Staff profile

• Systems biology

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., 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

Journal Article

• Liu, J., Moore, S., & Lindsey, K. (online). Modelling Plant Cell Growth. https://doi.org/10.1002/9780470015902.a0020107.pub2
• Moore, S., Zhang, X., Liu, J., & Lindsey, K. (online). Modelling plant hormone gradients. https://doi.org/10.1002/9780470015902.a0023733
• 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
• 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
• 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
• Liu, J., Lenzoni, G., & Knight, M. R. (2020). Design principles for decoding calcium signals to generate specific gene expression via transcription. Plant Physiology, 182(4), 1743-1761. https://doi.org/10.1104/pp.19.01003
• Lenzoni, G., Liu, J., & Knight, M. (2018). Predicting plant immunity gene expression by identifying the decoding mechanism of calcium signatures. New Phytologist, 217(4), 1598-1609. https://doi.org/10.1111/nph.14924
• 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
• 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
• 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
• 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
• Liu, J., Whalley, H., & Knight, M. (2015). Combining modelling and experimental approaches to explain how calcium signatures are decoded by calmodulin-binding transcription activators (CAMTAs) to produce specific gene expression responses. New Phytologist, 208(1), 174-187. https://doi.org/10.1111/nph.13428
• 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
• Liu, J., & Hussey, P. (2014). Dissecting the regulation of pollen tube growth by modeling the interplay of hydrodynamics, cell wall and ion dynamics. Frontiers in Plant Science, 5, Article 392. https://doi.org/10.3389/fpls.2014.00392
• 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
• 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
• Liu, J., Knight, H., Hurst, C., & Knight, M. (2012). Modelling and experimental analysis of the role of interacting cytosolic and vacuolar pools in shaping low temperature calcium signatures in plant cells. Molecular bioSystems, 2012(8), 2205-2220. https://doi.org/10.1039/c2mb25072a
• Liu, J., & Hussey, P. (2011). Towards the creation of a systems tip growth model for a pollen tube. Plant Signaling & Behavior, 6(4), 520-522. https://doi.org/10.4161/psb.6.4.14750
• Liu, J., Grieson, C. S., Webb, A. A., & Hussey, P. J. (2010). Modelling dynamic plant cells. Current Opinion in Plant Biology, 13(6), 744-749. https://doi.org/10.1016/j.pbi.2010.10.002
• Liu, J., Piette, B., Deeks, M., Franklin-Tong, V., & Hussey, P. (2010). A Compartmental Model Analysis of Integrative and Self-Regulatory Ion Dynamics in Pollen Tube Growth. PLoS ONE, 5(10), Article e13157. https://doi.org/10.1371/journal.pone.0013157
• 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
• Piette, B., Liu, J., Peeters, K., Smertenko, A., Hawkins, T., Deeks, M., Quinlan, R., Zakrzewski, W., & Hussey, P. (2009). A Thermodynamic Model of Microtubule Assembly and Disassembly. PLoS ONE, 4(8), Article e6378. https://doi.org/10.1371/journal.pone.0006378
• Liu, J., Brazier-Hicks, M., & Edwards, R. (2009). A kinetic model for the metabolism of the herbicide safener fenclorim in Arabidopsis thaliana. Biophysical Chemistry, 143(1-2), 85-94. https://doi.org/10.1016/j.bpc.2009.04.006
• Baxter, C., Liu, J., Fernie, A., & Sweetlove, L. (2007). Determination of metabolic fluxes in a non-steady-state system. Phytochemistry, 68(16-18), 2313-2319
• Baxter, C., Redestig, H., Schauer, N., Repsilber, D., Patil, K., Nielsen, J., Selbig, J., Liu, J., Fernie, A., & Sweetlove, L. (2007). The metabolic response of heterotrophic Arabidopsis cells to oxidative stress. Plant Physiology, 143(1), 312-325
• Liu, J. (2006). Dissipation and maintenance of stable states in an enzymatic system: Analysis and simulation. Biophysical Chemistry, 120(3), 207-214. https://doi.org/10.1016/j.bpc.2005.11.011
