Lionel Dupuy
I graduated in Timber Engineering from the École Supérieure du Bois (Nantes, France) in 2000 and was awarded a PhD in 2003 from the University of Bordeaux (School of Physics and Engineering Sciences) where I was developing biomechanical models of tree uprooting at the Laboratoire de Rheologie du Bois de Bordeaux (now Institute of Mechanics and Engineering of Bordeaux). I developed software for digitising the architecture of root systems and constructed finite element models of root soil interactions. In 2005 I took a post-doctoral position in Jim Haseloff's laboratory (University of Cambridge) to work on computational methods to analyse plant cell morphogenesis. I developed image analysis methods to track cell expansion and division from live microscopy data, and used these measurements to construct models that integrated genetic and biomechanical processes into dynamic multicellular architectures.
Current research interests
I develop models that predict how crops utilise environmental resources to grow and produce yield. I design experimental systems where such processes can be observed and quantified. For example, recent work has focused on the development of novel transparent soils that are suitable for the culture and live imaging of soil biological organisms.
My research also focuses on quantitative imaging to improve data resolution and throughput for models. I use techniques such as Optical Projection Tomography (OPT), Single Plane Illumination Microscopy (SPIM, in collaboration with Mike MacDonald), and Biospeckle Laser (BSL, in collaboration with Roberto Braga), and web-cam and scanner based systems to construct low cost high throughput phenotyping (Michael Adu, co-supervisors Martin Broadley, Malcolm Bennett, Philip White).
The main objective is to construct simple models that can be understood, calibrated easily using available data and integrated with existing software. To achieve this objective, I develop continuous models (PDE) where fundamental growth processes can be incorporated explicitly into conservation equations (in collaboration with Glyn Bengough, Xavier Draye, Tim George and Philip White).
See group pages for more information.
Software development
Archiroot: Software for the acquisition and visualisation of root architecture
BalloonPlugin: Fiji plugin for the segmentation of cell architecture
CellModeller2.0: Software platform for multicellular analysis modelling and computation
SIMUL3R : simulation of root architectures dynamics
More descriptions at: http://www.archiroot.org.uk/doku.php/navigation/architools
Bibliography
- Mimault, M.; Ptashnyk, M.; Dupuy, L. (2023) Particle-based model shows complex rearrangement of tissue mechanical properties are needed for roots to grow in hard soil, PLOS Computational Biology, 19(3), Art. E1010916
- Mimault, M.; Ptashnyk, M.; Dupuy, L. (2023) Particle-based model shows complex rearrangement of tissue mechanical properties are needed for roots to grow in hard soil, PLOS Computational Biology, 19(3), Art. E1010916
- Engelhardt, I.; Patko, D.; Liu, Y.; Mimault, M.; de las Heras Martinez, G.; George, T.; Macdonald, M.; Ptashnyk , M.; Sukhodub, T.; Stanley-Wall, N.; Holden, N.; Daniell, T.; Dupuy , L. (2022) Novel form of collective movement by soil bacteria, The ISME Journal, 16, pp. 2337-2347
- Patko, D.; Yang , Q.; Liu, Y.; Falireas, P.; Briou, B.; George, T.; Daniell, T.; Tawade, B.; MacDonald, M.; Ladmiral, V.; Ameduri, B.; Dupuy , L. (2022) Smart soils to observe hidden rhizosphere processes, bioRxiv, Art. 2021.11.19.468202
- Liu, Y.; Patko, D.; Engelhardt, I.; George, T.S.; Stanley-Wall, N.; Ladmiral, V.; Ameduri, B.; Daniell, T.; Holden, N.J.; MacDonald, M.P.; Dupuy, L.X. (2021) Plant–environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere. Proceedings of the National Academy of Sciences., Proceedings of the National Academy of Sciences, 118, Article No.e2109176118.
- Carroll, D.; Holden, N.J.; Gifford, M.L.; Dupuy, L.X. (2020) Framework for quantification of the dynamics of root colonization by Pseudomonas fluorescens isolate SBW25., Frontiers in Microbiology, 11, Article NO. 585443.
- O'Callaghan, F.E.; Neilson, R.; MacFarlane, S.A.; Dupuy, L.X. (2020) Dynamic biospeckle analysis, a new tool for the fast screening of plant nematicide selectivity., Plant Methods, 15, Article No. 155.
- Martins, A.D.; O'Callaghan, F.; Bengough, A.G.; Loades, K.W.; Pasqual, M.; Kolb, E.; Dupuy, L.X. (2020) The helical motions of roots are linked to avoidance of particle forces in soil., New Phytologist, 225, 2356-2367.
