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  1. Content type: Methodology

    Genome-wide characterization of tissue- or cell-specific gene expression is a recurrent bottleneck in biology. We have developed a sensitive approach based on ultra-low RNA sequencing coupled to laser assisted...

    Authors: Kaori Sakai, Ludivine Taconnat, Nero Borrega, Jennifer Yansouni, Véronique Brunaud, Christine Paysant-Le Roux, Etienne Delannoy, Marie-Laure Martin Magniette, Loïc Lepiniec, Jean Denis Faure, Sandrine Balzergue and Bertrand Dubreucq

    Citation: Plant Methods 2018 14:10

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  2. Content type: Methodology

    Due to the nature of viral RNA genomes, RNA viruses depend on many RNA-binding proteins (RBP) of viral and host origin for replication, dissemination and evasion of host RNA degradation pathways. Some viruses ...

    Authors: F. E. Marmisolle, M. L. García and C. A. Reyes

    Citation: Plant Methods 2018 14:9

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  3. Content type: Methodology

    The amino acid profile of plants is an important parameter in assessments of their growth potential, resource-use efficiency and/or quality as food and feed. Screening studies may involve large number of sampl...

    Authors: Rasmus Dahl-Lassen, Jan van Hecke, Henning Jørgensen, Christian Bukh, Birgit Andersen and Jan K. Schjoerring

    Citation: Plant Methods 2018 14:8

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  4. Content type: Methodology

    Leaf venation traits are important for many research fields such as systematics and evolutionary biology, plant physiology, climate change, and paleoecology. In spite of an increasing demand for vein trait dat...

    Authors: Julio V. Schneider, Renate Rabenstein, Jens Wesenberg, Karsten Wesche, Georg Zizka and Jörg Habersetzer

    Citation: Plant Methods 2018 14:7

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  5. Content type: Methodology

    Deep learning presents many opportunities for image-based plant phenotyping. Here we consider the capability of deep convolutional neural networks to perform the leaf counting task. Deep learning techniques ty...

    Authors: Jordan Ubbens, Mikolaj Cieslak, Przemyslaw Prusinkiewicz and Ian Stavness

    Citation: Plant Methods 2018 14:6

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  6. Content type: Methodology

    Miscanthus is a leading second generation bio-energy crop. It is mostly rhizome propagated; however, the increasing use of seed is resulting in a greater need to investigate germination. Miscanthus seed are small...

    Authors: Danny Awty-Carroll, John Clifton-Brown and Paul Robson

    Citation: Plant Methods 2018 14:5

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  7. Content type: Methodology

    Low pollen viability may limit grapevine yield under certain conditions, causing relevant economic losses to grape-growers. It is usually evaluated by the quantification of the number of viable and non-viable ...

    Authors: Javier Tello, María Ignacia Montemayor, Astrid Forneck and Javier Ibáñez

    Citation: Plant Methods 2018 14:3

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  8. Content type: Methodology

    Transient gene expression is a powerful tool to study gene function in plants. In citrus, Agrobacterium transformation is the method of choice for transient expression studies, but this method does not work effic...

    Authors: Amit Levy, Choaa El-Mochtar, Chunxia Wang, Michael Goodin and Vladimir Orbovic

    Citation: Plant Methods 2018 14:2

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  9. Content type: Software

    Plants demonstrate dynamic growth phenotypes that are determined by genetic and environmental factors. Phenotypic analysis of growth features over time is a key approach to understand how plants interact with ...

    Authors: Ji Zhou, Christopher Applegate, Albor Dobon Alonso, Daniel Reynolds, Simon Orford, Michal Mackiewicz, Simon Griffiths, Steven Penfield and Nick Pullen

    Citation: Plant Methods 2017 13:117

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  10. Content type: Methodology

    Fine-grained recognition of plants from images is a challenging computer vision task, due to the diverse appearance and complex structure of plants, high intra-class variability and small inter-class differenc...

