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Items: 26

1.

Shifting the limits in wheat research and breeding using a fully annotated reference genome.

International Wheat Genome Sequencing Consortium (IWGSC); IWGSC RefSeq principal investigators:, Appels R, Eversole K, Feuillet C, Keller B, Rogers J, Stein N; IWGSC whole-genome assembly principal investigators:, Pozniak CJ, Stein N, Choulet F, Distelfeld A, Eversole K, Poland J, Rogers J, Ronen G, Sharpe AG; Whole-genome sequencing and assembly:, Pozniak C, Ronen G, Stein N, Barad O, Baruch K, Choulet F, Keeble-Gagnère G, Mascher M, Sharpe AG, Ben-Zvi G, Josselin AA; Hi-C data-based scaffolding:, Stein N, Mascher M, Himmelbach A; Whole-genome assembly quality control and analyses:, Choulet F, Keeble-Gagnère G, Mascher M, Rogers J, Balfourier F, Gutierrez-Gonzalez J, Hayden M, Josselin AA, Koh C, Muehlbauer G, Pasam RK, Paux E, Pozniak CJ, Rigault P, Sharpe AG, Tibbits J, Tiwari V; Pseudomolecule assembly:, Choulet F, Keeble-Gagnère G, Mascher M, Josselin AA, Rogers J; RefSeq genome structure and gene analyses:, Spannagl M, Choulet F, Lang D, Gundlach H, Haberer G, Keeble-Gagnère G, Mayer KFX, Ormanbekova D, Paux E, Prade V, Šimková H, Wicker T; Automated annotation:, Choulet F, Spannagl M, Swarbreck D, Rimbert H, Felder M, Guilhot N, Gundlach H, Haberer G, Kaithakottil G, Keilwagen J, Lang D, Leroy P, Lux T, Mayer KFX, Twardziok S, Venturini L; Manual gene curation:, Appels R, Rimbert H, Choulet F, Juhász A, Keeble-Gagnère G; Subgenome comparative analyses:, Choulet F, Spannagl M, Lang D, Abrouk M, Haberer G, Keeble-Gagnère G, Mayer KFX, Wicker T; Transposable elements:, Choulet F, Wicker T, Gundlach H, Lang D, Spannagl M; Phylogenomic analyses:, Lang D, Spannagl M, Appels R, Fischer I; Transcriptome analyses and RNA-seq data:, Uauy C, Borrill P, Ramirez-Gonzalez RH, Appels R, Arnaud D, Chalabi S, Chalhoub B, Choulet F, Cory A, Datla R, Davey MW, Hayden M, Jacobs J, Lang D, Robinson SJ, Spannagl M, Steuernagel B, Tibbits J, Tiwari V, van Ex F, Wulff BBH; Whole-genome methylome:, Pozniak CJ, Robinson SJ, Sharpe AG, Cory A; Histone mark analyses:, Benhamed M, Paux E, Bendahmane A, Concia L, Latrasse D; BAC chromosome MTP IWGSC–Bayer Whole-Genome Profiling (WGP) tags:, Rogers J, Jacobs J, Alaux M, Appels R, Bartoš J, Bellec A, Berges H, Doležel J, Feuillet C, Frenkel Z, Gill B, Korol A, Letellier T, Olsen OA, Šimková H, Singh K, Valárik M, van der Vossen E, Vautrin S, Weining S; Chromosome LTC mapping and physical mapping quality control:, Korol A, Frenkel Z, Fahima T, Glikson V, Raats D, Rogers J; RH mapping:, Tiwari V, Gill B, Paux E, Poland J; Optical mapping:, Doležel J, Číhalíková J, Šimková H, Toegelová H, Vrána J; Recombination analyses:, Sourdille P, Darrier B; Gene family analyses:, Appels R, Spannagl M, Lang D, Fischer I, Ormanbekova D, Prade V; CBF gene family:, Barabaschi D, Cattivelli L; Dehydrin gene family:, Hernandez P, Galvez S, Budak H; NLR gene family:, Steuernagel B, Jones JDG, Witek K, Wulff BBH, Yu G; PPR gene family:, Small I, Melonek J, Zhou R; Prolamin gene family:, Juhász