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  • 2019
  • 2018
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  • 2016

Author

  • Philipp Bayer

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

Hane, J. K., Ming, Y., Kamphuis, L. G., Nelson, M. N., Garg, G., Atkins, C. A., Bayer, P. E., Bravo, A., Bringans, S. D., Cannon, S., Edwards, D., Foley, R., Gao, L. L., Harrison, M. J., Huang, W., Hurgobin, B., Li, S., Liu, C. W., McGrath, A., Morahan, G. & 4 others, Murray, J., Weller, J. L., Jian, J. & Singh, K. B., 1 Mar 2017, In : Plant Biotechnology Journal. 15, 3, p. 318-330 13 p.

Research output: Contribution to journalArticle

Open Access
63 Citations (Scopus)

Adapting legume crops to climate change using genomic approaches

Mousavi-Derazmahalleh, M., Bayer, P. E., Hane, J. K., Babu, V., Nguyen, H. T., Nelson, M. N., Erskine, W., Varshney, R. K., Papa, R. & Edwards, D., 30 Jan 2019, In : Plant Cell and Environment. 42, 1, p. 6-19

Research output: Contribution to journalReview article

Open Access
15 Citations (Scopus)

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

Kaur, P., Bayer, P. E., Milec, Z., Vrána, J., Yuan, Y., Appels, R., Edwards, D., Batley, J., Nichols, P., Erskine, W. & Doležel, J., 12 Jul 2017, In : Plant Biotechnology Journal. 15, 8, p. 1034-1046 13 p.

Research output: Contribution to journalArticle

Open Access
13 Citations (Scopus)

An efficient approach to BAC based assembly of complex genomes

Visendi, P., Berkman, P. J., Hayashi, S., Golicz, A. A., Bayer, P., Ruperao, P., Hurgobin, B., Montenegro, J., Chan, K., Staňková, H., Batley, J., Šimková, H., Doležel, J. & Edwards, D., 20 Jan 2016, In : Plant Methods. 12, 1, p. 1

Research output: Contribution to journalArticle

Open Access
7 Citations (Scopus)

A reference genome for pea provides insight into legume genome evolution

Kreplak, J., Madoui, M. A., Cápal, P., Novák, P., Labadie, K., Aubert, G., Bayer, P. E., Gali, K. K., Syme, R. A., Main, D., Klein, A., Bérard, A., Vrbová, I., Fournier, C., d’Agata, L., Belser, C., Berrabah, W., Toegelová, H., Milec, Z., Vrána, J. & 25 others, Lee, H. T., Kougbeadjo, A., Térézol, M., Huneau, C., Turo, C. J., Mohellibi, N., Neumann, P., Falque, M., Gallardo, K., McGee, R., Tar’an, B., Bendahmane, A., Aury, J. M., Batley, J., Le Paslier, M. C., Ellis, N., Warkentin, T. D., Coyne, C. J., Salse, J., Edwards, D., Lichtenzveig, J., Macas, J., Doležel, J., Wincker, P. & Burstin, J., 2 Sep 2019, In : Nature Genetics. 51, 9, p. 1411-1422 12 p.

Research output: Contribution to journalArticle

Open Access
30 Citations (Scopus)

Assembly and comparison of two closely related Brassica napus genomes

Bayer, P. E., Hurgobin, B., Golicz, A. A., Chan, C-K. K., Yuan, Y., Lee, H., Renton, M., Meng, J., Li, R., Long, Y., Zou, J., Bancroft, I., Chalhoub, B., King, G. J., Batley, J. & Edwards, D., Dec 2017, In : Plant Biotechnology Journal. 15, 12, p. 1-9 9 p.

Research output: Contribution to journalArticle

Open Access
46 Citations (Scopus)

Bias in resistance gene prediction due to repeat masking

Bayer, P. E., Edwards, D. & Batley, J., 1 Oct 2018, In : Nature Plants. 4, 10, p. 762-765 4 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

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

Yuan, Y., Bayer, P. E., Scheben, A., Chan, C. K. K. & Edwards, D., 30 Jun 2017, In : BMC Bioinformatics. 18, 1, 9 p., 323.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

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

Mason, A. S., Rousseau-Gueutin, M., Morice, J., Bayer, P., Besharat, N., Cousin, A., Pradhan, A., Parkin, I. A., Chevre, A. M., Batley, J. & Nelson, M., Feb 2016, In : Genetics. 202, 2, p. 513-523

Research output: Contribution to journalArticle

Open Access
16 Citations (Scopus)

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation

Dolatabadian, A., Bayer, P. E., Tirnaz, S., Hurgobin, B., Edwards, D. & Batley, J., 25 Sep 2019, In : Plant Biotechnology Journal. 14 p.

