Staff profile

For my first degree I read Botany at St. Catherine's College Oxford, and undertook a PhD at Edinburgh University. I carried out post-doc work in Edinburgh and then Rothamsted, before taking up a position as leader of the Plant Molecular Genetics Group at the Leicester Biocentre, and a lectureship at Leicester University (1989). I moved to a Chair in Durham in 1996.

Our research programme is focused on the developmental biology of plants, and in particular on molecular control mechanisms in embryogenesis and root development. We make use of a range of techniques in functional genomics, and exploit the many advantages of Arabidopsis thaliana as a model experimental organism. We developed promoter trap insertional mutagenesis in a forward genetics approach to identify genes required for correct embryogenesis and root development, and also use reverse genetics techniques (RNAi, identification of gene knockouts) to characterize the functions of genes identified by cDNA cloning. We also developed laser-capture microdissection in combination with expression profiling to identify transcription factors and signalling pathway components expressed in subdomains of developing embryos, and in roots. A current feature of our work is the development of predictive mathematical models to describe gene-hormone signalling network interactions, with Junli Liu and with Michael Goldstein and Ian Vernon in the Department of Mathematical Sciences. We are applying this to understand better the mechanisms regulating meristem function, including in response to environmental stresses. We also have a number of other collaborative projects, both with other academic laboratories and with industry, which build upon expertise and materials developed in our basic science programmes. In particular, we work on cotton genetics and biology with Prof. Xianlong Zhang, and on root biology with Prof. Chunli Chen at Huazhong Agricultural University, China, where I have been appointed Visiting Professor.

I am an Editor of the journal New Phytologist and Chair of the Board of Trustees for the New Phytologist Foundation. I was previously a member of BBSRC Council, the body that determines policy, priorities and strategy for BBSRC; Chair of BBSRC Appointments Board; and a member of the Defra Advisory Committee on Releases to the Environment (ACRE), which advises Government Ministers on GM and related issues. I am former President and Chair of Council of the Society for Experimental Biology. Some of my publications are listed below.

• Gene and hormone signalling networks
• Plant development
• Plant molecular genetics
• Root development

Authored book

• Lindsey, K., & Jones, M. (1989). Plant Biotechnology in Agriculture. Open University Press

Chapter in book

• Mehdi, S., Mudge, A., Rowe, J., Liu, J., Topping, J., & Lindsey, K. (2016). The POLARIS Peptide: Role in Hormone Signalling and Root Growth. In A. Huffaker, & G. Pearce (Eds.), Annual Plant Reviews: Peptide Signals in Plants. Wiley
• Lindsey, K. (2015). GM Futures - Perspectives from a plant molecular biologist. In P. MacNaughten, & S. Carro-Ripalda (Eds.), Governing Agricultural Sustainability: Global Lessons from GM Crops. Routledge
• Lindsey, K., Mehdi, S., Casson, S., Mudge, A., Topping, J., & Liu, J. (2013). POLARIS. In A. Kastin (Ed.), The Handbook of Biologically Active Peptides, 2nd Edition (40-45). (2nd.). Academic Press
• Fonseka, D., Yang, X., Mudge, A., Topping, J., & Lindsey, K. (2013). Embryogenesis in Arabidopsis: Signalling, Genes and the Control of Identity. In P. Becraft (Ed.), Seed Genomics (21-42). Wiley
• Casson, S., Spencer, M., & Lindsey, K. (2007). Laser-capture microdissection to study global transcriptional changes during plant embryogenesis. In M. Suarez, & P. Bozhkov (Eds.), Methods in Molecular Biology: Plant Embryogenesis Methods and Protocols (111-120). Harwood
• Lindsey, K., Casson, S., & Chilley, P. (2006). The POLARIS peptide. In A. Kastin (Ed.), The Handbook Of Biologically Active Peptides (23-27). Academic Press
• Gheysen, G., Abad, P., Bleve, T., Blok, V., Fenoll, C., Gatehouse, J., Grundler, F., Lindsey, K., Ohl, S., Sagen, K., Shields, R., & Helder, H. (2000). Concerted efforts to develop handles for plant parasitic nematode control. In G. de Vries, & K. Metzlaff (Eds.), Phytosphere ’99 – Highlights in European Biotechnology. Developments in Plant Genetics and Breeding 6 (159-167). Elsevier
• Lindsey, K., & Wei, W. (2000). Arabidopsis tissue culture, transformation and transient gene expression. In Z. Wilson (Ed.), Arabidopsis: A Practical Approach (123-141). Oxford University Press

Edited book

• Lindsey, K. (Ed.). (2004). Polarity in Plants. Blackwell
• Lindsey, K. (Ed.). (1998). Transgenic Plant Research. Harwood Academic Publishers
• Lindsey, K. (Ed.). (1991). Plant Tissue Culture Manual: Fundamentals and Applications. Kluwer Academic Publishers

