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  • 2020
  • 2018
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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)

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)

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
48 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

12 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)

Climate change and the need for agricultural adaptation

Anderson, R., Bayer, P. E. & Edwards, D., 11 Feb 2020, In : Current Opinion in Plant Biology.

Research output: Contribution to journalReview article

6 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)

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)

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
19 Citations (Scopus)
369 Downloads (Pure)

Genome-wide identification and comparative analysis of resistance genes in Brassica juncea

Inturrisi, F., Bayer, P. E., Yang, H., Tirnaz, S., Edwards, D. & Batley, J., Aug 2020, In : Molecular Breeding. 40, 8, 78.

Research output: Contribution to journalArticle

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
43 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

29 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

Legume pangenome construction using an iterative mapping and assembly approach

Hu, H., Yuan, Y., Bayer, P. E., Fernandez, C. T., Scheben, A., Golicz, A. A. & Edwards, D., 1 Jan 2020, Legume Genomics: Methods and Protocols. Jain, M. & Garg, R. (eds.). New York: Humana Press, Vol. 2107. p. 35-47 13 p. (Methods in Molecular Biology; vol. 2107).

Research output: Chapter in Book/Conference paperChapter

1 Citation (Scopus)

Method for Genome-Wide Association Study: A Soybean Example

Anderson, R., Fernandez, C. T., Yuan, Y., Golicz, A. A., Edwards, D. & Bayer, P. E., 2020, Methods in Molecular Biology . Humana, New York, NY, Vol. 2107. p. 147-158 12 p. (Methods in molecular biology (Clifton, N.J.)).

Research output: Chapter in Book/Conference paperChapter

Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications

Golicz, A. A., Bayer, P. E., Bhalla, P. L., Batley, J. & Edwards, D., Feb 2020, In : Trends in Genetics. 36, 2, p. 132-145 14 p.

Research output: Contribution to journalReview article

7 Citations (Scopus)

Plant pan-genomes are the new reference

Bayer, P. E., Golicz, A. A., Scheben, A., Batley, J. & Edwards, D., 1 Aug 2020, In : Nature Plants. 6, 8, p. 914-920

Research output: Contribution to journalReview article

Plant pangenomics: approaches, applications and advancements

Danilevicz, M. F., Tay Fernandez, C. G., Marsh, J. I., Bayer, P. E. & Edwards, D., Apr 2020, In : Current Opinion in Plant Biology. 54, p. 18-25 8 p.

Research output: Contribution to journalReview article

4 Citations (Scopus)
2 Downloads (Pure)

Resistance gene analogs in the Brassicaceae: Identification, characterization, distribution, and evolution

Tirnaz, S., Bayer, P., Inturrisi, F., Zhang, F., Yang, H., Dolatabadian, A., Neik, T. X., Severn-Ellis, A., Patel, D., Ibrahim, M. I., Pradhan, A., Edwards, D. & Batley, J., Oct 2020, In : Plant Physiology. 184, p. 909–922

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
687 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
27 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
103 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
86 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)

Trait associations in the pangenome of pigeon pea (Cajanus cajan)

Zhao, J., Bayer, P. E., Ruperao, P., Saxena, R. K., Khan, A. W., Golicz, A. A., Nguyen, H. T., Batley, J., Edwards, D. & Varshney, R. K., 5 Feb 2020, In : Plant Biotechnology Journal.

Research output: Contribution to journalArticle

Open Access
2 Citations (Scopus)