A, Belova T, Appels R, Olsen OA; WAK gene family:, Kanyuka K, King R; Stem solidness (SSt1) QTL team:, Nilsen K, Walkowiak S, Pozniak CJ, Cuthbert R, Datla R, Knox R, Wiebe K, Xiang D; Flowering locus C (FLC) gene team:, Rohde A, Golds T; Genome size analysis:, Doležel J, Čížková J, Tibbits J; MicroRNA and tRNA annotation:, Budak H, Akpinar BA, Biyiklioglu S; Genetic maps and mapping:, Muehlbauer G, Poland J, Gao L, Gutierrez-Gonzalez J, N'Daiye A; BAC libraries and chromosome sorting:, Doležel J, Šimková H, Číhalíková J, Kubaláková M, Šafář J, Vrána J; BAC pooling, BAC library repository, and access:, Berges H, Bellec A, Vautrin S; IWGSC sequence and data repository and access:, Alaux M, Alfama F, Adam-Blondon AF, Flores R, Guerche C, Letellier T, Loaec M, Quesneville H; Physical maps and BAC-based sequences:; 1A BAC sequencing and assembly:, Pozniak CJ, Sharpe AG, Walkowiak S, Budak H, Condie J, Ens J, Koh C, Maclachlan R, Tan Y, Wicker T; 1B BAC sequencing and assembly:, Choulet F, Paux E, Alberti A, Aury JM, Balfourier F, Barbe V, Couloux A, Cruaud C, Labadie K, Mangenot S, Wincker P; 1D, 4D, and 6D physical mapping:, Gill B, Kaur G, Luo M, Sehgal S; 2AL physical mapping:, Singh K, Chhuneja P, Gupta OP, Jindal S, Kaur P, Malik P, Sharma P, Yadav B; 2AS physical mapping:, Singh NK, Khurana J, Chaudhary C, Khurana P, Kumar V, Mahato A, Mathur S, Sevanthi A, Sharma N, Tomar RS; 2B, 2D, 4B, 5BL, and 5DL IWGSC–Bayer Whole-Genome Profiling (WGP) physical maps:, Rogers J, Jacobs J, Alaux M, Bellec A, Berges H, Doležel J, Feuillet C, Frenkel Z, Gill B, Korol A, van der Vossen E, Vautrin S; 3AL physical mapping:, Gill B, Kaur G, Luo M, Sehgal S; 3DS physical mapping and BAC sequencing and assembly:, Bartoš J, Holušová K, Plíhal O; 3DL BAC sequencing and assembly:, Clark MD, Heavens D, Kettleborough G, Wright J; 4A physical mapping, BAC sequencing, assembly, and annotation:, Valárik M, Abrouk M, Balcárková B, Holušová K, Hu Y, Luo M; 5BS BAC sequencing and assembly:, Salina E, Ravin N, Skryabin K, Beletsky A, Kadnikov V, Mardanov A, Nesterov M, Rakitin A, Sergeeva E; 6B BAC sequencing and assembly:, Handa H, Kanamori H, Katagiri S, Kobayashi F, Nasuda S, Tanaka T, Wu J; 7A physical mapping and BAC sequencing:, Appels R, Hayden M, Keeble-Gagnère G, Rigault P, Tibbits J; 7B physical mapping, BAC sequencing, and assembly:, Olsen OA, Belova T, Cattonaro F, Jiumeng M, Kugler K, Mayer KFX, Pfeifer M, Sandve S, Xun X, Zhan B; 7DS BAC sequencing and assembly:, Šimková H, Abrouk M, Batley J, Bayer PE, Edwards D, Hayashi S, Toegelová H, Tulpová Z, Visendi P; 7DL physical mapping and BAC sequencing:, Weining S, Cui L, Du X, Feng K, Nie X, Tong W, Wang L; Figures:, Borrill P, Gundlach H, Galvez S, Kaithakottil G, Lang D, Lux T, Mascher M, Ormanbekova D, Prade V, Ramirez-Gonzalez RH, Spannagl M, Stein N, Uauy C, Venturini L; Manuscript writing team:, Stein N, Appels R, Eversole K, Rogers J, Borrill P, Cattivelli L, Choulet F, Hernandez P, Kanyuka K, Lang D, Mascher M, Nilsen K, Paux E, Pozniak CJ, Ramirez-Gonzalez RH, Šimková H, Small I, Spannagl M, Swarbreck D, Uauy C.