Journal Article

• Farrar, K., Evans, I., Topping, J., Souter, M., Nielsen, J., & Lindsey, K. (online). EXORDIUM - a gene expressed in proliferating cells and with a role in meristem function, identified by promoter trapping in Arabidopsis. The Plant Journal, 61-73
• Moore, S., Zhang, X., Liu, J., & Lindsey, K. (online). Modelling plant hormone gradients. https://doi.org/10.1002/9780470015902.a0023733
• Liu, J., Moore, S., & Lindsey, K. (online). Modelling Plant Cell Growth. https://doi.org/10.1002/9780470015902.a0020107.pub2
• Mudge, A., Mehdi, S., Michaels, W., Orosa-Puente, B., Shen, W., Sadanandom, A., Hetherington, F., Hoppen, C., Unzen, B., Groth, G., Topping, J., Robinson, N., & Lindsey, K. (online). A peptide that regulates the metalation of the Arabidopsis ethylene receptor. bioRxiv (Preprint Server for Biology), https://doi.org/10.1101/2023.06.15.545071
• Wang, Y., Zhu, C., Chen, G., Li, X., Zhu, M., Alariqi, M., Hussian, A., Ma, W., Lindsey, K., Zhang, X., Nie, X., & Jin, S. (online). Cotton Bollworm ( H. armigera ) Effector PPI5 Targets FKBP17‐2 to Inhibit ER Immunity and JA/SA Responses, Enhancing Insect Feeding. Advanced Science, https://doi.org/10.1002/advs.202407826
• Sun, W., Xia, L., Deng, J., Sun, S., Yue, D., You, J., Wang, M., Jin, S., Zhu, L., Lindsey, K., Zhang, X., & Yang, X. (2024). Evolution and subfunctionalization of CIPK6 homologous genes in regulating cotton drought resistance. Nature Communications, 15(1), Article 5733. https://doi.org/10.1038/s41467-024-50097-3
• Moore, S., Jervis, G., Topping, J., Chen, C., Liu, J., & Lindsey, K. (2024). A predictive model for ethylene-mediated auxin and cytokinin patterning in the Arabidopsis root. Plant communications, 5(7), Article 100886. https://doi.org/10.1016/j.xplc.2024.100886
• Zhu, H., Wang, F., Xu, Z., Wang, G., Hu, L., Cheng, J., Ge, X., Liu, J., Chen, W., Li, Q., Xue, F., Liu, F., Li, W., Wu, L., Cheng, X., Tang, X., Yang, C., Lindsey, K., Zhang, X., Ding, F., …Jin, S. (2024). The complex hexaploid oil‐Camellia genome traces back its phylogenomic history and multi‐omics analysis of Camellia oil biosynthesis. Plant Biotechnology Journal, https://doi.org/10.1111/pbi.14412
• Xu, W., Miao, Y., Kong, J., Lindsey, K., Zhang, X., & Min, L. (2024). ROS signaling and its involvement in abiotic stress with emphasis on heat stress-driven anther sterility in plants. Crop and Environment, 3(2), 65-74. https://doi.org/10.1016/j.crope.2023.12.002
• Zhang, B., Long, Y., Pei, L., Huang, X., Li, B., Han, B., Zhang, M., Lindsey, K., Zhang, X., Wang, M., & Yang, X. (2024). Drought response revealed by chromatin organization variation and transcriptional regulation in cotton. BMC Biology, 22(1), Article 114. https://doi.org/10.1186/s12915-024-01906-0
• Tian, X., Ji, M., You, J., Zhang, Y., Lindsey, K., Zhang, X., Tu, L., & Wang, M. (2024). Synergistic interplay of redox homeostasis and polysaccharide synthesis promotes cotton fiber elongation. The Plant Journal, 118(2), 405-422. https://doi.org/10.1111/tpj.16615
• Qiu, P., Zheng, B., Yuan, H., Yang, Z., Lindsey, K., Wang, Y., Ming, Y., Zhang, L., Hu, Q., Shaban, M., Kong, J., Zhang, X., & Zhu, L. (2024). The elicitor VP2 from Verticillium dahliae triggers defence response in cotton. Plant Biotechnology Journal, 22(2), 497-511. https://doi.org/10.1111/pbi.14201
• Sun, L., Alariqi, M., Wang, Y., Wang, Q., Xu, Z., Zafar, M. N., Yang, G., Jia, R., Hussain, A., Chen, Y., Ding, X., Zhou, J., Wang, G., Wang, F., Li, J., Zou, J., Zhu, X., Yu, L., Sun, Y., Liang, S., …Jin, S. (2024). Construction of Host Plant Insect‐Resistance Mutant Library by High‐Throughput CRISPR/Cas9 System and Identification of A Broad‐Spectrum Insect Resistance Gene. Advanced Science, 11(4), Article 2306157. https://doi.org/10.1002/advs.202306157
• Li, Y., Ma, H., Wu, Y., Ma, Y., Yang, J., Li, Y., Yue, D., Zhang, R., Kong, J., Lindsey, K., Zhang, X., & Min, L. (2024). Single‐Cell Transcriptome Atlas and Regulatory Dynamics in Developing Cotton Anthers. Advanced Science, 11(3), Article 2304017. https://doi.org/10.1002/advs.202304017
• Chen, L., Zhang, B., Xia, L., Yue, D., Han, B., Sun, W., Wang, F., Lindsey, K., Zhang, X., & Yang, X. (2023). The GhMAP3K62-GhMKK16-GhMPK32 kinase cascade regulates drought tolerance by activating GhEDT1-mediated ABA accumulation in cotton. Journal of Advanced Research, 51, 13-25. https://doi.org/10.1016/j.jare.2022.11.002
• Palanivelu, S. D., Gan, S., Salleh, K. M., Lindsey, K., Sairi, F., Che-Othman, M. H., & Zakaria, S. (2023). Assessment of bio-based hydrogel as an alternative growth medium for seed germination and seedling growth in urban farming. Cellulose, 30(12), 7791-7803. https://doi.org/10.1007/s10570-023-05334-1