- Mimault, M.; Ptashnyk, M.; Bassel, G.W.; Dupuy, L. (2019) Smoothed particle hydrodynamics for root growth mechanics., Engineering Analysis with Boundary Elements, 105, 20-30.
- White, P.J.; Bradshaw, J.E.; Brown, L.K.; Dale, M.F.B.; Dupuy, L.X.; George, T.S.; Hammond, J.P.; Subramanian, N.K.; Thompson, J.A.; Wishart, J.; Wright, G. (2018) Juvenile root vigour improves phosphorus use efficiency of potato., Plant and Soil, 432, 45-63.
- De La Fuente Canto, C.; Kalogiros, D.I.; Ptashnyk, M.; George, T.S.; Waugh, R.; Bengough, A.G.; Russell, J.; Dupuy, L.X. (2018) Morphological and genetic characterisation of the root system architecture of selected barley recombinant chromosome substitution lines using an integrated phenotyping approach., Journal of Theoretical Biology, 447, 84-97.
- Giri, J.; Bhosale, R.; Huang, G.; Pandey, B.K.; Parker, H.; Zappala, S.; Yang, J.; Dievart, A.; Bureau, C.; Ljung, K.; Price, A.; Rose, T.; Larrieu, A.; Mairhofer, S.; Sturrock, C.J.; White, P.; Dupuy, L.; Hawkesford, M.J.; Perin, C.; Liang, W.; Peret, P.; Hodgman, C.T.; Lynch, J.; Wissuwa, M.; Zhang, D.; Pridmore, T.; Mooney, S.J.; Guidordoni, E.; Swarup, R.; Bennet, M.J. (2018) Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate., Nature Communications, 9, Article No. 1408.
- Dupuy L.X.; Mimault, M.; Patko, D.; Ladmiral, V.; Ameduri, B.; MacDonald, M.P.; Ptashnyk, M. (2018) Micromechanics of root development in soil., Current Opinion in Genetics and Development, 51, 18-25.
- Giles, C.D.; Dupuy, L.; Boitt, G.; Brown, L.K.; Condron, L.; Darch, T.; Blackwell, M.S.A.; Menezes-Blackburn, D.; Shand, C.A.; Stutter, M.I.; Lumsdon, D.G.; Wendler, R.; Cooper, P.; Wearing, C.; Zhang, H.; Haygarth, P.M.; George, T.S. (2018) Root development impacts on the distribution of phosphatase activity: Improvements in quantification using soil zymography., Soil Biology and Biochemistry, 116, 158-166.
- O'Callaghan, F.E.; Braga, R.A.; Neilson, R.; MacFarlane, S.A.; Dupuy, L.X. (2018) New live screening of plant-nematode interactions in the rhizosphere., Scientific Reports, 8, Article No. 1440.
- Bizet, F.; Dupuy, L. X.; Bengough, A. G.; Peaucelle, A.; Hummel, I.; Bogeat-Triboulot, M. (2017) Non-invasive protocol for kinematic monitoring of root growth under infrared light., Bio-protocol, 7, Article No. e2390.
- Banerjee, S.; Tawade, B.V.; Ladmiral, V.; Dupuy, L.X.; MacDonald, M.P.; Ameduri, B. (2017) Poly (fluoroacrylate)s with tunable surface hydrophobicity via radical copolymerization of 2, 2, 2-trifluoroethyl a-fluoroacrylate and 2-(trifluoromethyl) acrylic acid., Polymer Chemistry, 8, 1978-1988.
- Dupuy, L.X.; Wright, G.; Thompson, J.A.; Taylor, A.; Dekeyser, S.; White, C.P.; Thomas, W.T.B.; Nightingale, M.; Hammond, J.P.; Graham, N.S.; Thomas, C.L.; Broadley, M.R.; White, P.J. (2017) Accelerating root system phenotyping of seedlings through a computer-assisted processing pipeline., Plant Methods, 13, Article No. 57.
- Adu, M.O.; Yawson, D.O.; Bennett, MJ.; Broadley, M.R.; Dupuy, L.X.; White, P.J. (2017) A scanner-based rhizobox system enabling the quantification of root system development and response of Brassica rapa seedlings to external P availability., Plant Root, 11, 16-32.
- Bizet, F.; Bengough, A.G.; Hummel, I.; Bogeat-Triboulot, M.B.; Dupuy, L.X. (2016) 3D deformation field in growing plant roots reveals both mechanical and biological responses to axial mechanical forces., Journal of Experimental Botany, 67, 5605-5614.
