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Items: 34

1.

Bias in resistance gene prediction due to repeat masking.

Bayer PE, Edwards D, Batley J.

Nat Plants. 2018 Oct;4(10):762-765. doi: 10.1038/s41477-018-0264-0. Epub 2018 Oct 1.

PMID:
30287950
2.

High intraspecific diversity of Restorer-of-fertility-like genes in barley.

Melonek J, Zhou R, Bayer PE, Edwards D, Stein N, Small I.

Plant J. 2018 Oct 1. doi: 10.1111/tpj.14115. [Epub ahead of print]

PMID:
30276910
3.

Variation in abundance of predicted resistance genes in the Brassica oleracea pangenome.

Bayer PE, Golicz AA, Tirnaz S, Chan CK, Edwards D, Batley J.

Plant Biotechnol J. 2018 May 31. doi: 10.1111/pbi.13015. [Epub ahead of print]

4.

The western Mediterranean region provided the founder population of domesticated narrow-leafed lupin.

Mousavi-Derazmahalleh M, Nevado B, Bayer PE, Filatov DA, Hane JK, Edwards D, Erskine W, Nelson MN.

Theor Appl Genet. 2018 Dec;131(12):2543-2554. doi: 10.1007/s00122-018-3171-x. Epub 2018 Sep 17.

5.

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
6.

Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical Mapping.

Yuan Y, Milec Z, Bayer PE, Vrána J, Doležel J, Edwards D, Erskine W, Kaur P.

Front Plant Sci. 2018 Jul 17;9:971. doi: 10.3389/fpls.2018.00971. eCollection 2018.

7.

Genomic comparison of two independent seagrass lineages reveals habitat-driven convergent evolution.

Lee H, Golicz AA, Bayer PE, Severn-Ellis AA, Chan CK, Batley J, Kendrick GA, Edwards D.

J Exp Bot. 2018 Jun 27;69(15):3689-3702. doi: 10.1093/jxb/ery147.

8.

INDEL variation in the regulatory region of the major flowering time gene LanFTc1 is associated with vernalization response and flowering time in narrow-leafed lupin (Lupinus angustifolius L.).

Taylor CM, Kamphuis LG, Zhang W, Garg G, Berger JD, Mousavi-Derazmahalleh M, Bayer PE, Edwards D, Singh KB, Cowling WA, Nelson MN.

Plant Cell Environ. 2019 Jan;42(1):174-187. doi: 10.1111/pce.13320. Epub 2018 May 23.

PMID:
29677403
9.

Adapting legume crops to climate change using genomic approaches.

Mousavi-Derazmahalleh M, Bayer PE, Hane JK, Valliyodan B, Nguyen HT, Nelson MN, Erskine W, Varshney RK, Papa R, Edwards D.

Plant Cell Environ. 2019 Jan;42(1):6-19. doi: 10.1111/pce.13203. Epub 2018 Jun 13. Review.

PMID:
29603775
10.

Exploring the genetic and adaptive diversity of a pan-Mediterranean crop wild relative: narrow-leafed lupin.

Mousavi-Derazmahalleh M, Bayer PE, Nevado B, Hurgobin B, Filatov D, Kilian A, Kamphuis LG, Singh KB, Berger JD, Hane JK, Edwards D, Erskine W, Nelson MN.

Theor Appl Genet. 2018 Apr;131(4):887-901. doi: 10.1007/s00122-017-3045-7. Epub 2018 Jan 20.

11.

Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus.

Hurgobin B, Golicz AA, Bayer PE, Chan CK, Tirnaz S, Dolatabadian A, Schiessl SV, Samans B, Montenegro JD, Parkin IAP, Pires JC, Chalhoub B, King GJ, Snowdon R, Batley J, Edwards D.

Plant Biotechnol J. 2018 Jul;16(7):1265-1274. doi: 10.1111/pbi.12867. Epub 2018 Jan 10.

12.

Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia.