• Li, B., Zhang, M., Sun, W., Yue, D., Ma, Y., Zhang, B., Duan, L., Wang, M., Lindsey, K., Nie, X., Zhang, X., & Yang, X. (2023). N6‐methyladenosine RNA modification regulates cotton drought response in a Ca2+ and ABA‐dependent manner. Plant Biotechnology Journal, 21(6), 1270-1285. https://doi.org/10.1111/pbi.14036
• Xiao, S., Hu, Q., Ye, Z., Si, H., Liu, S., Zhang, X., Wang, W., Yu, Y., Kong, J., Klosterman, S., Lindsey, K., Aierxi, A., & Zhu, L. (2023). GhWRKY41 forms a positive feedback regulation loop and increases cotton defence response against Verticillium dahliae by regulating phenylpropanoid metabolism. Plant Biotechnology Journal, 21(5), 961-978. https://doi.org/10.1111/pbi.14008
• Thompson, H., Shen, W., Matus, R., Kakkar, M., Jones, C., Dolan, D., Grellscheid, S., Yang, X., Zhang, N., Mozaffari-Jovin, S., Chen, C., Zhang, X., Topping, J., & Lindsey, K. (2023). MERISTEM-DEFECTIVE regulates the balance between stemness and differentiation in the root meristem through RNA splicing control. Development, 150(7), Article dev201476. https://doi.org/10.1242/dev.201476
• You, J., Liu, Z., Qi, Z., Ma, Y., Sun, M., Su, L., Niu, H., Peng, Y., Luo, X., Zhu, M., Huang, Y., Chang, X., Hu, X., Zhang, Y., Pi, R., Liu, Y., Meng, Q., Li, J., Zhang, Q., Zhu, L., …Wang, M. (2023). Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton. Nature Genetics, 55, 1987-1997. https://doi.org/10.1038/s41588-023-01530-8
• Wang, N., Li, Y., Shen, C., Yang, Y., Wang, H., Yao, T., Zhang, X., Lindsey, K., & Lin, Z. (2023). High-resolution sequencing of nine elite upland cotton cultivars uncovers genic variations and breeding improvement targets. The Plant Journal, 113(1), 145-159. https://doi.org/10.1111/tpj.16041
• Xu, Z., Wang, G., Luo, J., Zhu, M., Hu, L., Liang, S., Li, B., Huang, X., Wang, Y., Zhang, G., Zhang, C., Zhou, Y., Yuan, D., Chen, T., Chen, L., Ma, W., Gao, W., Lindsey, K., Zhang, X., Ding, F., & Jin, S. (2023). The chromosome-scale reference genome of mirid bugs (Adelphocoris suturalis) genome provides insights into omnivory, insecticide resistance, and survival adaptation. BMC Biology, 21(1), Article 195. https://doi.org/10.1186/s12915-023-01666-3
• Zhu, X., Xu, Z., Wang, G., Cong, Y., Yu, L., Jia, R., Qin, Y., Zhang, G., Li, B., Yuan, D., Tu, L., Yang, X., Lindsey, K., Zhang, X., & Jin, S. (2023). Single-cell resolution analysis reveals the preparation for reprogramming the fate of stem cell niche in cotton lateral meristem. Genome Biology, 24, Article 194. https://doi.org/10.1186/s13059-023-03032-6
• Hu, L., Xu, Z., Fan, R., Wang, G., Wang, F., Qin, X., Yan, L., Ji, X., Meng, M., Sim, S., Chen, W., Hao, C., Wang, Q., Zhu, H., Zhu, S., Xu, P., Zhao, H., Lindsey, K., Daniell, H., Wendel, J., & Jin, S. (2023). The complex genome and adaptive evolution of polyploid Chinese pepper (Zanthoxylum armatum and Zanthoxylum bungeanum). Plant Biotechnology Journal, 21(1), 78-96. https://doi.org/10.1111/pbi.13926
• Qiu, P., Li, J., Zhang, L., Chen, K., Shao, J., Zheng, B., Yuan, H., Qi, J., Yue, L., Hu, Q., Ming, Y., Liu, S., Long, L., Gu, J., Zhang, X., Lindsey, K., Gao, W., Wu, H., & Zhu, L. (2023). Polyethyleneimine-coated MXene quantum dots improve cotton tolerance to Verticillium dahliae by maintaining ROS homeostasis. Nature Communications, 14(1), Article 7392. https://doi.org/10.1038/s41467-023-43192-4
• Qin, Y., Sun, M., Li, W., Xu, M., Shao, L., Liu, Y., Zhao, G., Liu, Z., Xu, Z., You, J., Ye, Z., Xu, J., Yang, X., Wang, M., Lindsey, K., Zhang, X., & Tu, L. (2022). Single-cell RNA-seq reveals fate determination control of an individual fiber cell initiation in cotton (Gossypium hirsutum). Plant Biotechnology Journal, 20(12), 2372-2388. https://doi.org/10.1111/pbi.13918
• Deng, J., Sun, W., Zhang, B., Sun, S., Xia, L., Miao, Y., He, L., Lindsey, K., Yang, X., & Zhang, X. (2022). GhTCE1-GhTCEE1 dimers regulate transcriptional reprogramming during wound-induced callus formation in cotton. The Plant Cell, 34(11), 4554-4568. https://doi.org/10.1093/plcell/koac252
• Palanivelu, S., Armir, N., Zulkifli, A., Hair, A., Salleh, K., Lindsey, K., Che-Othman, M., & Zakaria, S. (2022). Hydrogel Application in Urban Farming: Potentials and Limitations—A Review. Polymers, 14(13), Article 2590. https://doi.org/10.3390/polym14132590
• Wu, Y., Li, X., Li, Y., Ma, H., Chi, H., Ma, Y., Yang, J., Xie, S., Zhang, R., Liu, L., Su, X., Lv, R., Khan, A., Kong, J., Xiaoping, G., Lindsey, K., Min, L., & Zhang, X. (2022). Degradation of de-esterified pectin/homogalacturonan by the polygalacturonase GhNSP is necessary for pollen exine formation and male fertility in cotton. Plant Biotechnology Journal, 20(6), 1054-1068. https://doi.org/10.1111/pbi.13785
• Pei, L., Huang, X., Liu, Z., Tian, X., You, J., Li, J., Fang, D., Lindsey, K., Zhu, L., Zhang, X., & Wang, M. (2022). Dynamic 3D genome architecture of cotton fiber reveals subgenome-coordinated chromatin topology for 4-staged single-cell differentiation. Genome Biology, 23(1), Article 45. https://doi.org/10.1186/s13059-022-02616-y