- White, P.J.; Kawachi, T.; Thompson, J.A.; Wright, G.; Dupuy, L.X. (2016) Minimizing the treatments required to determine the responses of different crop genotypes to potassium supply., Communications in Soil Science and Plant Analysis, 47, 104-111.
- Thomas, C.L.; Graham, N.S.; Hayden, R.; Meacham, M.C.; Neugebauer, K.; Nightingale, M.; Dupuy, L.X.; Hammond, J.P.; White, P.J.; Broadley, M.R. (2016) High-throughput phenotyping (HTP) identifies seedling root traits linked to variation in seed yield and nutrient capture in field-grown oilseed rape (Brassica napus L.)., Annals of Botany, 118, 655-665.
- Kalogiros, D.I.; Adu, M.O.; White, P.J.; Broadley, M.R.; Draye, X.; Ptashnyk, M.; Bengough, A.G.; Dupuy, L.X. (2016) Analysis of root growth from a phenotyping data set using a density-based model., Journal of Experimental Botany, 67, 1045-1058.
- Adu, M.O.; Yawson, D.O.; Armah, F.A.; Asare, P.A.; Bennett, M.J.; Broadley, M.R.; White, P.J.; Dupuy, L.X. (2016) Effects of rooting media on root growth and morphology of Brassica rapa seedlings., South African Journal of Plant and Soil, 33, 219-227.
- Dupuy, L.X.; Silk, W.K. (2016) Mechanisms of early microbial establishment on growing root surfaces., Vadose Zone Journal, 15(2). Open access.
- Thomas, C.L.; Alcock, T.D.; Graham, N.S.; Hayden, R.; Matterson, S.; Wilson, L.; Young, S.D.; Dupuy, L.X.; White, P.J.; Hammond, J.P.; Danku, J.M.C.; Salt, D.E.; Sweeney, A.; Bancroft, I.; Broadley, M.R. (2016) Root morphology and seed and leaf ionomic traits in a Brassica napus L. diversity panel show wide phenotypic variation and are characteristic of crop habit., BMC Plant Biology, 16, Article No. 214.
- Downie, H.F.; Adu, M.O.; Schmidt, S.; Otten, W.; Dupuy, L.X.; White, P.J.; Valentine, T.A. (2015) Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis., Plant, Cell and Environment, 38, 1213-1232.
- Adu, M.O.; Wiesel, L.; Bennett, M.J.; Broadley, M.R.; White, P.J.; Dupuy, L.X. (2015) Scanner-based time-lapse root phenotyping., Bio-protocol, 5, Article No. e1424.
- Valentine, T.A.; Upton, C.; Binnie, K.; Dupuy, L.X.; Karley, A.J.; Schmidt, S.; White, P.; Bengough, G. (2015) Tools and techniques for phenotyping plant:soil interactions., Integrated Plant and Algal Phenomics (IPAP) Meeting, Prague, Czech Republic, 27-30 June 2015.
- Valentine, T.A.; Upton, C.; Bentley, S.; Greenland, A.; Otten, W.; Schmidt, S.; Squire, G.; Dupuy, L.X.; Karley, A.J. (2015) Recent developments in root phenotyping pipelines of cereal crops: transparent soil and rhizotubes., ISSR 2015. 9th International Symposium of the ISRR. "Roots down under - Belowground solutions to global challenges", Canberra, Australia, 6-9 October 2015. Paper O-23.
- Valentine, T.A.; Bengough, A.G.; Dupuy, L.X.; Hallett, P.; Karley, A.J.; McKenzie, B.M.; Newton, A.; Schmidt, S.; Stobart, R.; Squire, G.; Young, M.; Hawes, C. (2015) Evaluating interactions at the plant:soil interface., UK-India Initiative in Agroecology, Centre for Pollination Studies, Calcutta University, Kolkata, India, 21-23 February 2015.
- Valentine, T.A.; Upton, C.; Binnie, K.; Dupuy, L.X.; Karley, A.K.; Schmidt, S.; White, P.; Bengough, A.G. (2015) Tools and techniques for phenotyping plant:soil interactions. , International Plant and Algal Phenomics Meeting, Prague, Czech Republic, 27-30 June 2015.
- Valentine, T.A.; Upton, C.M.; Bentley, S.; Greenland, A.; Otten, W.; Schmidt, S.; Squire, G.; Dupuy, L.X.; Karley, A.J. (2015) Recent developments in root phenotyping pipelines of cereal crops: Transparent soil and rhizotubes., 9th International Symposium of the International Society of Root Research, Roots Down Under - Belowground Solutions to Global Chanllenges, Canberra, Australia 6-9 October 2015.
