An SGSGeneloss-Based Method for Constructing a Gene Presence—Absence Table Using Mosdepth

Authors: Fernandez, Cassandria G. Tay, Marsh, Jacob I., Nestor, Benjamin J., Gill, Mitchell, Golicz, Agnieszka A., Bayer, Philipp E., Edwards, David

Source: Methods in molecular biology. 2512:73-80

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN629741882&indx=1&recIds=ETOCRN629741882

Tandem LTR-retrotransposon structures are common and highly polymorphic in plant genomes.

Authors: Morales-Díaz, Noemia, Sushko, Svitlana, Campos-Dominguez, Lucía, Kopalli, Venkataramana, Golicz, Agnieszka A., Castanera, Raúl, Casacuberta, Josep M.

Source: Mobile DNA; 3/12/2025, Vol. 16 Issue 1, p1-11, 11p

Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids

Authors: Bayer, Philipp E., Scheben, Armin, Golicz, Agnieszka A., Yuan, Yuxuan, Faure, Sebastien, Lee, HueyTyng, Chawla, Harmeet Singh, Anderson, Robyn, Bancroft, Ian, Raman, Harsh, Lim, Yong Pyo, Robbens, Steven, Jiang, Lixi, Liu, Shengyi, Barker, Michael S., Schranz, M. Eric, Wang, Xiaowu, King, Graham J., Pires, J. Chris, Chalhoub, Boulos, Snowdon, Rod J., Batley, Jacqueline, Edwards, David

Source: Plant biotechnology journal. 19(12):2488-2500

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100135814053.0x000001&indx=1&recIds=ETOCvdc_100135814053.0x000001

On the Role of Transposable Elements in the Regulation of Gene Expression and Subgenomic Interactions in Crop Genomes

Authors: Gill, Rafaqat A., Scossa, Federico, King, Graham J., Golicz, Agnieszka A., Tong, Chaobo, Snowdon, Rod J., Fernie, Alisdair R., Liu, Shengyi

Source: Critical reviews in plant sciences. 40(2):157-189

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100131785326.0x000001&indx=1&recIds=ETOCvdc_100131785326.0x000001

Analysis of the winter oilseed rape recombination landscape suggests maternal–paternal bias.

Authors: Abdollahi sisi, Nayyer, Herzog, Eva, Abbadi, Amine, Snowdon, Rod J., Golicz, Agnieszka A.

Source: Genome; 2024, Vol. 67 Issue 12, p445-453, 9p

Subject Terms: RAPESEED, HOMOLOGOUS chromosomes, GENETIC variation, CHROMOSOMES, MEIOSIS

Benchmarking Oxford Nanopore read alignment‐based insertion and deletion detection in crop plant genomes

Authors: Yildiz, Gözde, Zanini, Silvia F., Afsharyan, Nazanin P., Obermeier, Christian, Snowdon, Rod J., Golicz, Agnieszka A.

Source: œplant genome. 16(2)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100185454259.0x000001&indx=1&recIds=ETOCvdc_100185454259.0x000001

Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement

Authors: Khan, Aamir W., Garg, Vanika, Roorkiwal, Manish, Golicz, Agnieszka A., Edwards, David, Varshney, Rajeev K.

Source: In Trends in Plant Science February 2020 25(2):148-158

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

Authors: Golicz, Agnieszka A., Bayer, Philipp E., Bhalla, Prem L., Batley, Jacqueline, Edwards, David

Source: In Trends in Genetics February 2020 36(2):132-145

Building pangenome graphs

Authors: Garrison, Erik, Guarracino, Andrea, Heumos, Simon, Villani, Flavia, Bao, Zhigui, Tattini, Lorenzo, Hagmann, Jörg, Vorbrugg, Sebastian, Marco-Sola, Santiago, Kubica, Christian, Ashbrook, David G., Thorell, Kaisa, Rusholme-Pilcher, Rachel L., Liti, Gianni, Rudbeck, Emilio, Golicz, Agnieszka A., Nahnsen, Sven, Yang, Zuyu, Mwaniki, Moses Njagi, Nobrega, Franklin L., Wu, Yi, Chen, Hao, de Ligt, Joep, Sudmant, Peter H., Huang, Sanwen, Weigel, Detlef, Soranzo, Nicole, Colonna, Vincenza, Williams, Robert W., Prins, Pjotr

Source: Nature Methods; November 2024, Vol. 21 Issue: 11 p2008-2012, 5p

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

Authors: Zhao, Junliang, Bayer, Philipp E., Ruperao, Pradeep, Saxena, Rachit K., Khan, Aamir W., Golicz, Agnieszka A., Nguyen, Henry T., Batley, Jacqueline, Edwards, David, Varshney, Rajeev K.