• Wang, G., Xu, Z., Wang, F., Huang, Y., Xin, Y., Liang, S., Li, B., Si, H., Sun, L., Wang, Q., Ding, X., Zhu, X., Chen, L., Yu, L., Lindsey, K., Zhang, X., & Jin, S. (2022). Development of an efficient and precise adenine base editor (ABE) with expanded target range in allotetraploid cotton (Gossypium hirsutum). BMC Biology, 20(1), Article 45. https://doi.org/10.1186/s12915-022-01232-3
• Ma, Y., Min, L., Wang, J., Li, Y., Wu, Y., Hu, Q., Ding, Y., Wang, M., Liang, Y., Gong, Z., Xie, S., Su, X., Khan, A., Lindsey, K., Zhu, L., Li, X., & Zhang, X. (2021). Combined transcriptome GWAS and TWAS reveal genetic elements leading to male sterility during high temperature stress in cotton. New Phytologist, 231(1), 165-181. https://doi.org/10.1111/nph.17325
• Jacobsen, A., Jervis, G., Xu, J., Topping, J., & Lindsey, K. (2021). Root growth responses to mechanical impedance are regulated by a network of ROS, ethylene and auxin signalling in Arabidopsis. New Phytologist, 231(1), 225-242. https://doi.org/10.1111/nph.17180
• Pei, L., Li, G., Lindsey, K., Zhang, X., & Wang, M. (2021). Plant 3D genomics: the exploration and application of chromatin organization. New Phytologist, 230(5), 1772-1786. https://doi.org/10.1111/nph.17262
• Gu, X., Fonseka, K., Agneessens, J., Casson, S., Smertenko, A., Guo, G., Topping, J., Hussey, P., & Lindsey, K. (2021). The Arabidopsis R-SNARE VAMP714 is essential for polarization of PIN proteins and auxin responses. New Phytologist, 230(2), 550-566. https://doi.org/10.1111/nph.17205
• Hetherington, F., Kakkar, M., Topping, J., & Lindsey, K. (2021). Gibberellin signaling mediates lateral root inhibition in response to K+-deprivation. Plant Physiology, 185(3), 1198-1215. https://doi.org/10.1093/plphys/kiaa093
• Hashem, A., Moore, S., Chen, S., Hu, C., Zhao, Q., IE Elasawi, I., Feng, Y., Topping, J., Liu, J., Lindsey, K., & Chen, C. (2021). Putrescine depletion affects Arabidopsis root meristem size by modulating auxin and cytokinin signaling and ROS accumulation. International Journal of Molecular Sciences, 22(8), Article 4094. https://doi.org/10.3390/ijms22084094
• Li, J., Yuan, D., Wang, P., Wang, Q., Sun, M., Liu, Z., Si, H., Xu, Z., Ma, Y., Zhang, B., Pei, L., Tu, L., Zhu, L., Chen, L.-L., Lindsey, K., Zhang, X., Jin, S., & Wang, M. (2021). Cotton pan-genome retrieves the lost sequences and genes during domestication and selection. Genome Biology, 22, Article 119. https://doi.org/10.1186/s13059-021-02351-w
• Liu, S., Zhang, X., Xiao, S., Ma, J., Shi, W., Qin, T., Xi, H., Nie, X., You, C., Xu, Z., Wang, T., Wang, Y., Zhang, Z., Li, J., Kong, J., Aierxi, A., Yu, Y., Lindsey, K., Klosterman, S., & Zhu, L. (2021). A single-nucleotide mutation in GLUTAMATE RECEPTOR-LIKE protein gene confers resistance to Fusarium wilt in Gossypium hirsutum. Advanced Science, 8(7), Article 2020723. https://doi.org/10.1002/advs.202002723
• Wang, Q., Alariqi, M., Wang, F., Li, B., Ding, X., Rui, H., Li, Y., Xu, Z., Qin, L., Sun, L., Li, J., Zou, J., Lindsey, K., Zhang, X., & Jin, S. (2020). The application of a heat‐inducible CRISPR/Cas12b (C2c1) genome editing system in tetraploid cotton (G.hirsutum) plants. Plant Biotechnology Journal, 18(12), 2436-2443. https://doi.org/10.1111/pbi.13417
• Andrews, M., Condron, L., Kemp, P., Topping, J., Lindsey, K., Hodge, S., & Raven, J. (2020). Will rising atmospheric CO2 concentration inhibit nitrate assimilation in shoots but enhance it in roots of C3 plants?. Physiologia Plantarum, 170(1), 40-45. https://doi.org/10.1111/ppl.13096
• Li, Z., Wang, P., You, C., Yu, J., Zhang, X., Yan, F., Ye, Z., Shen, C., Li, B., Guo, K., Liu, N., Thyssen, G., Fang, D., Lindsey, K., Wang, M., & Tu, L. (2020). Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton. New Phytologist, 226(6), 1738-1752. https://doi.org/10.1111/nph.16468
• Jackson, S., Vernon, I., Liu, J., & Lindsey, K. (2020). Understanding hormonal crosstalk in Arabidopsis root development via emulation and history matching. Statistical Applications in Genetics and Molecular Biology, 19(2), Article 20180053. https://doi.org/10.1515/sagmb-2018-0053
• Manghwar, H., Li, B., Ding, X., Hussain, A., Lindsey, K., Zhang, X., & Jin, S. (2020). CRISPR/Cas systems in genome editing: methodologies and tools for sgRNA design, off-target evaluation and strategies to mitigate off-target effects. Advanced Science, 7(6), Article 1902312. https://doi.org/10.1002/advs.201902312
• Wang, L., Sun, J., Chen, S., Huang, J., Yuan, H., Lindsey, K., Alenius, H., & Chen, C. (2020). Silver nanoparticles regulate Arabidopsis root growth by concentration-dependent modification of reactive oxygen species accumulation and cell division. Ecotoxicology and Environmental Safety, 190, Article 110072. https://doi.org/10.1016/j.ecoenv.2019.110072