Science. 2018 Aug 17;361(6403). pii: eaar7191. doi: 10.1126/science.aar7191. Epub 2018 Aug 16.

PMID:
30115783
2.

The transcriptional landscape of polyploid wheat.

Ramírez-González RH, Borrill P, Lang D, Harrington SA, Brinton J, Venturini L, Davey M, Jacobs J, van Ex F, Pasha A, Khedikar Y, Robinson SJ, Cory AT, Florio T, Concia L, Juery C, Schoonbeek H, Steuernagel B, Xiang D, Ridout CJ, Chalhoub B, Mayer KFX, Benhamed M, Latrasse D, Bendahmane A; International Wheat Genome Sequencing Consortium, Wulff BBH, Appels R, Tiwari V, Datla R, Choulet F, Pozniak CJ, Provart NJ, Sharpe AG, Paux E, Spannagl M, Bräutigam A, Uauy C.

Science. 2018 Aug 17;361(6403). pii: eaar6089. doi: 10.1126/science.aar6089.

PMID:
30115782
3.

An improved assembly and annotation of the melon (Cucumis melo L.) reference genome.

Ruggieri V, Alexiou KG, Morata J, Argyris J, Pujol M, Yano R, Nonaka S, Ezura H, Latrasse D, Boualem A, Benhamed M, Bendahmane A, Cigliano RA, Sanseverino W, Puigdomènech P, Casacuberta JM, Garcia-Mas J.

Sci Rep. 2018 May 24;8(1):8088. doi: 10.1038/s41598-018-26416-2.

4.

The Rosa genome provides new insights into the domestication of modern roses.

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.

Nat Genet. 2018 Jun;50(6):772-777. doi: 10.1038/s41588-018-0110-3. Epub 2018 Apr 30.

PMID:
29713014
5.

At-MINI ZINC FINGER2 and Sl-INHIBITOR OF MERISTEM ACTIVITY, a Conserved Missing Link in the Regulation of Floral Meristem Termination in Arabidopsis and Tomato.

Bollier N, Sicard A, Leblond J, Latrasse D, Gonzalez N, Gévaudant F, Benhamed M, Raynaud C, Lenhard M, Chevalier C, Hernould M, Delmas F.

Plant Cell. 2018 Jan;30(1):83-100. doi: 10.1105/tpc.17.00653. Epub 2018 Jan 3.

PMID:
29298836
6.

Plant-Specific Histone Deacetylases HDT1/2 Regulate GIBBERELLIN 2-OXIDASE2 Expression to Control Arabidopsis Root Meristem Cell Number.

Li H, Torres-Garcia J, Latrasse D, Benhamed M, Schilderink S, Zhou W, Kulikova O, Hirt H, Bisseling T.

Plant Cell. 2017 Sep;29(9):2183-2196. doi: 10.1105/tpc.17.00366. Epub 2017 Aug 30.

7.

Arabidopsis ATRX Modulates H3.3 Occupancy and Fine-Tunes Gene Expression.

Duc C, Benoit M, Détourné G, Simon L, Poulet A, Jung M, Veluchamy A, Latrasse D, Le Goff S, Cotterell S, Tatout C, Benhamed M, Probst AV.