- Graham, N.S.; Hammond, J.P.; Lysenko, A.; Mayes, S.; O'Lochlainn, S.; Blasco, B.; Bowen, H.C.; Rawlings, C.J.; Rios, J.J.; Welham, S.; Carion, P.W.C.; Dupuy, L.X.; King, G.J.; White, P.J.; Broadley, M.R. (2014) Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs., The Plant Cell, 26, 2818-2830.
- Downie, H.; Valentine, T.A.; Otten, W.; Spiers, A.J.; Dupuy, L.X. (2014) Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo., Plant Signaling and Behavior, 9, Article No. e29878.
- Ribeiro, K.M.; Baretto, B.; Pasqual, M.; White, P.J.; Braga, R.A.; Dupuy, L.X. (2014) Continuous, high-resolution biospeckle imaging reveals a discrete zone of activity at the root apex that responds to contact with obstacles., Annals of Botany, 113, 555-563.
- Adu,M.O.; Chatot, A.; Wiesel, L.; Bennett, M.J.; Broadley, M.R.; White, P.J.; Dupuy, L.X. (2014) A scanner system for high-resolution quantification of variation in root growth dynamics of Brassica rapa genotypes., Journal of Experimental Botany, 65, 2039-2048.
- Upton, C.M., Dupuy, L.X.; Schmidt, S.; Downie, H.; Otten, W.; Valentine, T.A. (2014) Quantifying 3D root system architecture of roots grown in transparent soil - current progress, challenges and future work., Society for Experimental Biology (SEB) Conference, University of Manchester, July 2014. Scientific Session - Roots for global food security (a tribute to Bill Davies). Http://www.sebiology.org/meetings/Manchester/sessions.html
- Brown, L.K.; George, T.S.; Dupuy, L.; White, P.J. (2014) A conceptual model of root hair ideotypes for future agricultural environments., Phosphorus in Soils and Plants, 5th International Symposium, 4th Sustainable Phosphorus Summit, Montpellier, France, 26 August - 3 September 2014.
- Sargent, F.; Davidson, F.A.; Kelly, C.L.; Binny, R.; Christodoulides, N.; Gibson, D.; Johansson, E.; Kozyrska, K.; Lado, L.L.; MacCallum, J.; Montague, R.; Ortmann, B.; Owen, R.; Coulthurst, S.J.; Dupuy, L.; Prescott, A.R.; Palmer, T. (2013) A synthetic system for expression of components of a bacterial microcompartment., Microbiology-SGM, 159, 2427-2436.
- Mimault, M.; Ptashnyk, M.; Dupuy, L. (2023) Particle-based model shows complex rearrangement of tissue mechanical properties are needed for roots to grow in hard soil, PLOS Computational Biology, 19(3), Art. E1010916
- Mimault, M.; Ptashnyk, M.; Dupuy, L. (2023) Particle-based model shows complex rearrangement of tissue mechanical properties are needed for roots to grow in hard soil, PLOS Computational Biology, 19(3), Art. E1010916
- Engelhardt, I.; Patko, D.; Liu, Y.; Mimault, M.; de las Heras Martinez, G.; George, T.; Macdonald, M.; Ptashnyk , M.; Sukhodub, T.; Stanley-Wall, N.; Holden, N.; Daniell, T.; Dupuy , L. (2022) Novel form of collective movement by soil bacteria, The ISME Journal, 16, pp. 2337-2347
- Patko, D.; Yang , Q.; Liu, Y.; Falireas, P.; Briou, B.; George, T.; Daniell, T.; Tawade, B.; MacDonald, M.; Ladmiral, V.; Ameduri, B.; Dupuy , L. (2022) Smart soils to observe hidden rhizosphere processes, bioRxiv, Art. 2021.11.19.468202
- Liu, Y.; Patko, D.; Engelhardt, I.; George, T.S.; Stanley-Wall, N.; Ladmiral, V.; Ameduri, B.; Daniell, T.; Holden, N.J.; MacDonald, M.P.; Dupuy, L.X. (2021) Plant–environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere. Proceedings of the National Academy of Sciences., Proceedings of the National Academy of Sciences, 118, Article No.e2109176118.
- Carroll, D.; Holden, N.J.; Gifford, M.L.; Dupuy, L.X. (2020) Framework for quantification of the dynamics of root colonization by Pseudomonas fluorescens isolate SBW25., Frontiers in Microbiology, 11, Article NO. 585443.