    Authors: Milan Šulc and Jiří Matas

    Citation: Plant Methods 2017 13:115

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  11. Content type: Software

    Developmental biology has made great strides in recent years towards the quantification of cellular properties during development. This requires tissues to be imaged and segmented to generate computerised vers...

    Authors: Annamária Kiss, Typhaine Moreau, Vincent Mirabet, Cerasela Iliana Calugaru, Arezki Boudaoud and Pradeep Das

    Citation: Plant Methods 2017 13:114

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  12. Content type: Methodology

    Switchgrass (Panicum virgatum), a robust perennial C4-type grass, has been evaluated and designated as a model bioenergy crop by the U.S. DOE and USDA. Conventional breeding of switchgrass biomass is difficult be...

    Authors: Chien-Yuan Lin, Bryon S. Donohoe, Neha Ahuja, Deborah M. Garrity, Rongda Qu, Melvin P. Tucker, Michael E. Himmel and Hui Wei

    Citation: Plant Methods 2017 13:113

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  13. Content type: Methodology

    To investigate translational regulation of gene expression in plant mitochondria, a mitochondrial polysome isolation protocol was established for tobacco to investigate polysomal mRNA loading as a proxy for tr...

    Authors: Muhammad Waqar Hameed, Ilona Juszczak, Ralph Bock and Joost Thomas van Dongen

    Citation: Plant Methods 2017 13:112

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  14. Content type: Methodology

    The morphological analysis of olive leaves, fruits and endocarps may represent an efficient tool for the characterization and discrimination of cultivars and the establishment of relationships among them. In r...

    Authors: Konstantinos N. Blazakis, Maria Kosma, George Kostelenos, Luciana Baldoni, Marina Bufacchi and Panagiotis Kalaitzis

    Citation: Plant Methods 2017 13:111

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  15. Content type: Research

    The development of cell pattern in the surface cell layer of the shoot apex can be investigated in vivo by use of a time-lapse confocal images, showing naked meristem in 3D in successive times. However, how th...

    Authors: Krzysztof Kucypera, Marcin Lipowczan, Anna Piekarska-Stachowiak and Jerzy Nakielski

    Citation: Plant Methods 2017 13:110

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  16. Content type: Methodology

    Sorghum (Sorghum bicolor L.) is one of the world’s most important cereal crops grown for multiple applications and has been identified as a potential biofuel crop. Despite several decades of study, sorghum has be...

    Authors: Srinivas Belide, Thomas Vanhercke, James Robertson Petrie and Surinder Pal Singh

    Citation: Plant Methods 2017 13:109

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  17. Content type: Methodology

    Plant extracts contain a huge variety of pharmacologically active substances. Conventionally, various chromatographic methods must be applied several times to purify functional compounds to measure their funct...

    Authors: Ye Ji Park, Si Hyun Seong, Min Sun Kim, Sang Wan Seo, Mee Ree Kim and Hyun Sik Kim

    Citation: Plant Methods 2017 13:108

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  18. Content type: Methodology

    The proportion of granule types in wheat starch is an important characteristic that can affect its functionality. It is widely accepted that granule types are either large, disc-shaped A-type granules or small...

    Authors: Emi Tanaka, Jean-Phillippe F. Ral, Sean Li, Raj Gaire, Colin R. Cavanagh, Brian R. Cullis and Alex Whan

    Citation: Plant Methods 2017 13:107

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  19. Content type: Methodology

    Several high-throughput molecular genetic analyses rely on high-quality genomic DNA. Copurification of other molecules can negatively impact the functionality of plant DNA preparations employed in these proced...

    Authors: Kelvin T. Chiong, Mona B. Damaj, Carmen S. Padilla, Carlos A. Avila, Shankar R. Pant, Kranthi K. Mandadi, Ninfa R. Ramos, Denise V. Carvalho and T. Erik Mirkov

    Citation: Plant Methods 2017 13:106

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  20. Content type: Research

    Rice panicle phenotyping is important in rice breeding, and rice panicle segmentation is the first and key step for image-based panicle phenotyping. Because of the challenge of illumination differentials, pani...