• Li, B., Liang, S., Alariqi, M., Wang, F., Wang, G., Wang, Q., Xu, Z., Yu, L., Zafar, M., Sun, L., Si, H., Yuan, D., Guo, W., Wang, Y., Lindsey, K., Zhang, X., & Jin, S. (2020). The application of temperature sensitivity CRISPR/LbCpf1 (LbCas12a) mediated genome editing in allotetraploid cotton (G. hirsutum) and creation of nontransgenic, gossypol‐free cotton. Plant Biotechnology Journal, 19(2), 221-223. https://doi.org/10.1111/pbi.13470
• Qin, L., Li, J., Wang, Q., Xu, Z., Sun, L., Alariqi, M., Manghwar, H., Wang, G., Li, B., Ding, X., Rui, H., Huang, H., Lu, T., Lindsey, K., Daniell, H., Zhang, X., & Jin, S. (2020). High efficient and precise base editing of C•G to T•A in the allotetraploid cotton (Gossypium hirsutum) genome using a modified CRISPR/Cas9 system. Plant Biotechnology Journal, 18(1), 45-56. https://doi.org/10.1111/pbi.13168
• Gu, X., Brennan, A., Wei, W., Guo, G., & Lindsey, K. (2020). Vesicle transport in plants: A revised phylogeny of SNARE proteins. Evolutionary Bioinformatics, 16, 1-11. https://doi.org/10.1177/1176934320956575
• Manghwar, H., Lindsey, K., Zhang, X., & Jin, S. (2019). CRISPR/Cas system: recent advances and prospects for genome editing. Trends in Plant Science, 24(12), 1102-1125. https://doi.org/10.1016/j.tplants.2019.09.006
• Hu, L., Xu, Z., Wang, M., Fan, R., Yuan, D., Wu, B., Wu, H., Qin, X., Yan, L., Tan, L., Sim, S., Li, W., Saski, C., Daniell, H., Wendel, J., Lindsey, K., Zhang, X., Hao, C., & Jin, S. (2019). The chromosome-scale reference genome of black pepper (Piper nigrum L.) provides further insight into piperine biosynthesis. Nature Communications, 10, Article 4702. https://doi.org/10.1038/s41467-019-12607-6
• Li, J., Manghwar, H., Sun, L., Wang, P., Wang, G., Sheng, H., Zhang, J., Liu, H., Qin, L., Rui, H., Lindsey, K., Daniell, H., Jin, S., & Zhang, X. (2019). Whole genome sequencing reveals rare off-target mutations and considerable inherent genetic and/or somaclonal variations in CRISPR/Cas9-edited cotton plants. Plant Biotechnology Journal, 17(5), 858-868. https://doi.org/10.1111/pbi.13020
• Li, J., Wang, M., Li, Y., Zhang, Q., Lindsey, K., Daniell, H., Jin, S., & Zhang, X. (2019). Multi‐omics analyses reveal epigenomics basis for cotton somatic embryogenesis through successive regeneration acclimation process. Plant Biotechnology Journal, 17(2), 435-450. https://doi.org/10.1111/pbi.12988
• Wang, M., Tu, L., Yuan, D., Zhu, D., Shen, C., Li, J., Liu, F., Pei, L., Wang, P., Zhao, G., Ye, Z., Huang, H., Yan, F., Ma, Y., Zhang, L., Liu, M., You, J., Yang, Y., Liu, Z., Huang, F., …Zhang, X. (2019). Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nature Genetics, 51, 224-229. https://doi.org/10.1038/s41588-018-0282-x
• Qin, T., Liu, S., Zhang, Z., Sun, L., He, X., Lindsey, K., Zhu, L., & Zhang, X. (2019). GhCyp3 improves the resistance of cotton to Verticillium dahliae by inhibiting ubiquitin ligase activity of GhPUB17. Plant Molecular Biology, 99, 379-393
• Zhang, L., Wang, M., Li, N., Wang, H., Qiu, P., Hu, Q., Pei, L., Xu, Z., Wang, T., Gao, E., Liu, J., Liu, S., Miao, Y., Lindsey, K., Tu, L., Zhu, L., & Zhang, X. (2018). Long noncoding RNAs involved in resistance to Verticillium dahliae, a fungal disease in cotton. Plant Biotechnology Journal, 16(6), 1172-1185. https://doi.org/10.1111/pbi.12861
• Short, E., Pullen, M., Imriz, G., Liu, D., Cope-Selby, N., Hetherington, F., Smertenko, A., Hussey, P., Topping, J., & Lindsey, K. (2018). Epidermal expression of a sterol biosynthesis gene regulates root growth by a non-cell autonomous mechanism in Arabidopsis. Development, 145(10), Article dev160572. https://doi.org/10.1242/dev.160572
• Wang, L., Liu, N., Wang, T., Li, J., Wen, T., Yang, X., Lindsey, K., & Zhang, X. (2018). The GhmiR157a–GhSPL10 regulatory module controls initial cellular dedifferentiation and callus proliferation in cotton by modulating ethylene-mediated flavonoid biosynthesis. Journal of Experimental Botany, 69(5), 1081-1093. https://doi.org/10.1093/jxb/erx475
• Hu, Q., Min, L., Yang, X., Jin, S., Zhang, L., Li, Y., Ma, Y., Qi, X., Li, D., Liu, H., Lindsey, K., Zhu, L., & Zhang, X. (2018). Laccase GhLac1 modulates broad-spectrum biotic stress tolerance via manipulating phenylpropanoid pathway and jasmonic acid synthesis. Plant Physiology, 176(2), 1808-1823. https://doi.org/10.1104/pp.17.01628
• Vernon, I., Liu, J., Goldstein, M., Rowe, J., Topping, J., & Lindsey, K. (2018). Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions. BMC systems biology, 12, Article 1. https://doi.org/10.1186/s12918-017-0484-3
• Andrews, M., Condron, L., Kemp, P., Topping, J., Lindsey, K., Hodge, S., & Raven, J. (2018). Elevated CO2 effects on nitrogen (N) assimilation and growth of C3 vacular plants are similar regardless of N-form assimilated. Journal of Experimental Botany, 70, 683-690. https://doi.org/10.1093/jxb/ery371
