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Atkinson, Jonathan A., Pound, Michael P., Bennett, Malcolm J. and Wells, Darren M. (2019) Uncovering the hidden half of plants using new advances in root phenotyping. Current Opinion in Biotechnology, 55 . pp. 1-8. ISSN 1879-0429

Pridmore, Tony P., Gibbs, Jonathon, Pound, Michael P., French, Andrew P., Wells, Darren M. and Murchie, Erik H. (2018) Plant phenotyping: an active vision cell for three-dimensional plant shoot reconstruction. Plant Physiology . ISSN 1532-2548 (In Press)

Muller, Lukas, Bennett, Malcolm J., French, Andy, Wells, Darren M. and Swarup, Ranjan (2018) Root gravitropism: quantification, challenges, and solutions. Methods in Molecular Biology, 1761 . pp. 103-112. ISSN 1940-6029

von Wangenheim, Daniel, Wells, Darren M. and Bennett, Malcolm J. (2017) Adding a piece to the leaf epidermal cell shape puzzle. Developmental Cell, 43 (3). pp. 255-256. ISSN 1878-1551

Kenobi, Kim, Atkinson, Jonathan A., Wells, Darren M., Gaju, Oorbessy, deSilva, Jayalath G., Foulkes, M. John, Dryden, Ian L., Wood, Andrew T.A. and Bennett, Malcolm J. (2017) Linear discriminant analysis reveals differences in root architecture in wheat seedlings by nitrogen uptake efficiency. Journal of Experimental Botany, 68 (17). pp. 4969-4981. ISSN 1460-2431

Atkinson, Jonathan A. and Wells, Darren M. (2017) An updated protocol for high throughput plant tissue sectioning. Frontiers in Plant Science, 8 . p. 1721. ISSN 1664-462X

Pound, Michael P., Atkinson, Jonathan A., Townsend, Alexandra J., Wilson, Michael H., Griffiths, Marcus, Jackson, Aaron S., Bulat, Adrian, Tzimiropoulos, Georgios, Wells, Darren M., Murchie, Erik H., Pridmore, Tony P. and French, Andrew P. (2017) Deep machine learning provides state-of-the-art performance in image-based plant phenotyping. GigaScience, 6 (10). pp. 1-10. ISSN 2047-217X

Morris, Emily C., Griffiths, Marcus, Golebiowska, Agata, Mairhofer, Stefan, Burr-Hersey, Jasmine, Goh, Tatsuaki, von Wangenheim, Daniel, Atkinson, Brian, Sturrock, Craig J., Lynch, Jonathan P., Vissenberg, Kris, Ritz, Karl, Wells, Darren M., Mooney, Sacha J. and Bennett, Malcolm J. (2017) Shaping 3D root system architecture. Current Biology, 27 (17). R919-R930. ISSN 1879-0445

Atkinson, Jonathan A., Lobet, Guillaume, Noll, Manuel, Meyer, Patrick E., Griffiths, Marcus and Wells, Darren M. (2017) Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large-scale genetic studies. GigaScience, 6 (10). pp. 1-7. ISSN 2047-217X

Dietrich, Daniela, Pang, Lei, Kobayashi, Akie, Fozard, John A., Boudolf, Véronique, Bhosale, Rahul, Antoni, Regina, Nguyen, Tuan, Hiratsuka, Sotaro, Fujii, Nobuharu, Miyazawa, Yutaka, Bae, Tae-Woong, Wells, Darren M., Owen, Markus R., Band, Leah R., Dyson, Rosemary J., Jensen, Oliver E., King, John R., Tracy, Saoirse R., Sturrock, Craig, Mooney, Sacha J., Roberts, Jeremy A., Bhalerao, Rishikesh P., Dinneny, José R., Rodriguez, Pedro L., Nagatani, Akira, Hosokawa, Yoichiroh, Baskin, Tobias I., Pridmore, Tony P., De Veylder, Lieven, Takahashi, Hideyuki and Bennett, Malcolm J. (2017) Root hydrotropism is controlled via a cortex-specific growth mechanism. Nature Plants, 3 . p. 17057. ISSN 2055-0278

