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  • Philipp Bayer

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 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)

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)

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
6 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)

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
3 Citations (Scopus)
37 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
6 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 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)
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

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)

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
1 Citation (Scopus)

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

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 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)

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
22 Citations (Scopus)