    Authors: Xiong Xiong, Lingfeng Duan, Lingbo Liu, Haifu Tu, Peng Yang, Dan Wu, Guoxing Chen, Lizhong Xiong, Wanneng Yang and Qian Liu

    Citation: Plant Methods 2017 13:104

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  21. Content type: Research

    Accurately segmenting vegetation from the background within digital images is both a fundamental and a challenging task in phenotyping. The performance of traditional methods is satisfactory in homogeneous env...

    Authors: Pouria Sadeghi-Tehran, Nicolas Virlet, Kasra Sabermanesh and Malcolm J. Hawkesford

    Citation: Plant Methods 2017 13:103

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  22. Content type: Methodology

    Root systems are highly plastic and adapt according to their soil environment. Studying the particular influence of soils on root development necessitates the adaptation and evaluation of imaging methods for m...

    Authors: Daniel Pflugfelder, Ralf Metzner, Dagmar van Dusschoten, Rüdiger Reichel, Siegfried Jahnke and Robert Koller

    Citation: Plant Methods 2017 13:102

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  23. Content type: Correction

    After publication of this article [1], the authors noted the following error. Due to a calculation error in the temperature term f(TL) of the emission standardization algorithm (Eq. 3 of the original paper), the ...

    Authors: Marvin Lüpke, Rainer Steinbrecher, Michael Leuchner and Annette Menzel

    Citation: Plant Methods 2017 13:100

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    The original article was published in Plant Methods 2017 13:14

  24. Content type: Methodology

    The compressional modulus of elasticity is an important mechanical property for understanding stalk lodging, but this property is rarely available for thin-walled plant stems such as maize and sorghum because ...

    Authors: Loay A. Al-Zube, Daniel J. Robertson, Jean N. Edwards, Wenhuan Sun and Douglas D. Cook

    Citation: Plant Methods 2017 13:99

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  25. Content type: Methodology

    Plant science uses increasing amounts of phenotypic data to unravel the complex interactions between biological systems and their variable environments. Originally, phenotyping approaches were limited by manua...

    Authors: Benoît Valle, Thierry Simonneau, Romain Boulord, Francis Sourd, Thibault Frisson, Maxime Ryckewaert, Philippe Hamard, Nicolas Brichet, Myriam Dauzat and Angélique Christophe

    Citation: Plant Methods 2017 13:98

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  26. Content type: Research

    Automated species identification is a long term research subject. Contrary to flowers and fruits, leaves are available throughout most of the year. Offering margin and texture to characterize a species, they a...

    Authors: Michael Rzanny, Marco Seeland, Jana Wäldchen and Patrick Mäder

    Citation: Plant Methods 2017 13:97

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  27. Content type: Methodology

    In maize, silks are hundreds of filaments that simultaneously emerge from the ear for collecting pollen over a period of 1–7 days, which largely determines grain number especially under water deficit. Silk gro...

    Authors: Nicolas Brichet, Christian Fournier, Olivier Turc, Olivier Strauss, Simon Artzet, Christophe Pradal, Claude Welcker, François Tardieu and Llorenç Cabrera-Bosquet

    Citation: Plant Methods 2017 13:96

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  28. Content type: Methodology

    Improvements in high-throughput phenotyping technologies are rapidly expanding the scope and capacity of plant biology studies to measure growth traits. Nevertheless, the costs of commercial phenotyping equipm...

    Authors: Andrei Dobrescu, Livia C. T. Scorza, Sotirios A. Tsaftaris and Alistair J. McCormick

    Citation: Plant Methods 2017 13:95

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  29. Content type: Methodology article

    Accurate and quantitative phenotypic data in plant breeding programmes is vital in breeding to assess the performance of genotypes and to make selections. Traditional strawberry phenotyping relies on the human...