Schneider MV, Griffin PC, Tyagi S, Flannery M, Dayalan S, Gladman S, Watson-Haigh N, Bayer PE, Charleston M, Cooke I, Cook R, Edwards RJ, Edwards D, Gorse D, McConville M, Powell D, Wilkins MR, Lonie A.

Brief Bioinform. 2017 Jun 30. doi: 10.1093/bib/bbx071. [Epub ahead of print]

PMID:
29106479
13.

Climate Clever Clovers: New Paradigm to Reduce the Environmental Footprint of Ruminants by Breeding Low Methanogenic Forages Utilizing Haplotype Variation.

Kaur P, Appels R, Bayer PE, Keeble-Gagnere G, Wang J, Hirakawa H, Shirasawa K, Vercoe P, Stefanova K, Durmic Z, Nichols P, Revell C, Isobe SN, Edwards D, Erskine W.

Front Plant Sci. 2017 Sep 5;8:1463. doi: 10.3389/fpls.2017.01463. eCollection 2017.

14.

BioNanoAnalyst: a visualisation tool to assess genome assembly quality using BioNano data.

Yuan Y, Bayer PE, Scheben A, Chan CK, Edwards D.

BMC Bioinformatics. 2017 Jun 30;18(1):323. doi: 10.1186/s12859-017-1735-4.

15.

runBNG: a software package for BioNano genomic analysis on the command line.

Yuan Y, Bayer PE, Lee HT, Edwards D.

Bioinformatics. 2017 Oct 1;33(19):3107-3109. doi: 10.1093/bioinformatics/btx366.

PMID:
28605539
16.

Assembly and comparison of two closely related Brassica napus genomes.

Bayer PE, Hurgobin B, Golicz AA, Chan CK, Yuan Y, Lee H, Renton M, Meng J, Li R, Long Y, Zou J, Bancroft I, Chalhoub B, King GJ, Batley J, Edwards D.

Plant Biotechnol J. 2017 Dec;15(12):1602-1610. doi: 10.1111/pbi.12742. Epub 2017 Jun 14.

17.

Improvements in Genomic Technologies: Application to Crop Genomics.

Yuan Y, Bayer PE, Batley J, Edwards D.

Trends Biotechnol. 2017 Jun;35(6):547-558. doi: 10.1016/j.tibtech.2017.02.009. Epub 2017 Mar 9. Review.

PMID:
28284542
18.

The pangenome of hexaploid bread wheat.

Montenegro JD, Golicz AA, Bayer PE, Hurgobin B, Lee H, Chan CK, Visendi P, Lai K, Doležel J, Batley J, Edwards D.

Plant J. 2017 Jun;90(5):1007-1013. doi: 10.1111/tpj.13515. Epub 2017 Apr 5.

19.

Genome-Wide Association Study of Genetic Control of Seed Fatty Acid Biosynthesis in Brassica napus.

Gacek K, Bayer PE, Bartkowiak-Broda I, Szala L, Bocianowski J, Edwards D, Batley J.

Front Plant Sci. 2017 Jan 20;7:2062. doi: 10.3389/fpls.2016.02062. eCollection 2016.

20.

An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance.

Kaur P, Bayer PE, Milec Z, Vrána J, Yuan Y, Appels R, Edwards D, Batley J, Nichols P, Erskine W, Doležel J.

Plant Biotechnol J. 2017 Aug;15(8):1034-1046. doi: 10.1111/pbi.12697. Epub 2017 Mar 23.

21.

The pangenome of an agronomically important crop plant Brassica oleracea.

Golicz AA, Bayer PE, Barker GC, Edger PP, Kim H, Martinez PA, Chan CK, Severn-Ellis A, McCombie WR, Parkin IA, Paterson AH, Pires JC, Sharpe AG, Tang H, Teakle GR, Town CD, Batley J, Edwards D.

Nat Commun. 2016 Nov 11;7:13390. doi: 10.1038/ncomms13390.

22.

A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant-microbe interactions and legume evolution.

Hane JK, Ming Y, Kamphuis LG, Nelson MN, Garg G, Atkins CA, Bayer PE, Bravo A, Bringans S, Cannon S, Edwards D, Foley R, Gao LL, Harrison MJ, Huang W, Hurgobin B, Li S, Liu CW, McGrath A, Morahan G, Murray J, Weller J, Jian J, Singh KB.

