Publications

Full list of publications can be found here:
https://scholar.google.com/citations?user=KR_W0jIAAAAJ&hl=en

Selected manuscripts:

Jayakodi, M.*, Golicz, A.A.*, Kreplak, J.*, Fechete, L.I., Angra, D., Bednar, P., Bornhofen, E., Zhang, H., Boussageon, R., Kaur, S., Cheung, K., Cizkova, J., Gundlach, H., Hallab, A., Imbert, B., Keeble-Gagnere, G., Koblizkova, A., Kobrlova, L., Krejci, P., Mouritzen, T.W., Neumann, P., Nadzieja, M., Nielsen, L.K., Novak, P., Orabi, J., Padmarasu, S., Robertson-Shersby-Harvie, T., Robledillo, L.A., Schiemann, A., Tanskanen, J., Toronen, P., Warsame, A.O., Wittenberg, A.H., Himmelbach, A., Aubert, G., Courty, P.-E., Dolezel, J., Holm, L.U., Janss, L.L., Khazaei, H., Macas, J., Mascher, M., Smykal, P., Snowdon, R.J., Stein, N., Stoddard, F.L., Stougaard, J., Tayeh, N., Torres, A.M., Usadel, B., Schubert, I., O’Sullivan, D.M., Schulman, A.H. and Andersen, S.U. (2023) The giant diploid faba genome unlocks variation in a global protein crop. Nature. *Co-first author. https://doi.org/10.1038/s41586-023-05791-5
Here we describe assembly, annotation and comparative analyses of two faba bean genomes.

Yildiz, G., Zanini, S.F., Afsharyan, N.P., Obermeier, C., Snowdon, R.J. and Golicz, A.A. (2022) Benchmarking Oxford Nanopore Read Alignment-Based Structural Variant Detection Tools in Crop Plant Genomes. bioRxiv, 2022.09.23.508909. https://doi.org/10.1101/2022.09.23.508909
In this manuscript we compare different structural variant discovery algorithms using crop plant genome data,

Zanini, S.F., Bayer, P.E., Wells, R., Snowdon, R.J., Batley, J., Varshney, R.K., Nguyen, H.T., Edwards, D. and Golicz, A.A. (2021) Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs. Plant Genome, e20177. https://doi.org/10.1002/tpg2.20177
This manuscript outlines advances in the use of pangenome graphs for crop plant research.

Bayer, P.E., Scheben, A., Golicz, A.A., Yuan, Y., Faure, S., Lee, H., Chawla, H.S., Anderson, R., Bancroft, I., Raman, H., Lim, Y.P., Robbens, S., Jiang, L., Liu, S., Barker, M.S., Schranz, M.E., Wang, X., King, G.J., Pires, J.C., Chalhoub, B., Snowdon, R.J., Batley, J. and Edwards, D. (2021) Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids. Plant Biotechnol J. https://doi.org/10.1111/pbi.13674
This manuscript describes pangenome for three Brassica species and suggests possible features associated with gene presence/absence variation in diploids and polyploids.

Gill, R.A., Scossa, F., King, G.J., Golicz, A.A., Tong C., Snowdon R.J., Fernie A.R. and Liu S. (2021) On the Role of Transposable Elements in the Regulation of Gene Expression and Subgenomic Interactions in Crop Genomes. Critical Reviews in Plant Sciences, 40, 157-189. https://doi.org/10.1080/07352689.2021.1920731
This manuscript provides a comprehensive review of the role of transposable elements in regulation of genome structure and gene expression.

Golicz, A.A., Bayer, P.E., Bhalla, P.L., Batley, J. and Edwards, D. (2020) Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications. Trends in Genetics, 36, 132–145. https://doi.org/10.1016/j.tig.2019.11.006
This manuscript describes recent developments in plant and animal pangenomics.

Golicz, A.A., Bhalla, P.L., Edwards, D. and Singh, M.B. (2020) Rice 3D chromatin structure correlates with sequence variation and meiotic recombination rate. Communications Biology, 3, 235. https://doi.org/10.1038/s42003-020-0932-2
This manuscript reports correlation between sequence variation (single nucleotide and structural variants) and 3D genome structure in rice.

Golicz, A.A., Bayer, P.E., Barker, G.C., Edger, P.P., Kim, H., 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. and Edwards, D. (2016) The pangenome of an agronomically important crop plant Brassica oleracea. Nature Communications, 7, 13390. https://doi.org/10.1038/ncomms13390
This manuscript reports one of first plant pangenomes constructed and a suite of methods developed for pangenome analysis.