• Wang, M., Wang, P., Liang, F., Ye, Z., Li, J., Shen, C., Pei, L., Wang, F., Hu, J., Tu, L., Lindsey, K., He, D., & Zhang, X. (2018). A global survey of alternative splicing in allopolyploid cotton: landscape, complexity and regulation. New Phytologist, 217(1), 163-178. https://doi.org/10.1111/nph.14762
• Liu, J., Moore, S., Chen, C., & Lindsey, K. (2017). Crosstalk complexities between auxin, cytokinin and ethylene in Arabidopsis root development: from experiments to systems modelling, and back again. Molecular Plant, 10(12), 1480-1496. https://doi.org/10.1016/j.molp.2017.11.002
• Lobine, D., Howes, M.-J., Cummins, I., Govinden-Soulange, J., Ranghoo-Sanmukhiya, M., Lindsey, K., & Chazot, P. (2017). Bio-prospecting endemic Mascarene Aloes for potential neuroprotectants. Phytotherapy Research, 31(12), 1926-1934. https://doi.org/10.1002/ptr.5941
• Luo, J., Liang, S., Li, J., Xu, Z., Li, L., Zhu, B., Li, Z., Lei, C., Lindsey, K., Chen, L., Jin, S., & Zhang, X. (2017). A transgenic strategy for controlling plant bugs (Adelphocoris suturalis) through expression of double-stranded RNA homologous to fatty acyl-coenzyme A reductase in cotton. New Phytologist, 215(3), 1173-1185. https://doi.org/10.1111/nph.14636
• Wang, M., Tu, L., Lin, M., Lin, Z., Wang, P., Yang, Q., Ye, Z., Shen, C., Zhou, X., Zhang, L., Li, J., Nie, X., Li, Z., Guo, K., Ma, Y., Jin, S., Zhu, L., Yang, X., Min, L., Zhang, Q., …Zhang, X. (2017). Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nature Genetics, 49(4), 579-587. https://doi.org/10.1038/ng.3807
• Moore, S., Liu, J., Zhang, X., & Lindsey, K. (2017). A recovery principle provides insight into auxin pattern control in the Arabidopsis root. Scientific Reports, 7, Article 43004. https://doi.org/10.1038/srep43004
• Rowe, J., Topping, J., Liu, J., & Lindsey, K. (2016). Abscisic acid regulates root growth under osmotic stress conditions via an interacting hormonal network with cytokinin, ethylene and auxin. New Phytologist, 211(1), 225-239. https://doi.org/10.1111/nph.13882
• Zhou, T., Yang, X., Guo, K., Deng, J., Xu, J., Gao, W., Lindsey, K., & Zhang, X. (2016). ROS homeostasis regulates somatic embryogenesis via the regulation of auxin signaling in cotton. Molecular and Cellular Proteomics, 15(6), 2108-2124. https://doi.org/10.1074/mcp.m115.049338
• Gao, W., Long, L., Xu, L., Lindsey, K., Zhang, X., & Zhu, L. (2016). Suppression of the homeobox gene HDTF1 enhances resistance to Verticillium dahliae and Botrytis cinerea in cotton. Journal of Integrative Plant Biology, 58(5), 503-513. https://doi.org/10.1111/jipb.12432
• Moore, S., Zhang, X., Liu, J., & Lindsey, K. (2015). Some fundamental aspects of modelling auxin patterning in the context of auxin-ethylene-cytokinin crosstalk. Plant Signaling & Behavior, 10(10), Article e1056424. https://doi.org/10.1080/15592324.2015.1056424
• Moore, S., Zhang, X., Mudge, A., Rowe, J., Topping, J., Liu, J., & Lindsey, K. (2015). Spatiotemporal modelling of hormonal crosstalk explains the level and patterning of hormones and gene expression in Arabidopsis thaliana wildtype and mutant roots. New Phytologist, 207(4), 1110-1122. https://doi.org/10.1111/nph.13421
• Wang, M., Yuan, D., Tu, L., Gao, W., He, Y., Hu, H., Wang, P., Liu, N., Lindsey, K., & Zhang, X. (2015). Long non-coding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.). New Phytologist, 207(4), 1181-1197. https://doi.org/10.1111/nph.13429
• Lima, N., Trindade, F., da Cunha, M., Oliviera, A., Lindsey, K., Topping, J., & Fernandes, K. (2015). Programmed cell death during development of cowpea (Vigna unguiculata L. (Walp.)) seed coat. Plant, Cell and Environment, 38(4), 718-728. https://doi.org/10.1111/pce.12432
• Liu, N., Tu, L., Tang, W., Gao, W., Lindsey, K., & Zhang, X. (2014). Small RNA and degradome profiling reveals a role for miRNAs and their targets in the developing fibers of Gossypium barbadense. The Plant Journal, 80(2), 331-344. https://doi.org/10.1111/tpj.12636
• Tang, W., Tu, L., Yang, X., Tan, J., Deng, F., Hao, J., Guo, K., Lindsey, K., & Zhang, X. (2014). The calcium sensor GhCaM7 promotes cotton fiber elongation by modulating reactive oxygen species (ROS) production. New Phytologist, 202(2), 509-520. https://doi.org/10.1111/nph.12676
• Liu, J., Rowe, J., & Lindsey, K. (2014). Hormonal crosstalk for root development: a combined experimental and modeling perspective. Frontiers in Plant Science, 5, Article 116. https://doi.org/10.3389/fpls.2014.00116
• Liu, J., Lindsey, K., & Hussey, P. J. (2014). Elucidating the regulation of complex signalling systems in plant cells. Biochemical Society Transactions, 42(1), 219-223. https://doi.org/10.1042/bst20130090
• Ji, H., Kyndt, T., Denil, S., Lindsey, K., Topping, J., Nahar, K., Haegeman, A., Van Criekinge, W., Trooskens, G., De Meyer, T., & Gheysen, G. (2013). Transcriptional analysis through RNA sequencing of giant cells induced by Meloidogyne graminicola in rice roots. Journal of Experimental Botany, 64(13), 3885-3898. https://doi.org/10.1093/jxb/ert219