Goh, Tatsuaki, Toyokura, Koichi, Wells, Darren M., Swarup, Kamal, Yamamoto, Mayuko, Mimura, Tetsuro, Weijers, Dolf, Fukaki, Hidehiro, Laplaze, Laurent, Bennett, Malcolm J. and Guyomarc'h, Soazig (2016) Quiescent center initiation in the Arabidopsislateral root primordia is dependent on the SCARECROW transcription factor. Development, 143 (18). pp. 3363-3371. ISSN 1477-9129

Gibbs, Jonathon, Pound, Michael P., French, Andrew P., Wells, Darren M., Murchie, Erik H. and Pridmore, Tony P. (2016) Approaches to three-dimensional reconstruction of plant shoot topology and geometry. Functional Plant Biology . ISSN 1445-4408

Passot, Sixtine, Gnacko, Fatoumata, Moukouanga, Daniel, Lucas, Mikaël, Guyomarc’h, Soazig, Ortega, Beatriz Moreno, Atkinson, Jonathan A., Belko, Marème N., Bennett, Malcolm J., Gantet, Pascal, Wells, Darren M., Guédon, Yann, Vigouroux, Yves, Verdeil, Jean-Luc, Muller, Bertrand and Laplaze, Laurent (2016) Characterization of pearl millet root architecture and anatomy reveals three types of lateral roots. Frontiers in Plant Science, 7 . p. 829. ISSN 1664-462X

Voß, Ute, Wilson, Michael H., Kenobi, Kim, Gould, Peter D., Robertson, Fiona C., Peer, Wendy A., Lucas, Mikaël, Swarup, Kamal, Casimiro, Ilda, Holman, Tara J., Wells, Darren M., Péret, Benjamin, Goh, Tatsuaki, Fukaki, Hidehiro, Hodgman, T. Charlie, Laplaze, Laurent, Halliday, Karen J., Ljung, Karin, Murphy, Angus S., Hall, Anthony J., Webb, Alex A. R. and Bennett, Malcolm J. (2015) The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana. Nature Communications, 6 . 7641/1-7641/9. ISSN 2041-1723

Atkinson, Jonathan A., Wingen, Luzie U., Griffiths, Marcus, Pound, Michael P., Gaju, Oorbessy, Foulkes, John, Le Gouis, Jacques, Griffiths, Simon, Bennett, Malcolm J., King, Julie and Wells, Darren M. (2015) Phenotyping pipeline reveals major seedling root growth QTL in hexaploid wheat. Journal of Experimental Botany, 66 (8). pp. 2283-2292. ISSN 1460-2431

Wilson, Michael H., Holman, Tara J., Sørensen, Iben, Cancho-Sanchez, Ester, Wells, Darren M., Swarup, Ranjan, Knox, J. Paul, Willats, William G.T., Ubeda-Tomás, Susana, Holdsworth, Michael J., Bennett, Malcolm J., Vissenberg, Kris and Hodgman, T. Charlie (2015) Multi-omics analysis identifies genes mediating the extension of cell walls in the Arabidopsis thaliana root elongation zone. Frontiers in Cell and Developmental Biology, 3 . 10/1-10/12. ISSN 2296-634X

Mairhofer, Stefan, Sturrock, Craig, Wells, Darren M., Bennett, Malcolm J., Mooney, Sacha J. and Pridmore, Tony (2014) On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images. Functional Plant Biology, 42 (5). pp. 460-470. ISSN 1445-4408