Plant Cell. 2017 Jul;29(7):1773-1793. doi: 10.1105/tpc.16.00877. Epub 2017 Jul 6.

8.

MAPK-triggered chromatin reprogramming by histone deacetylase in plant innate immunity.

Latrasse D, Jégu T, Li H, de Zelicourt A, Raynaud C, Legras S, Gust A, Samajova O, Veluchamy A, Rayapuram N, Ramirez-Prado JS, Kulikova O, Colcombet J, Bigeard J, Genot B, Bisseling T, Benhamed M, Hirt H.

Genome Biol. 2017 Jul 6;18(1):131. doi: 10.1186/s13059-017-1261-8.

9.

Natural and induced loss of function mutations in SlMBP21 MADS-box gene led to jointless-2 phenotype in tomato.

Roldan MVG, Périlleux C, Morin H, Huerga-Fernandez S, Latrasse D, Benhamed M, Bendahmane A.

Sci Rep. 2017 Jun 30;7(1):4402. doi: 10.1038/s41598-017-04556-1.

10.

The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility.

Jégu T, Veluchamy A, Ramirez-Prado JS, Rizzi-Paillet C, Perez M, Lhomme A, Latrasse D, Coleno E, Vicaire S, Legras S, Jost B, Rougée M, Barneche F, Bergounioux C, Crespi M, Mahfouz MM, Hirt H, Raynaud C, Benhamed M.

Genome Biol. 2017 Jun 15;18(1):114. doi: 10.1186/s13059-017-1246-7.

11.

The quest for epigenetic regulation underlying unisexual flower development in Cucumis melo.

Latrasse D, Rodriguez-Granados NY, Veluchamy A, Mariappan KG, Bevilacqua C, Crapart N, Camps C, Sommard V, Raynaud C, Dogimont C, Boualem A, Benhamed M, Bendahmane A.

Epigenetics Chromatin. 2017 Jun 6;10:22. doi: 10.1186/s13072-017-0132-6. eCollection 2017.

12.

Plant programmed cell death from a chromatin point of view.

Latrasse D, Benhamed M, Bergounioux C, Raynaud C, Delarue M.

J Exp Bot. 2016 Oct;67(20):5887-5900. Epub 2016 Sep 17. Review.

PMID:
27639093
13.

The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 Subunit LHP1 Function in Concert to Regulate the Transcription of Stress-Responsive Genes.

Molitor AM, Latrasse D, Zytnicki M, Andrey P, Houba-Hérin N, Hachet M, Battail C, Del Prete S, Alberti A, Quesneville H, Gaudin V.

Plant Cell. 2016 Sep;28(9):2197-2211. doi: 10.1105/tpc.16.00244. Epub 2016 Aug 5.

14.

LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome.

Veluchamy A, Jégu T, Ariel F, Latrasse D, Mariappan KG, Kim SK, Crespi M, Hirt H, Bergounioux C, Raynaud C, Benhamed M.

PLoS One. 2016 Jul 13;11(7):e0158936. doi: 10.1371/journal.pone.0158936. eCollection 2016.

15.

Put your 3D glasses on: plant chromatin is on show.

Rodriguez-Granados NY, Ramirez-Prado JS, Veluchamy A, Latrasse D, Raynaud C, Crespi M, Ariel F, Benhamed M.

J Exp Bot. 2016 May;67(11):3205-21. doi: 10.1093/jxb/erw168. Epub 2016 Apr 29. Review.

PMID:
27129951
16.

Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop.

Ariel F, Jegu T, Latrasse D, Romero-Barrios N, Christ A, Benhamed M, Crespi M.

Mol Cell. 2014 Aug 7;55(3):383-96. doi: 10.1016/j.molcel.2014.06.011. Epub 2014 Jul 10.

17.

The BAF60 subunit of the SWI/SNF chromatin-remodeling complex directly controls the formation of a gene loop at FLOWERING LOCUS C in Arabidopsis.