- O'Callaghan, F.E.; Neilson, R.; MacFarlane, S.A.; Dupuy, L.X. (2020) Dynamic biospeckle analysis, a new tool for the fast screening of plant nematicide selectivity., Plant Methods, 15, Article No. 155.
- Martins, A.D.; O'Callaghan, F.; Bengough, A.G.; Loades, K.W.; Pasqual, M.; Kolb, E.; Dupuy, L.X. (2020) The helical motions of roots are linked to avoidance of particle forces in soil., New Phytologist, 225, 2356-2367.
- Mimault, M.; Ptashnyk, M.; Bassel, G.W.; Dupuy, L. (2019) Smoothed particle hydrodynamics for root growth mechanics., Engineering Analysis with Boundary Elements, 105, 20-30.
- White, P.J.; Bradshaw, J.E.; Brown, L.K.; Dale, M.F.B.; Dupuy, L.X.; George, T.S.; Hammond, J.P.; Subramanian, N.K.; Thompson, J.A.; Wishart, J.; Wright, G. (2018) Juvenile root vigour improves phosphorus use efficiency of potato., Plant and Soil, 432, 45-63.
- De La Fuente Canto, C.; Kalogiros, D.I.; Ptashnyk, M.; George, T.S.; Waugh, R.; Bengough, A.G.; Russell, J.; Dupuy, L.X. (2018) Morphological and genetic characterisation of the root system architecture of selected barley recombinant chromosome substitution lines using an integrated phenotyping approach., Journal of Theoretical Biology, 447, 84-97.
- Giri, J.; Bhosale, R.; Huang, G.; Pandey, B.K.; Parker, H.; Zappala, S.; Yang, J.; Dievart, A.; Bureau, C.; Ljung, K.; Price, A.; Rose, T.; Larrieu, A.; Mairhofer, S.; Sturrock, C.J.; White, P.; Dupuy, L.; Hawkesford, M.J.; Perin, C.; Liang, W.; Peret, P.; Hodgman, C.T.; Lynch, J.; Wissuwa, M.; Zhang, D.; Pridmore, T.; Mooney, S.J.; Guidordoni, E.; Swarup, R.; Bennet, M.J. (2018) Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate., Nature Communications, 9, Article No. 1408.
- Dupuy L.X.; Mimault, M.; Patko, D.; Ladmiral, V.; Ameduri, B.; MacDonald, M.P.; Ptashnyk, M. (2018) Micromechanics of root development in soil., Current Opinion in Genetics and Development, 51, 18-25.
- Giles, C.D.; Dupuy, L.; Boitt, G.; Brown, L.K.; Condron, L.; Darch, T.; Blackwell, M.S.A.; Menezes-Blackburn, D.; Shand, C.A.; Stutter, M.I.; Lumsdon, D.G.; Wendler, R.; Cooper, P.; Wearing, C.; Zhang, H.; Haygarth, P.M.; George, T.S. (2018) Root development impacts on the distribution of phosphatase activity: Improvements in quantification using soil zymography., Soil Biology and Biochemistry, 116, 158-166.
- O'Callaghan, F.E.; Braga, R.A.; Neilson, R.; MacFarlane, S.A.; Dupuy, L.X. (2018) New live screening of plant-nematode interactions in the rhizosphere., Scientific Reports, 8, Article No. 1440.
- Bizet, F.; Dupuy, L. X.; Bengough, A. G.; Peaucelle, A.; Hummel, I.; Bogeat-Triboulot, M. (2017) Non-invasive protocol for kinematic monitoring of root growth under infrared light., Bio-protocol, 7, Article No. e2390.
- Banerjee, S.; Tawade, B.V.; Ladmiral, V.; Dupuy, L.X.; MacDonald, M.P.; Ameduri, B. (2017) Poly (fluoroacrylate)s with tunable surface hydrophobicity via radical copolymerization of 2, 2, 2-trifluoroethyl a-fluoroacrylate and 2-(trifluoromethyl) acrylic acid., Polymer Chemistry, 8, 1978-1988.
- Dupuy, L.X.; Wright, G.; Thompson, J.A.; Taylor, A.; Dekeyser, S.; White, C.P.; Thomas, W.T.B.; Nightingale, M.; Hammond, J.P.; Graham, N.S.; Thomas, C.L.; Broadley, M.R.; White, P.J. (2017) Accelerating root system phenotyping of seedlings through a computer-assisted processing pipeline., Plant Methods, 13, Article No. 57.