Research output: Contribution to journalArticle

Open Access
5 Citations (Scopus)

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, P. E., Keeble-Gagnere, G., Wang, J., Hirakawa, H., Shirasawa, K., Vercoe, P., Stefanova, K., Durmic, Z., Nichols, P., Revell, C., Isobe, S. N., Edwards, D. & Erskine, W., 5 Sep 2017, In : Frontiers in Plant Science. 8, 10 p., 1463.

Research output: Contribution to journalArticle

Open Access
4 Citations (Scopus)

Construction and comparison of three reference-quality genome assemblies for soybean

Valliyodan, B., Cannon, S. B., Bayer, P. E., Shu, S., Brown, A. V., Ren, L., Jenkins, J., Chung, C. Y-L., Chan, T-F., Daum, C. G., Plott, C., Hastie, A., Baruch, K., Barry, K. W., Huang, W., Patil, G., Varshney, R. K., Hu, H., Batley, J., Yuan, Y. & 10 others, Song, Q., Stupar, R. M., Goodstein, D. M., Stacey, G., Lam, H-M., Jackson, S. A., Schmutz, J., Grimwood, J., Edwards, D. & Nguyen, H. T., Dec 2019, In : The Plant Journal. 100, 5, p. 1066-1082 39 p.

Research output: Contribution to journalArticle

Open Access
File
2 Citations (Scopus)
36 Downloads (Pure)

CropSNPdb: a database of SNP array data for Brassica crops and hexaploid bread wheat

Scheben, A., Verpaalen, B., Lawley, C. T., Chan, C-K. K., Bayer, P. E., Batley, J. & Edwards, D., Apr 2019, In : Plant Journal. 98, 1, p. 142-152 11 p.

Research output: Contribution to journalArticle

Open Access
5 Citations (Scopus)

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

Schneider, M. V., Griffin, P. C., Tyagi, S., Flannery, M., Dayalan, S., Gladman, S., Watson-Haigh, N., Bayer, P. E., Charleston, M., Cooke, I., Cook, R., Edwards, R. J., Edwards, D., Gorse, D., McConville, M., Powell, D., Wilkins, M. R. & Lonie, A., Mar 2019, In : Briefings in Bioinformatics. 20, 2, p. 384-389 6 p.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

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

Mousavi-Derazmahalleh, M., Bayer, P. E., Nevado, B., Hurgobin, B., Filatov, D., Kilian, A., Kamphuis, L. G., Singh, K. B., Berger, J. D., Hane, J. K., Edwards, D., Erskine, W. & Nelson, M. N., Apr 2018, In : Theoretical and Applied Genetics. 131, 4, p. 887–901 15 p.

Research output: Contribution to journalArticle

Open Access
11 Citations (Scopus)
Open Access
1 Citation (Scopus)
19 Downloads (Pure)

Genome‐Wide Association Studies in Plants

Anderson, R., Edwards, D., Batley, J. & Bayer, P., 15 Feb 2019, eLS. John Wiley & Sons, p. 1-7 7 p.

Research output: Chapter in Book/Conference paperChapter

File
175 Downloads (Pure)

Genome-wide association study of genetic control of seed fatty acid biosynthesis in Brassica napus

Gacek, K., Bayer, P. E., Bartkowiak-Broda, I., Szala, L., Bocianowski, J., Edwards, D. & Batley, J., 20 Jan 2017, In : Frontiers in Plant Science. 7, 2062.

Research output: Contribution to journalArticle

Open Access
25 Citations (Scopus)

Genome-wide identification and comparative analysis of NBS-LRR resistance genes in Brassica napus

Alamery, S., Tirnaz, S., Bayer, P., Tollenaere, R., Chaloub, B., Edwards, D. & Batley, J., 1 Jan 2018, In : Crop and Pasture Science. 69, S1, p. 79-93 15 p.

Research output: Contribution to journalConference article

Open Access
File
17 Citations (Scopus)
369 Downloads (Pure)

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

Lee, H., Golicz, A. A., Bayer, P. E., Severn-Ellis, A. A., Chan, C. K. K., Batley, J., Kendrick, G. A. & Edwards, D., 27 Jun 2018, In : Journal of Experimental Botany. 69, 15, p. 3689-3702 14 p.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)
Open Access
5 Citations (Scopus)
282 Downloads (Pure)

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

Hurgobin, B., Golicz, A. A., Bayer, P. E., Chan, C-K. K., Tirnaz, S., Dolatabadian, A., Schiessl, S. V., Samans, B., Montenegro, J. D., Parkin, I. A. P., Pires, J. C., Chalhoub, B., King, G. J., Snowdon, R., Batley, J. & Edwards, D., 10 Jan 2018, In : Plant Biotechnology Journal. p. 1-10