Atkinson, Jonathan A., Rasmussen, Amanda, Traini, Richard, Voss, Ute, Sturrock, Craig, Mooney, Sacha J., Wells, Darren M. and Bennett, Malcolm J. (2014) Branching out in roots: uncovering form, function, and regulation. Plant Physiology, 166 (2). pp. 538-550. ISSN 0032-0889

Dyson, Rosemary J., Vizcay-Barrena, Gema, Band, Leah R., Fernandes, Anwesha N., French, Andrew P., Fozard, John A., Hodgman, T. Charlie, Kenobi, Kim, Pridmore, Tony P., Stout, Michael, Wells, Darren M., Wilson, Michael H., Bennett, Malcolm J. and Jensen, Oliver E. (2014) Mechanical modelling quantifies the functional importance of outer tissue layers during root elongation and bending. New Phytologist, 202 (4). pp. 1212-1222. ISSN 1469-8137

Band, Leah R., Wells, Darren M., Fozard, John A., Ghetiu, Teodor, French, Andrew P., Pound, Michael P., Wilson, Michael H., Yu, Lei, Li, Wenda, Hijazi, Hussein I., Oh, Jaesung, Pearce, Simon P., Perez-Amador, Miguel A., Yun, Jeonga, Kramer, Eric, Alonso, Jose M., Godin, Christophe, Vernoux, Teva, Hodgman, T. C., Pridmore, Tony P., Swarup, Ranjan, King, John R. and Bennett, Malcolm J. (2014) Systems analysis of auxin transport in the Arabidopsis root apex. Plant Cell, 26 (3). pp. 862-875. ISSN 1040-4651

Peret, Benjamin, Middleton, Alistair M., French, Andrew P., Larrieu, Antoine, Bishopp, Antony, Njo, Maria, Wells, Darren M., Porco, Silvana, Mellor, Nathan., Band, Leah R., Casimiro, Ilda, Kleine-Vehn, Jurgen, Vanneste, Steffen, Sairanen, Ilkka, Mallet, Romain, Sandberg, Goran, Ljung, Karin, Beeckman, Tom, Benkova, Eva, Friml, Jiri, Kramer, Eric, King, John R., De Smet, Ive, Pridmore, Tony, Owen, Markus R. and Bennett, Malcolm J. (2013) Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology, 9 (1). 699/1-699/15. ISSN 1744-4292

Conference or Workshop Item

Pound, Michael P., Atkinson, Jonathan A., Wells, Darren M., Pridmore, Tony P. and French, Andrew P. (2017) Deep learning for multi-task plant phenotyping. In: ICCV 2017 International Conference on Computer Vision, 22-29 October, 2017, Venice, Italy.

Gibbs, Jonathon, Pound, Michael P., Wells, Darren M., Murchie, Erik H., French, Andrew P. and Pridmore, Tony P. (2015) Three-dimensional reconstruction of plant shoots from multiple images using an active vision system. In: Agri-Food Robotics Workshop, 2 Oct 2015, Hamburg, Germany.

Book Section

Atkinson, Jonathan A., Jackson, Robert J., Bentley, Alison R., Ober, Eric and Wells, Darren M. (2018) Field phenotyping for the future. In: Annual Plant Reviews Online. Annual Plant Reviews Online (51). Wiley. ISBN 9781119312994 (In Press)

Other

Atkinson, Jonathan A., Lobet, Guillaume, Noll, Manuel, Meyer, Patrick E., Griffiths, Marcus and Wells, Darren M. (2017) Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large scale genetic studies. bioRxiv, Cold Spring Harbor, N.Y., USA.

Pound, Michael P., Burgess, Alexandra J., Wilson, Michael H., Atkinson, Jonathan A., Griffiths, Marcus, Jackson, Aaron S., Bulat, Adrian, Tzimiropoulos, Yorgos, Wells, Darren M., Murchie, Erik H., Pridmore, Tony P. and French, Andrew P. (2016) Deep machine learning provides state-of-the art performance in image-based plant phenotyping. Cold Spring Harbor Laboratory.