- Adu, M.O.; Yawson, D.O.; Bennett, MJ.; Broadley, M.R.; Dupuy, L.X.; White, P.J. (2017) A scanner-based rhizobox system enabling the quantification of root system development and response of Brassica rapa seedlings to external P availability., Plant Root, 11, 16-32.
- Bizet, F.; Bengough, A.G.; Hummel, I.; Bogeat-Triboulot, M.B.; Dupuy, L.X. (2016) 3D deformation field in growing plant roots reveals both mechanical and biological responses to axial mechanical forces., Journal of Experimental Botany, 67, 5605-5614.
- White, P.J.; Kawachi, T.; Thompson, J.A.; Wright, G.; Dupuy, L.X. (2016) Minimizing the treatments required to determine the responses of different crop genotypes to potassium supply., Communications in Soil Science and Plant Analysis, 47, 104-111.
- Thomas, C.L.; Graham, N.S.; Hayden, R.; Meacham, M.C.; Neugebauer, K.; Nightingale, M.; Dupuy, L.X.; Hammond, J.P.; White, P.J.; Broadley, M.R. (2016) High-throughput phenotyping (HTP) identifies seedling root traits linked to variation in seed yield and nutrient capture in field-grown oilseed rape (Brassica napus L.)., Annals of Botany, 118, 655-665.
- Kalogiros, D.I.; Adu, M.O.; White, P.J.; Broadley, M.R.; Draye, X.; Ptashnyk, M.; Bengough, A.G.; Dupuy, L.X. (2016) Analysis of root growth from a phenotyping data set using a density-based model., Journal of Experimental Botany, 67, 1045-1058.
- Adu, M.O.; Yawson, D.O.; Armah, F.A.; Asare, P.A.; Bennett, M.J.; Broadley, M.R.; White, P.J.; Dupuy, L.X. (2016) Effects of rooting media on root growth and morphology of Brassica rapa seedlings., South African Journal of Plant and Soil, 33, 219-227.
- Dupuy, L.X.; Silk, W.K. (2016) Mechanisms of early microbial establishment on growing root surfaces., Vadose Zone Journal, 15(2). Open access.
- Thomas, C.L.; Alcock, T.D.; Graham, N.S.; Hayden, R.; Matterson, S.; Wilson, L.; Young, S.D.; Dupuy, L.X.; White, P.J.; Hammond, J.P.; Danku, J.M.C.; Salt, D.E.; Sweeney, A.; Bancroft, I.; Broadley, M.R. (2016) Root morphology and seed and leaf ionomic traits in a Brassica napus L. diversity panel show wide phenotypic variation and are characteristic of crop habit., BMC Plant Biology, 16, Article No. 214.
- Downie, H.F.; Adu, M.O.; Schmidt, S.; Otten, W.; Dupuy, L.X.; White, P.J.; Valentine, T.A. (2015) Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis., Plant, Cell and Environment, 38, 1213-1232.
- Adu, M.O.; Wiesel, L.; Bennett, M.J.; Broadley, M.R.; White, P.J.; Dupuy, L.X. (2015) Scanner-based time-lapse root phenotyping., Bio-protocol, 5, Article No. e1424.
- Graham, N.S.; Hammond, J.P.; Lysenko, A.; Mayes, S.; O'Lochlainn, S.; Blasco, B.; Bowen, H.C.; Rawlings, C.J.; Rios, J.J.; Welham, S.; Carion, P.W.C.; Dupuy, L.X.; King, G.J.; White, P.J.; Broadley, M.R. (2014) Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs., The Plant Cell, 26, 2818-2830.
- Downie, H.; Valentine, T.A.; Otten, W.; Spiers, A.J.; Dupuy, L.X. (2014) Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo., Plant Signaling and Behavior, 9, Article No. e29878.
- Ribeiro, K.M.; Baretto, B.; Pasqual, M.; White, P.J.; Braga, R.A.; Dupuy, L.X. (2014) Continuous, high-resolution biospeckle imaging reveals a discrete zone of activity at the root apex that responds to contact with obstacles., Annals of Botany, 113, 555-563.
- Adu,M.O.; Chatot, A.; Wiesel, L.; Bennett, M.J.; Broadley, M.R.; White, P.J.; Dupuy, L.X. (2014) A scanner system for high-resolution quantification of variation in root growth dynamics of Brassica rapa genotypes., Journal of Experimental Botany, 65, 2039-2048.