Plant Biotechnol J. 2017 Mar;15(3):318-330. doi: 10.1111/pbi.12615. Epub 2016 Sep 23.

23.

The Genome of a Southern Hemisphere Seagrass Species (Zostera muelleri).

Lee H, Golicz AA, Bayer PE, Jiao Y, Tang H, Paterson AH, Sablok G, Krishnaraj RR, Chan CK, Batley J, Kendrick GA, Larkum AW, Ralph PJ, Edwards D.

Plant Physiol. 2016 Sep;172(1):272-83. doi: 10.1104/pp.16.00868. Epub 2016 Jul 3.

24.

An efficient approach to BAC based assembly of complex genomes.

Visendi P, Berkman PJ, Hayashi S, Golicz AA, Bayer PE, Ruperao P, Hurgobin B, Montenegro J, Chan CK, Staňková H, Batley J, Šimková H, Doležel J, Edwards D.

Plant Methods. 2016 Jan 20;12:2. doi: 10.1186/s13007-016-0107-9. eCollection 2016.

25.

Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis.

Mason AS, Rousseau-Gueutin M, Morice J, Bayer PE, Besharat N, Cousin A, Pradhan A, Parkin IA, Chèvre AM, Batley J, Nelson MN.

Genetics. 2016 Feb;202(2):513-23. doi: 10.1534/genetics.115.183210. Epub 2015 Nov 27.

26.
27.

High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus.

Bayer PE, Ruperao P, Mason AS, Stiller J, Chan CK, Hayashi S, Long Y, Meng J, Sutton T, Visendi P, Varshney RK, Batley J, Edwards D.

Theor Appl Genet. 2015 Jun;128(6):1039-47. doi: 10.1007/s00122-015-2488-y. Epub 2015 Mar 10.

PMID:
25754422
28.

Skim-based genotyping by sequencing.

Golicz AA, Bayer PE, Edwards D.

Methods Mol Biol. 2015;1245:257-70. doi: 10.1007/978-1-4939-1966-6_19.

PMID:
25373763
29.

Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat.

Lai K, Lorenc MT, Lee HC, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan CK, Manoli S, Stiller J, Batley J, Edwards D.

Plant Biotechnol J. 2015 Jan;13(1):97-104. doi: 10.1111/pbi.12240. Epub 2014 Aug 22.

30.

Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.

Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier MC, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee TH, Thi VH, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CH, Wang X, Canaguier A, Chauveau A, Bérard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Wang X, Meng J, Ma J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury JM, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C, Wincker P.

Science. 2014 Aug 22;345(6199):950-3. doi: 10.1126/science.1253435. Epub 2014 Aug 21.

31.

openSNP--a crowdsourced web resource for personal genomics.

Greshake B, Bayer PE, Rausch H, Reda J.

PLoS One. 2014 Mar 19;9(3):e89204. doi: 10.1371/journal.pone.0089204. eCollection 2014.

32.

High-resolution molecular karyotyping uncovers pairing between ancestrally related Brassica chromosomes.

Mason AS, Batley J, Bayer PE, Hayward A, Cowling WA, Nelson MN.

New Phytol. 2014 May;202(3):964-74. doi: 10.1111/nph.12706. Epub 2014 Jan 28.

33.

Acclimation to different depths by the marine angiosperm Posidonia oceanica: transcriptomic and proteomic profiles.

Dattolo E, Gu J, Bayer PE, Mazzuca S, Serra IA, Spadafora A, Bernardo L, Natali L, Cavallini A, Procaccini G.

Front Plant Sci. 2013 Jun 17;4:195. doi: 10.3389/fpls.2013.00195. eCollection 2013.

34.

Cell differentiation in the embryonic midgut of the tobacco hornworm, Manduca sexta.

Hakim RS, Baldwin KM, Bayer PE.

Tissue Cell. 1988;20(1):51-62.

PMID:
18620227

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