• Liu, J., Mehdi, S., Topping, J., Friml, J., & Lindsey, K. (2013). Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. Frontiers in Plant Science, 4, Article 75. https://doi.org/10.3389/fpls.2013.00075
• Yang, X., Wang, L., Yuan, D., Lindsey, K., & Zhang, X. (2013). Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis. Journal of Experimental Botany, 64(6), 1521-1536. https://doi.org/10.1093/jxb/ert013
• Portillo, M., Cabrera, J., Lindsey, K., Topping, J., Andrés, M., Emiliozzi, M., Oliveros, J., García-Casado, G., Solano, R., Koltai, H., Resnick, N., Fenoll, C., & Escobar, C. (2013). Distinct and conserved transcriptomic changes during nematode-induced giant cell development in tomato compared with Arabidopsis: a functional role for gene repression. New Phytologist, 197(4), 1276-1290. https://doi.org/10.1111/nph.12121
• Chapman, N., Miller, A., Lindsey, K., & Whalley, R. (2012). Roots, water, and nutrient acquisition: let’s get physical. Trends in Plant Science, 16, 701-710
• Zhang, R., Xia, X., Lindsey, K., & Ferreira da Rocha, P. (2012). Functional complementation of the dwf4-102 mutant of Arabidopsis by overexpression of CYP724A1. Journal of Plant Physiology, 169, 421-428
• Osbourn, A., O'Maille, P., Rosser, S., & Lindsey, K. (2012). Synthetic Biology. New Phytologist, 196, 671-677. https://doi.org/10.1111/j.1469-8137.2012.04374.x
• Chapman, N., Whalley, W., Lindsey, K., & Miller, A. (2011). Water supply and not nitrate concentration determines primary root growth in Arabidopsis. Plant, Cell and Environment, 34, 1630-1638
• Pullen, M., Clark, N., Zarinkamar, F., Topping, J., & Lindsey, K. (2010). Analysis of vascular development in the hydra sterol biosynthetic mutants of Arabidopsis. PLoS ONE, 5(8), Article e12227. https://doi.org/10.1371/journal.pone.0012227
• Liu, J., Mehdi, S., Topping, J., Tarkowski, P., & Lindsey, K. (2010). Modelling and experimental analysis of hormonal crosstalk in Arabidopsis. Molecular Systems Biology, 6(1), Article 373. https://doi.org/10.1038/msb.2010.26
• Barcala, M., Garcia, A., Cabrera, J., Casson, S., Lindsey, K., Favery, B., García-Casado, G., Solano, R., Fenoll, C., & Escobar, C. (2010). Early transcriptomic events in microdissected Arabidopsis nematode-induced giant cells. The Plant Journal, 61(4), 698-712. https://doi.org/10.1111/j.1365-313x.2009.04098.x
• Chivasa, S., Simon, J., Murphy, A., Lindsey, K., Carr, J., & Slabas, A. (2010). The effects of extracellular adenosine 5'-triphosphate on the tobacco proteome. Proteomics, 10(2), 235-244. https://doi.org/10.1002/pmic.200900454
• Lindsey, K., & Consortium, T. I. A. I. (2010). An international bioinformatics infrastructure to underpin the Arabidopsis community. The Plant Cell, 22, 2530-2536
• Casson, S., Topping, J., & Lindsey, K. (2009). MERISTEM-DEFECTIVE, an RS domain protein, is required for the correct meristem patterning and function in Arabidopsis. The Plant Journal, 57(5), 857-869. https://doi.org/10.1111/j.1365-313x.2008.03738.x
• Portillo, M., Lindsey, K., Casson, S., Fenoll, C., & Escobar, C. (2009). A rapid protocol for laser-capture microdissection of giant cells and root vascular cells from tomato (Solanum lycopersicum). Molecular Plant Pathology, 10, 523-535
• Chivasa, S., Tomé, D., Murphy, A., Hamilton, J., Lindsey, K., Carr, J., & Slabas, A. (2009). Extracellular ATP: a modulator of cell death and pathogen defense in plants. Plant Signaling & Behavior, 4(11), 1078-1080. https://doi.org/10.4161/psb.4.11.9784
• Chivasa, S., Murphy, A., Hamilton, J., Lindsey, K., Carr, J., & Slabas, A. (2009). Extracellular ATP is a regulator of pathogen defence in plants. The Plant Journal, 60(3), 436-448. https://doi.org/10.1111/j.1365-313x.2009.03968.x
• Spencer, M., Casson, S., & Lindsey, K. (2007). Transcriptional profiling of the Arabidopsis embryo. Plant Physiology, 143, 924-940
• Chilley, P., Casson, S., Tarkowski, P., Wang, K.-C., Hawkins, N., Hussey, P., Beale, M., Ecker, J., Sandberg, G., & Lindsey, K. (2006). The POLARIS peptide of Arabidopsis regulates auxin transport and root growth via effects on ethylene signaling. The Plant Cell, 18(11), 3058-3072. https://doi.org/10.1105/tpc.106.040790
• Vaughan, S., James, D., Lindsey, K., & Massiah, A. (2006). Characterization of FaRB7, a near root-specific gene from strawberry (Fragaria x ananassa Duch.) and promoter activity analysis in homologous and heterologous hosts. Journal of Experimental Botany, 57, 3901-3910
• Chivasa, S., Hamilton, J., Pringle, R., Ndimba, B., Simon, J., Lindsey, K., & Slabas, A. (2006). Proteomic analysis of differentially expressed proteins in fungal elicitor-treated Arabidopsis cell cultures. Journal of Experimental Botany, 57, 1553-1562