- Sargent, F.; Davidson, F.A.; Kelly, C.L.; Binny, R.; Christodoulides, N.; Gibson, D.; Johansson, E.; Kozyrska, K.; Lado, L.L.; MacCallum, J.; Montague, R.; Ortmann, B.; Owen, R.; Coulthurst, S.J.; Dupuy, L.; Prescott, A.R.; Palmer, T. (2013) A synthetic system for expression of components of a bacterial microcompartment., Microbiology-SGM, 159, 2427-2436.
- Brown, L.K.; George, T.S.; Dupuy, L.X.; White, P.J. (2013) A conceptual model of root hair ideotypes for future agricultural environments: what combination of traits should be targeted to cope with limited P availability?, Annals of Botany, 112, 317-330.
- Dresboll, D.B.; Thorup-Kristensen, K.; McKenzie, B.M.; Dupuy, L.X.; Bengough, A.G. (2013) Timelapse scanning reveals spatial variation in tomato (Solanum lycopersicum L.) root elongation rates during partial waterlogging., Plant and Soil, 369, 467-477.
- Yang, Z.; Downie, H.; Dupuy, L.; MacDonald, M. (2013) Light-sheet tomography for in situ imaging of Arabidopsis Thaliana roots., Optics Express, 21, 16239-16247.
- White, P.J.; George, T.S.; Dupuy, L.X.; Karley, A.J.; Valentine, T.A.; Wiesel, L.; Wishart, J. (2013) Root traits for infertile soils., Frontiers in Plant Science, 4, 193.
- Chavarria-Krauser, A.; Dupuy, L.; Ptashnyk, M. (2013) Preface., Mathematical Modelling of Natural Phenoma, 8, 1-4.
- Downie, H.; Holden, N.; Otten, W.; Spiers, A.J.; Valentine, T.A.; Dupuy, L.X. (2012) Transparent soil for imaging the rhizosphere., PLoS ONE, 7, Article No. e44276.
- Dupuy, L.X.; Vignes, M. (2012) An algorithm for the simulation of the growth of root systems on deformable domains., Journal of Theoretical Biology, 310, 164-174.
- Valentine, T.A.; Upton, C.; Binnie, K.; Dupuy, L.X.; Karley, A.J.; Schmidt, S.; White, P.; Bengough, G. (2015) Tools and techniques for phenotyping plant:soil interactions., Integrated Plant and Algal Phenomics (IPAP) Meeting, Prague, Czech Republic, 27-30 June 2015.
- Valentine, T.A.; Upton, C.; Bentley, S.; Greenland, A.; Otten, W.; Schmidt, S.; Squire, G.; Dupuy, L.X.; Karley, A.J. (2015) Recent developments in root phenotyping pipelines of cereal crops: transparent soil and rhizotubes., ISSR 2015. 9th International Symposium of the ISRR. "Roots down under - Belowground solutions to global challenges", Canberra, Australia, 6-9 October 2015. Paper O-23.
- Valentine, T.A.; Bengough, A.G.; Dupuy, L.X.; Hallett, P.; Karley, A.J.; McKenzie, B.M.; Newton, A.; Schmidt, S.; Stobart, R.; Squire, G.; Young, M.; Hawes, C. (2015) Evaluating interactions at the plant:soil interface., UK-India Initiative in Agroecology, Centre for Pollination Studies, Calcutta University, Kolkata, India, 21-23 February 2015.
- Valentine, T.A.; Upton, C.; Binnie, K.; Dupuy, L.X.; Karley, A.K.; Schmidt, S.; White, P.; Bengough, A.G. (2015) Tools and techniques for phenotyping plant:soil interactions. , International Plant and Algal Phenomics Meeting, Prague, Czech Republic, 27-30 June 2015.
- Valentine, T.A.; Upton, C.M.; Bentley, S.; Greenland, A.; Otten, W.; Schmidt, S.; Squire, G.; Dupuy, L.X.; Karley, A.J. (2015) Recent developments in root phenotyping pipelines of cereal crops: Transparent soil and rhizotubes., 9th International Symposium of the International Society of Root Research, Roots Down Under - Belowground Solutions to Global Chanllenges, Canberra, Australia 6-9 October 2015.
- Upton, C.M., Dupuy, L.X.; Schmidt, S.; Downie, H.; Otten, W.; Valentine, T.A. (2014) Quantifying 3D root system architecture of roots grown in transparent soil - current progress, challenges and future work., Society for Experimental Biology (SEB) Conference, University of Manchester, July 2014. Scientific Session - Roots for global food security (a tribute to Bill Davies). Http://www.sebiology.org/meetings/Manchester/sessions.html
- Brown, L.K.; George, T.S.; Dupuy, L.; White, P.J. (2014) A conceptual model of root hair ideotypes for future agricultural environments., Phosphorus in Soils and Plants, 5th International Symposium, 4th Sustainable Phosphorus Summit, Montpellier, France, 26 August - 3 September 2014.
