiðarsdóttir GE, Barbey S, Dozias D, Cobo E, Reversé P, Catros O, Marchand JL, Soulas P, Roy P, Marquant-Leguienne B, Le Bourhis D, Clément L, Salas-Cortes L, Venot E, Pannetier M, Phocas F, Klopp C, Rocha D, Fouchet M, Journaux L, Bernard-Capel C, Ponsart C, Eggen A, Blum H, Gallard Y, Boichard D, Pailhoux E, Capitan A.

PLoS One. 2013 May 22;8(5):e63512. doi: 10.1371/journal.pone.0063512. Print 2013.

18.

Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing.

Djari A, Esquerré D, Weiss B, Martins F, Meersseman C, Boussaha M, Klopp C, Rocha D.

BMC Genomics. 2013 May 7;14:307. doi: 10.1186/1471-2164-14-307.

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