    Authors: Joe Q. He, Richard J. Harrison and Bo Li

    Citation: Plant Methods 2017 13:93

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  30. Content type: Research

    Wheat is one of the most widely grown crop in temperate climates for food and animal feed. In order to meet the demands of the predicted population increase in an ever-changing climate, wheat production needs ...

    Authors: Nathan Hughes, Karen Askew, Callum P. Scotson, Kevin Williams, Colin Sauze, Fiona Corke, John H. Doonan and Candida Nibau

    Citation: Plant Methods 2017 13:76

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  31. Content type: Methodology

    Hyperspectral imaging is a technology that can be used to monitor plant responses to stress. Hyperspectral images have a full spectrum for each pixel in the image, 400–2500 nm in this case, giving detailed inf...

    Authors: Dominic Williams, Avril Britten, Susan McCallum, Hamlyn Jones, Matt Aitkenhead, Alison Karley, Ken Loades, Ankush Prashar and Julie Graham

    Citation: Plant Methods 2017 13:74

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  32. Content type: Research

    Flos Chrysanthemi, as a part of Chinese culture for a long history, is valuable for not only environmental decoration but also the medicine and food additive. Due to their voluminously...

    Authors: Heng Zhang, Zhenyi Chen, Taihao Li, Na Chen, Wenjie Xu and Shupeng Liu

    Citation: Plant Methods 2017 13:92

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  33. Content type: Research

    Cultivated strawberry (Fragaria × ananassa Duch.) has homoeologous chromosomes because of allo-octoploidy. For example, two homoeologous chromosomes that belong to different sub-genome of allopolyploids have simi...

    Authors: Tomohiro Yanagi, Kenta Shirasawa, Mayuko Terachi and Sachiko Isobe

    Citation: Plant Methods 2017 13:91

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  34. Content type: Research

    There is currently a high requirement for field phenotyping methodologies/technologies to determine quantitative traits related to crop yield and plant stress responses under field conditions.

    Authors: Jorge Gago, Alisdair R. Fernie, Zoran Nikoloski, Takayuki Tohge, Sebastiá Martorell, José Mariano Escalona, Miquel Ribas-Carbó, Jaume Flexas and Hipólito Medrano

    Citation: Plant Methods 2017 13:90

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  35. Content type: Methodology

    Cytokinins play many essential roles in plant growth and development, mainly through signal transduction pathways. Although the cytokinin signaling pathway in rice has been clarified, no synthetic reporter for...

    Authors: Jinyuan Tao, Huwei Sun, Pengyuan Gu, Zhihao Liang, Xinni Chen, Jiajing Lou, Guohua Xu and Yali Zhang

    Citation: Plant Methods 2017 13:89

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  36. Content type: Methodology

    The oomycete Phytophthora infestans causes late blight on potato and tomato. Despite extensive research, the P. infestans-host interaction is still poorly understood. To find new ways to further unravel this inte...

    Authors: Charikleia Schoina, Klaas Bouwmeester and Francine Govers

    Citation: Plant Methods 2017 13:88

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  37. Content type: Methodology

    Most current methods for constructing guide RNAs (gRNA) for the CRISPR/Cas9 genome editing system, depend on traditional cloning using specific type IIS restriction enzymes and DNA ligation. These methods cons...

    Authors: Aftab A. Khan, Ashraf El-Sayed, Asma Akbar, Arianna Mangravita-Novo, Shaheen Bibi, Zunaira Afzal, David J. Norman and Gul Shad Ali

    Citation: Plant Methods 2017 13:86

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  38. Content type: Methodology

    Genomic DNA extracted from species of Cactaceae is often contaminated with significant amounts of mucilage and pectin. Pectin is one of the main components of cellular walls, whereas mucilage is a complex poly...

    Authors: César Ramiro Martínez-González, Rosario Ramírez-Mendoza, Jaime Jiménez-Ramírez, Clemente Gallegos-Vázquez and Isolda Luna-Vega

    Citation: Plant Methods 2017 13:82

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