Source: Plant biotechnology journal. 18(9):1946-1954

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100108143906.0x000001&indx=1&recIds=ETOCvdc_100108143906.0x000001

Legume Pangenome Construction Using an Iterative Mapping and Assembly Approach

Authors: Hu, Haifei, Yuan, Yuxuan, Bayer, Philipp E., Fernandez, Cassandria T., Scheben, Armin, Golicz, Agnieszka A., Edwards, David

Source: Methods in molecular biology. 2107:35-48

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN622550683&indx=1&recIds=ETOCRN622550683

Method for Genome-Wide Association Study: A Soybean Example

Authors: Anderson, Robyn, Fernandez, Cassandria Tay, Yuan, Yuxuan, Golicz, Agnieszka A., Edwards, David, Bayer, Philipp E.

Source: Methods in molecular biology. 2107:147-158

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN622550724&indx=1&recIds=ETOCRN622550724

Plant pan-genomes are the new reference

Authors: Bayer, Philipp E., Golicz, Agnieszka A., Scheben, Armin, Batley, Jacqueline, Edwards, David

Source: Nature plants. 6(8):914-920

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100183675617.0x000001&indx=1&recIds=ETOCvdc_100183675617.0x000001

Analysis of the quinoa genome reveals conservation and divergence of the flowering pathways

Authors: Golicz, Agnieszka A., Steinfort, Ursula, Arya, Hina, Singh, Mohan B., Bhalla, Prem L.

Source: Functional & integrative genomics. 20(2):245-258

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100161934939.0x000001&indx=1&recIds=ETOCvdc_100161934939.0x000001

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

Authors: Lee, HueyTyng, Golicz, Agnieszka A., Bayer, Philipp E., Severn-Ellis, Anita A., Chan, Chon-Kit Kenneth, Batley, Jacqueline, Kendrick, Gary A., Edwards, David

Source: Journal of Experimental Botany, 2018 Jul 01. 69(15), 3689-3702.

Access URL: https://www.jstor.org/stable/26932817

lncRNAs in Plant and Animal Sexual Reproduction

Authors: Golicz, Agnieszka A., Bhalla, Prem L., Singh, Mohan B.

Source: In Trends in Plant Science March 2018 23(3):195-205

Insight into the evolution and functional characteristics of the pan‐genome assembly from sesame landraces and modern cultivars

Authors: Yu, Jingyin, Golicz, Agnieszka A., Lu, Kun, Dossa, Komivi, Zhang, Yanxin, Chen, Jinfeng, Wang, Linhai, You, Jun, Fan, Dingding, Edwards, David, Zhang, Xiurong

Source: Plant biotechnology journal. 17(5):881-892

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100090607581.0x000001&indx=1&recIds=ETOCvdc_100090607581.0x000001

Genome-wide analysis of the Hsf gene family in Brassica oleracea and a comparative analysis of the Hsf gene family in B. oleracea, B. rapa and B. napus

Authors: Lohani, Neeta, Golicz, Agnieszka A., Singh, Mohan B., Bhalla, Prem L.

Source: Functional & integrative genomics. 19(3):515-531

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100126231003.0x000001&indx=1&recIds=ETOCvdc_100126231003.0x000001

Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs

Authors: Zanini, Silvia F., Bayer, Philipp E., Wells, Rachel, Snowdon, Rod J., Batley, Jacqueline, Varshney, Rajeev K., Nguyen, Henry T., Edwards, David, Golicz, Agnieszka A.

Source: œplant genome. 15(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100145999680.0x000001&indx=1&recIds=ETOCvdc_100145999680.0x000001

The Long Intergenic Noncoding RNA (LincRNA) Landscape of the Soybean Genome

Authors: Golicz, Agnieszka A., Singh, Mohan B., Bhalla, Prem L.

Source: Plant Physiology, 2018 Mar 01. 176(3), 2133-2147.

Access URL: https://www.jstor.org/stable/26393499