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Items: 19

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.

Conservation analysis of long non-coding RNAs in plants.

Deng P, Liu S, Nie X, Weining S, Wu L.

Sci China Life Sci. 2018 Feb;61(2):190-198. doi: 10.1007/s11427-017-9174-9. Epub 2017 Oct 31.

PMID:
29101587
3.

Identification and Analysis of RNA Editing Sites in the Chloroplast Transcripts of Aegilops tauschii L.

Wang M, Liu H, Ge L, Xing G, Wang M, Weining S, Nie X.

Genes (Basel). 2016 Dec 30;8(1). pii: E13. doi: 10.3390/genes8010013.

4.

Characterization of microRNAs and their targets in wild barley (Hordeum vulgare subsp. spontaneum) using deep sequencing.

Deng P, Bian J, Yue H, Feng K, Wang M, Du X, Weining S, Nie X.

Genome. 2016 May;59(5):339-48. doi: 10.1139/gen-2015-0224. Epub 2016 Mar 18.

PMID:
27100818
5.

Global Identification of MicroRNAs and Their Targets in Barley under Salinity Stress.

Deng P, Wang L, Cui L, Feng K, Liu F, Du X, Tong W, Nie X, Ji W, Weining S.

PLoS One. 2015 Sep 15;10(9):e0137990. doi: 10.1371/journal.pone.0137990. eCollection 2015.

6.

Preparation of high molecular weight gDNA and bacterial artificial chromosome (BAC) libraries in plants.

Biradar SS, Nie X, Feng K, Weining S.

Methods Mol Biol. 2014;1099:41-63. doi: 10.1007/978-1-62703-715-0_6.

PMID:
24243195
7.

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor.

Luo MC, Gu YQ, You FM, Deal KR, Ma Y, Hu Y, Huo N, Wang Y, Wang J, Chen S, Jorgensen CM, Zhang Y, McGuire PE, Pasternak S, Stein JC, Ware D, Kramer M, McCombie WR, Kianian SF, Martis MM, Mayer KF, Sehgal SK, Li W, Gill BS, Bevan MW, Simková H, Dolezel J, Weining S, Lazo GR, Anderson OD, Dvorak J.

Proc Natl Acad Sci U S A. 2013 May 7;110(19):7940-5. doi: 10.1073/pnas.1219082110. Epub 2013 Apr 22.

8.

Dispersion and domestication shaped the genome of bread wheat.

Berkman PJ, Visendi P, Lee HC, Stiller J, Manoli S, Lorenc MT, Lai K, Batley J, Fleury D, Simková H, Kubaláková M, Weining S, Doležel J, Edwards D.

Plant Biotechnol J. 2013 Jun;11(5):564-71. doi: 10.1111/pbi.12044. Epub 2013 Jan 24.

9.

Development of chromosome-arm-specific microsatellite markers in Triticum aestivum (Poaceae) using NGS technology.

Nie X, Li B, Wang L, Liu P, Biradar SS, Li T, Dolezel J, Edwards D, Luo M, Weining S.

Am J Bot. 2012 Sep;99(9):e369-71. doi: 10.3732/ajb.1200077. Epub 2012 Aug 30.

10.

Complete chloroplast genome sequence of a major invasive species, crofton weed (Ageratina adenophora).

Nie X, Lv S, Zhang Y, Du X, Wang L, Biradar SS, Tan X, Wan F, Weining S.

PLoS One. 2012;7(5):e36869. doi: 10.1371/journal.pone.0036869. Epub 2012 May 11.

11.

Identification and characterization of microRNAs from barley (Hordeum vulgare L.) by high-throughput sequencing.

Lv S, Nie X, Wang L, Du X, Biradar SS, Jia X, Weining S.

Int J Mol Sci. 2012;13(3):2973-84. doi: 10.3390/ijms13032973. Epub 2012 Mar 6.

12.

Genetic diversity of mitochondrial cytochrome b gene in Chinese native buffalo.

Lei CZ, Zhang CM, Weining S, Campana MG, Bower MA, Zhang XM, Liu L, Lan XY, Chen H.

Anim Genet. 2011 Aug;42(4):432-6. doi: 10.1111/j.1365-2052.2011.02174.x. Epub 2011 Mar 7.

PMID:
21749426
13.

Multiple maternal origins of native modern and ancient horse populations in China.

Lei CZ, Su R, Bower MA, Edwards CJ, Wang XB, Weining S, Liu L, Xie WM, Li F, Liu RY, Zhang YS, Zhang CM, Chen H.

Anim Genet. 2009 Dec;40(6):933-44. doi: 10.1111/j.1365-2052.2009.01950.x. Epub 2009 Sep 10.

PMID:
19744143
14.

A MAPK gene from Dead Sea fungus confers stress tolerance to lithium salt and freezing-thawing: Prospects for saline agriculture.

Jin Y, Weining S, Nevo E.

Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):18992-7. Epub 2005 Dec 19.

15.

Wild barley eibi1 mutation identifies a gene essential for leaf water conservation.

Chen G, Sagi M, Weining S, Krugman T, Fahima T, Korol AB, Nevo E.

Planta. 2004 Aug;219(4):684-93. Epub 2004 Jun 9.

PMID:
15197591
16.

Anchor primer associated problems in differential display reverse transcription polymerase chain reaction.

Chen Y, Wang B, Weining S, Daggard G.

Anal Biochem. 2004 Jun 1;329(1):145-7. No abstract available.

PMID:
15136178
17.
18.

Polymorphisms in the α-amy1 gene of wild and cultivated barley revealed by the polymerase chain reaction.

Weining S, Ko L, Henry RJ.

Theor Appl Genet. 1994 Oct;89(4):509-13. doi: 10.1007/BF00225388.

PMID:
24177902
19.

Identification and mapping of polymorphisms in cereals based on the polymerase chain reaction.

Weining S, Langridge P.

Theor Appl Genet. 1991 Aug;82(2):209-16. doi: 10.1007/BF00226215.

PMID:
24213068

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