• Friml, J., Benfey, P., Benkova, E., Bennett, M., Berleth, T., Geldner, N., Grebe, M., Heisler, M., Hejato, J., Juergens, G., Laux, T., Lindsey, K., Lukowitz, W., Luschnig, C., Offringa, R., Scheres, B., Swarup, R., Torres-Ruiz, R., Weijers, D., & Zazimalova, E. (2006). Apical-basal polarity - why plant cells don't stand on their heads. Trends in Plant Science, 11, 12-14
• Casson, S., & Lindsey, K. (2006). The turnip mutant of Arabidopsis reveals that LEC1 expression mediates the effects of auxin and sugars to promote embryonic cell identity. Plant Physiology, 142, 526-541
• Chivasa, S., Ndimba, B., Simon, J., Lindsey, K., & Slabas, A. (2005). Extracellular ATP functions as an endogenous external metabolite regulating plant cell viability. The Plant Cell, 17(11), 3019-3034. https://doi.org/10.1105/tpc.105.036806
• Casson, S., Spencer, M., Walker, K., & Lindsey, K. (2005). Laser capture microdissection for the analysis of gene expression during embryogenesis of Arabidopsis. The Plant Journal, 42(1), 111-123. https://doi.org/10.1111/j.1365-313x.2005.02355.x
• Chivasa, S., Ndimba, B., Simon, W., Lindsey, K., & Slabas, A. (2005). Extracellular ATP defines a novel endogenous extracellular metabolite regulating plant cell viability. The Plant Cell, 17, 3019-3034
• Souter, M., Pullen, M., Topping, J., Zhang, X., & Lindsey, K. (2004). Rescue of defective auxin-mediated gene expression and root meristem function by inhibition of ethylene sugnalling in sterol biosynthesis mutants of Arabidopsis. Planta, 219, 773-783
• Dean, G., Casson, S., & Lindsey, K. (2004). KNAT6 gene of Arabidopsis is expressed in roots and is required for correct lateral root formation. Plant Molecular Biology, 54, 71-84
• Lindsey, K., Topping, J., & Pullen, M. (2003). Importance of plant sterols in pattern formation and hormone signalling. Trends in Plant Science, 8, 521-525
• Casson, S., & Lindsey, K. (2003). Tansley Review: Genes and signalling in root development. New Phytologist, 158, 11-38
• Casson, S., Chilley, P., Topping, J., Evans, I., Souter, M., & Lindsey, K. (2002). The POLARIS gene of Arabidopsis encodes a predicted peptide required for correct root growth and leaf vascular patterning. The Plant Cell, 14(8), 1705-1721. https://doi.org/10.1105/tpc.002618
• Souter, M., Topping, J., Pullen, M., Friml, J., Palme, K., Hackett, R., Grierson, D., & Lindsey, K. (2002). hydra mutants of Arabidopsis are defective in sterol profiles and auxin and ethylene signaling. The Plant Cell, 14(5), 1017-1031. https://doi.org/10.1105/tpc.001248
• Lindsey, K., Casson, S., & Chilley, P. (2002). Peptides: new signalling molecules in plants. Trends in Plant Science, 7, 78-83
• Topping, J., & Lindsey, K. (1997). Promoter trap markers differentiate structural and positional components of polar development in Arabidopsis. The Plant Cell, 9, 1713-1725
• Topping, J., May, V., Muskett, P., & Lindsey, K. (1997). Mutations in the HYDRA1 gene of Arabidopsis perturb cell shape and disrupt embryonic and seedling morphogenesis. Development, 124, 4415-4424
• Wei, W., Twell, D., & Lindsey, K. (1997). A novel nucleic acid helicase gene identified by promoter trapping in Arabidopsis. The Plant Journal, 11, 1307-1314
• Barthels, N., van der Lee, F., Klap, J., Goddijn, O., Karimi, M., Puzio, P., Grundler, F., Ohl, S., Lindsey, K., Robertson, L., Robertson, W., Van Montagu, M., Gheysen, G., & Sijmons, P. (1997). Regulatory sequences of Arabidopsis drive reporter gene expression in nematode feeding structures. The Plant Cell, 9, 2119-2134
• Fuerst, R., Soni, R., Murray, J., & Lindsey, K. (1996). Modulation of cyclin transcript levels in cultured cells of Arabidopsis thaliana. Plant Physiology, 112, 1023-1033
• Topping, J., & Lindsey, K. (1995). Insertional mutagenesis and promoter trapping in plants for the isolation of genes and the study of development. Transgenic Research, 4, 291-305
• Topping, J., Agyeman, F., Henricot, B., & Lindsey, K. (1994). Identification of molecular markers of embryogenesis in Arabidopsis thaliana by promoter trapping. The Plant Journal, 57, 895-903
• Lindsey, K., & Topping, J. (1993). Embryogenesis: a question of pattern. Journal of Experimental Botany, 44, 359-374. https://doi.org/10.1093/jxb/44.2.359
• Goddijn, O., Lindsey, K., van der Lee, F., Klap, J., & Sijmons, P. (1993). Differential gene expression in nematode-induced feeding structures of transgenic plants harbouring promoter-gusA fusion constructs. The Plant Journal, 4, 863-873
• Lindsey, K., Wei, W., Clarke, M., McArdle, H., Rooke, L., & Topping, J. (1993). Tagging genomic sequences that direct transgene expression by activation of a promoter trap in plants. Transgenic Research, 2, 33-47
• Clarke, M., Wei, W., & Lindsey, K. (1992). High frequency transformation of Arabidopsis thaliana by Agrobacterium tumefaciens. Plant Molecular Biology Reporter, 10, 178-189
• Topping, J., Wei, W., & Lindsey, K. (1991). Functional tagging of regulatory elements in the plant genome. Development, 112, 1109-1119