Research output: Contribution to journalArticle

Open Access
40 Citations (Scopus)

Improvements in Genomic Technologies: Application to Crop Genomics

Yuan, Y., Bayer, P. E., Batley, J. & Edwards, D., Jun 2017, In : Trends in Biotechnology. 35, 6, p. 547-558

Research output: Contribution to journalReview article

28 Citations (Scopus)
Open Access
14 Citations (Scopus)

Large-scale structural variation detection in subterranean clover subtypes using optical mapping

Yuan, Y., Milec, Z., Bayer, P. E., Vrána, J., Doležel, J., Edwards, D., Erskine, W. & Kaur, P., 17 Jul 2018, In : Frontiers in Plant Science. 9, 971.

Research output: Contribution to journalArticle

Open Access

Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics

Mousavi-Derazmahalleh, M., Chang, S., Thomas, G., Derbyshire, M., Bayer, P. E., Edwards, D., Nelson, M. N., Erskine, W., Lopez-Ruiz, F. J., Clements, J. & Hane, J. K., 17 May 2019, In : BMC Genomics. 20, 11 p., 385.

Research output: Contribution to journalArticle

Open Access

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

Yuan, Y., Bayer, P. E., Lee, H-T. & Edwards, D., 1 Oct 2017, In : Bioinformatics. 33, 19, p. 3107-3109 3 p.

Research output: Contribution to journalArticle

Open Access
2 Citations (Scopus)

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

International Wheat Genome Sequencing Consortium (IWGSC), 17 Aug 2018, In : Science. 361, 6403, eaar7191.

Research output: Contribution to journalArticle

Open Access
675 Citations (Scopus)

Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions, and Improve Genome Assemblies

Bayer, P. E., 2016, Plant Bioinformatics: Methods and Protocols. Edwards, D. (ed.). 2nd ed. New York: Humana Press, Vol. 1374. p. 285-292 8 p. (Methods in Molecular Biology).

Research output: Chapter in Book/Conference paperChapter

1 Citation (Scopus)

The genome of a southern hemisphere seagrass species (Zostera muelleri)

Lee, H., Golicz, A. A., Bayer, P. E., Jiao, Y., Tang, H., Paterson, A. H., Sablok, G., Krishnaraj, R. R., Chan, C-K. K., Batley, J., Kendrick, G. A., Larkum, A. W. D., Ralph, P. J. & Edwards, D., Sep 2016, In : Plant Physiology. 172, 1, p. 272-283

Research output: Contribution to journalArticle

Open Access
26 Citations (Scopus)

The More the Merrier? Investigating Copy Number Variation in Brassica Disease Resistance

Batley, J., Dolatabadian, A., Yang, H., Severn-Ellis, A., Alamery, S., Tollenaere, R., Bayer, P., Hurgobin, B., Golicz, A. A. & Edwards, D., 2016.

Research output: Contribution to conferencePoster

The pangenome of an agronomically important crop plant Brassica oleracea

Golicz, A. A., Bayer, P. E., Barker, G. C., Edger, P. P., Kim, H. R., Martinez, P. A., Chan, C. K. K., Severn-Ellis, A., McCombie, W. R., Parkin, I. A. P., Paterson, A. H., Pires, J. C., Sharpe, A. G., Tang, H., Teakle, G. R., Town, C. D., Batley, J. & Edwards, D., 11 Nov 2016, In : Nature Communications. 7, 13390.

Research output: Contribution to journalArticle

Open Access
100 Citations (Scopus)

The pangenome of hexaploid bread wheat

Montenegro, J. D., Golicz, A. A., Bayer, P. E., Hurgobin, B., Lee, H., Chan, C. K. K., Visendi, P., Lai, K., Doležel, J., Batley, J. & Edwards, D., Jun 2017, In : The Plant Journal. 90, 5, p. 1007-1013

Research output: Contribution to journalArticle

Open Access
82 Citations (Scopus)

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

Mousavi-Derazmahalleh, M., Nevado, B., Bayer, P. E., Filatov, D. A., Hane, J. K., Edwards, D., Erskine, W. & Nelson, M. N., Dec 2018, In : Theoretical and Applied Genetics. 131, 12, p. 2543-2554

Research output: Contribution to journalArticle

Open Access
5 Citations (Scopus)

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

Bayer, P. E., Golicz, A. A., Tirnaz, S., Chan, C. K. K., Edwards, D. & Batley, J., Apr 2019, In : Plant Biotechnology Journal. p. 789-800 12 p.

Research output: Contribution to journalArticle

Open Access
21 Citations (Scopus)