- Adu, M.O.; Broadley, M.R.; Bennett, M.J.; White, P.J.; Dupuy, L.X. (2013) Developing a low cost high throughput root phenotyping system for selection of phosphorus efficient Brassica rapa lines., In: XVII International Plant Nutrition Colloquium and Boron Satellite Meeting, Sabanci University, Istanbul, Turkey, 19-22 August 2013. Proceedings, pp227-228.
- Dupuy, L.X.; Bengough, A.G.; Draye, X.; Kalogiros, D.; Ptashnyk, M. (2013) Density-based approaches to interface models and data in root biology., Annual Meeting of the Society for Experimental Biology, Valencia, Spain, 3-6 July 2013.
- Thomas, C.L.; Neugebauer, K.; Graham, N.S.; Hayden, R.; Hammond, J.P.; Nightingale, M.; Meacham, M.C.; White, P.J.; Dupuy, L.; Broadley, M.R. (2013) Developing root phenotyping techniques for Brassica napus., In: XVII International Plant Nutrition Colloquium and Boron Satellite Meeting, Sabanci University, Istanbul, Turkey, 19-22 August 2013. Proceedings, pp290-291.
- Adu, M.; Bennett, M.; Hammond, J.; White, P.; Dupuy, L.; Broadley, M. (2012) High throughput imaging and analysis of Brassica rapa root system architecture in response to (P) ext., The 8th Symposium of the International Society of Root Research (ISRR); Roots to the Future, The James Hutton Institute, Dundee, 26-29 June 2012.
- Adu M.; Bennett M.; Hammond, J.P.; White, P.J.; Dupuy, L.; Broadley, M.R. (2011) Variation in root system architecture of a single genotype of Brassica rapa., Joint Meeting of BSSS Scottish Soils Discussion Group and the Scottish Root Group, Edinburgh, 2 November 2011.
- Dupuy, L.X. (2011) Modelling root systems using oriented density distributions., 9th International Conference of Numerical Analysis and Applied Mathematics, Halkidiki, Greece, 19-25 September 2011. AIP Conference Proceedings, 1389, p726.
- Dupuy, L. (2010) Modelling root systems using continuous deformable plant models (CDPM)., 6th International Workshop on Functional - Structural Plant Models (FSPM). University of California, Davis, California, USA, 12-17 September 2010 (Talk).
- Dupuy, L. (2009) New approaches for the modelling of root architecture., The 20th International Conference on Arabidopsis Research. EICC, Edinburgh, 30 June-4 July 2009 (Invited talk).
- Dupuy, L.; Vignes, M. (2009) Simplified root architectural models using continuous deformable domains., IEEE, 3rd International Symposium Plant Growth Modeling, Simulation, Visualization and Applications. Beijing, China, 9-13 November 2009 (Talk).
- Dupuy, L.; Vignes, M.; McKenzie, B.M.; White, P.J. (2009) The dynamics of plant root meristems., French Annual Meeting of Biology, Informatics and Mathematics, Nantes, France, 9-11 June 2009.
- Bengough, A.G.; Roberts, T.J.; Wuyts, N.; Hans, J.; McKenna, S.J.; Valentine, T.A.; Bransby, M.F.; Dupuy, L.; Haseloff, J. (2007) Computer visualisation and modelling of plant morphogenesis: Motion analysis of time-lapse confocal microscopy images., BBSRC Joint Bioinformatics and e-Science, Proteomics and Cell Function Grantholders Workshop, Cheshire, 8-10 January 2007.
- Valentine, T.A.; Bengough, A.G.; Bransby, F.; Dupuy, L.; Hans, J.; Haseloff, J.; McKenna, S.; Roberts, T.J. (2005) Computer visualisation and modelling of plant morphogenesis: Optical flow analysis of time-lapse confocal microscopy images., BBSRC/SCRI Bioinformatics and Escience Workshop, Manchester, 18-19 October 2005.
- Roberts, T.J.; Bengough, A.G.; Bransby, F.; Dupuy, L.; Hans, J.; Haseloff, J.; McKenna, S.; Valentine, T.A. (2005) Computer visualisation and modelling of plant morphogenesis: in-vivo segmentation and tracking of cells using confocal microscopy., BBSRC/SCRI Bioinformatics and Escience Workshop, Manchester, 18-19 October 2005.