Jégu T, Latrasse D, Delarue M, Hirt H, Domenichini S, Ariel F, Crespi M, Bergounioux C, Raynaud C, Benhamed M.

Plant Cell. 2014 Feb;26(2):538-51. doi: 10.1105/tpc.113.114454. Epub 2014 Feb 7.

18.

Chromatin meets the cell cycle.

Raynaud C, Mallory AC, Latrasse D, Jégu T, Bruggeman Q, Delarue M, Bergounioux C, Benhamed M.

J Exp Bot. 2014 Jun;65(10):2677-89. doi: 10.1093/jxb/ert433. Epub 2014 Feb 4. Review.

PMID:
24497647
19.

Multiple functions of Kip-related protein5 connect endoreduplication and cell elongation.

Jégu T, Latrasse D, Delarue M, Mazubert C, Bourge M, Hudik E, Blanchet S, Soler MN, Charon C, De Veylder L, Raynaud C, Bergounioux C, Benhamed M.

Plant Physiol. 2013 Apr;161(4):1694-705. doi: 10.1104/pp.112.212357. Epub 2013 Feb 20.

20.

Dual function of MIPS1 as a metabolic enzyme and transcriptional regulator.

Latrasse D, Jégu T, Meng PH, Mazubert C, Hudik E, Delarue M, Charon C, Crespi M, Hirt H, Raynaud C, Bergounioux C, Benhamed M.

Nucleic Acids Res. 2013 Mar 1;41(5):2907-17. doi: 10.1093/nar/gks1458. Epub 2013 Jan 21.

21.

Arabidopsis histone deacetylase HDA9 regulates flowering time through repression of AGL19.

Kim W, Latrasse D, Servet C, Zhou DX.

Biochem Biophys Res Commun. 2013 Mar 8;432(2):394-8. doi: 10.1016/j.bbrc.2012.11.102. Epub 2012 Dec 10.

PMID:
23237803
22.

The Arabidopsis ortholog of the YEATS domain containing protein YAF9a regulates flowering by controlling H4 acetylation levels at the FLC locus.

Zacharaki V, Benhamed M, Poulios S, Latrasse D, Papoutsoglou P, Delarue M, Vlachonasios KE.

Plant Sci. 2012 Nov;196:44-52. doi: 10.1016/j.plantsci.2012.07.010. Epub 2012 Aug 3.

PMID:
23017898
23.

Control of flowering and cell fate by LIF2, an RNA binding partner of the polycomb complex component LHP1.

Latrasse D, Germann S, Houba-Hérin N, Dubois E, Bui-Prodhomme D, Hourcade D, Juul-Jensen T, Le Roux C, Majira A, Simoncello N, Granier F, Taconnat L, Renou JP, Gaudin V.

PLoS One. 2011 Jan 31;6(1):e16592. doi: 10.1371/journal.pone.0016592.

24.

Histone acetyltransferase GCN5 interferes with the miRNA pathway in Arabidopsis.

Kim W, Benhamed M, Servet C, Latrasse D, Zhang W, Delarue M, Zhou DX.

Cell Res. 2009 Jul;19(7):899-909. doi: 10.1038/cr.2009.59.

PMID:
19436261
25.

The MYST histone acetyltransferases are essential for gametophyte development in Arabidopsis.

Latrasse D, Benhamed M, Henry Y, Domenichini S, Kim W, Zhou DX, Delarue M.

BMC Plant Biol. 2008 Nov 28;8:121. doi: 10.1186/1471-2229-8-121.

26.

Characterization of a phosphatase 2C protein as an interacting partner of the histone acetyltransferase GCN5 in Arabidopsis.

Servet C, Benhamed M, Latrasse D, Kim W, Delarue M, Zhou DX.

Biochim Biophys Acta. 2008 Jun-Jul;1779(6-7):376-82. doi: 10.1016/j.bbagrm.2008.04.007. Epub 2008 May 2.

PMID:
18498779

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