• Liu, J., Crawford, J., & Leontiou, K. (2005). Collapse of single stable states via a fractal attraction basin: analysis of a representative metabolic network. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 461(2060), 2327-2338. https://doi.org/10.1098/rspa.2004.1436
• Liu, J. (2005). Kinetic constraints for formation of steady states in biochemical networks. Biophysical Journal, 88(5), 3212-3223. https://doi.org/10.1529/biophysj.104.056085
• Stoleriu, I., Davidson, F., & Liu, J. (2005). Effects of periodic input on the quasi-steady state assumptions for enzyme-catalysed reactions. Journal of Mathematical Biology, 50(2), 115-132
• Roessner-Tunali, U., Liu, J., Leisse, A., Balbo, I., Perez-Melis, A., Willmitzer, L., & Fernie, A. (2004). Kinetics of labelling of organic and amino acids in potato tubers by gas chromatography-mass spectrometry following incubation in 13C labelled isotopes. The Plant Journal, 39(4), 668-679. https://doi.org/10.1111/j.1365-313x.2004.02157.x
• Stoleriu, I., Davidson, F., & Liu, J. (2004). Quasi-steady state assumptions for non-isolated enzyme-catalysed reactions. Journal of Mathematical Biology, 48(1), 82-104
• Liu, J., & Marshall, D. (2003). Sufficient conditions for coordination of coupled nonlinear biochemicalsystems: Analysis of a simple, representative example. Journal of Biological Systems, 11(3), 275-291
• Marion, G., Mao, X., Renshaw, E., & Liu, J. (2002). Spatial heterogeneity and the stability of reaction states inautocatalysis. Physical review E: Statistical physics, plasmas, fluids, and related interdisciplinary topics, 66(5),
• Davidson, F., & Liu, J. (2002). Global stability of the attracting set of an enzyme-catalysed reactionsystem. Mathematical and computer modelling, 35(13), 1467-1481
• Davidson, F., Xu, R., & Liu, J. (2002). Existence and uniqueness of limit cycles in an enzyme-catalysedreaction system. Applied Mathematics and Computation, 127(2-3), 165-179
• Liu, J. (2002). State selection in coupled identical biochemical systems withcoexisting stable states. BioSystems, 65(1), 49-60. https://doi.org/10.1016/s0303-2647%2802%2900003-5
• Peksel, A., Torres, N., Liu, J., Juneau, G., & Kubicek, C. (2002). C-13-NMR analysis of glucose metabolism during citric acid productionby Aspergillus niger. Applied Microbiology and Biotechnology, 58(2), 157-163
• Liu, J. (2001). Enhancement and restriction of system coordination by interaction ofpathways. Journal of Biological Systems, 9(3), 169-186
• Liu, J. (2000). Sufficient conditions for coordination of a forced biochemical systemwith the interplay of activation and inhibition. Journal of Biological Systems, 8(3), 237-253
• Liu, J., & Crawford, J. (2000). Sufficient conditions for coordination of a nonlinear biochemicalsystem under external forcing. Journal of Physical Chemistry B (Soft Condensed Matter and Biophysical Chemistry), 104(12), 2623-2629
• Liu, J. (1999). Dependence of flux distribution and system coordination on dynamicalstates for biochemical systems with multiple coexisting states. Journal of Biological Systems, 7(1), 67-84
• Liu, J. (1999). Coordination restriction of enzyme-catalysed reaction systems asnonlinear dynamical systems. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 455(1981), 285-298
• Liu, J., & Crawford, J. (1998). Stability of an autocatalytic biochemical system in the presence ofnoise perturbations. IMA journal of mathematics applied in medicine and biology, 15(4), 339-350
• Liu, J., & Crawford, J. (1997). Transitions and new dynamical states induced by noise in a multiplyregulated biochemical system. Biophysical Chemistry, 69(2-3), 97-106
• Liu, J., & Crawford, J. (1997). Stability of an autocatalytic system under noise perturbations and itsdependence on the basin of attraction. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 453(1961), 1195-1203
• Liu, J., Crawford, J., Viola, R., & Goodman, B. (1997). Prospects for advancing the understanding of complex biochemical systems. Plant Molecular Biology, 33(4), 573-581