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false/arabidopsis thaliana
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Assessing the Performances of Protein Function Prediction Algorithms from the Perspectives of Identification Accuracy and False Discovery Rate.
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The function of a protein is of great interest in the cutting-edge research of biological mechanisms, disease development and drug/target discovery. Besides experimental explorations, a variety of computational methods have been designed to predict protein function. Among these in silico methods,
High Throughput Screening Method for Identifying Potential Agonists and Antagonists of Arabidopsis thaliana Cytokinin Receptor CRE1/AHK4.
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The CRE1/AHK4 cytokinin receptor is an important component of plants' hormone signaling systems, and compounds that can alter its activity have potential utility for studying the receptor's functions and/or developing new plant growth regulators. A high throughput method was developed for screening
UvHrip1, an Effector Secreted by Ustilaginoidea Virens, Suppresses Basal Defense and Promotes Disease Development in Arabidopsis Thaliana
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Rice false smut (RFS), caused by Ustilaginoidea virens, is one of the most detrimental rice fungal diseases and pose a severe threat to rice production and quality. Effectors in U. virens often act as a set of essential virulence factors that play crucial roles in the interaction between host and
Computational analysis of auxin responsive elements in the Arabidopsis thaliana L. genome.
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Auxin responsive elements (AuxRE) were found in upstream regions of target genes for ARFs (Auxin response factors). While Chip-seq data for most of ARFs are still unavailable, prediction of potential AuxRE is restricted by consensus models that detect too many false positive sites. Using sequence
Response to the note to editor: Comments on "transcriptomic response of Arabidopsis thaliana exposed to hydroxylated polychlorinated biphenyls (OH-PCBs)".
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In response to Dr. Yang et al.'s comments on our article "Transcriptomic response of Arabidopsis thaliana exposed to hydroxylated polychlorinated biphenyls (OH-PCBs)", additional details were provided regarding the analysis of the gene expression level (One-Way
Workflow for large scale detection and validation of peptide modifications by RPLC-LTQ-Orbitrap: application to the Arabidopsis thaliana leaf proteome and an online modified peptide library.
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Post-translational modifications (PTMs) of proteins add to the complexity of proteomes, thereby complicating the task of proteome characterization. An efficient strategy to identify this peptide heterogeneity is important for determination of protein function, as well as for mass spectrometry-based
A rapid and non-destructive screenable marker, FAST, for identifying transformed seeds of Arabidopsis thaliana.
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The creation of transgenic plants has contributed extensively to the advancement of plant science. Establishing homozygous transgenic lines is time-consuming and laborious, and using antibiotics or herbicides to select transformed plants may adversely affect the growth of some transgenic plants.
Large expression differences in genes for iron and zinc homeostasis, stress response, and lignin biosynthesis distinguish roots of Arabidopsis thaliana and the related metal hyperaccumulator Thlaspi caerulescens.
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The micronutrient zinc has an essential role in physiological and metabolic processes in plants as a cofactor or structural element in 300 catalytic and noncatalytic proteins, but it is very toxic when available in elevated amounts. Plants tightly regulate their internal zinc concentrations in a
Prediction of operon-like gene clusters in the Arabidopsis thaliana genome based on co-expression analysis of neighboring genes.
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Operon-like arrangements of genes occur in eukaryotes ranging from yeasts and filamentous fungi to nematodes, plants, and mammals. In plants, several examples of operon-like gene clusters involved in metabolic pathways have recently been characterized, e.g. the cyclic hydroxamic acid pathways in
SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines.
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BACKGROUND
Many tools exist to predict structural variants (SVs), utilizing a variety of algorithms. However, they have largely been developed and tested on human germline or somatic (e.g. cancer) variation. It seems appropriate to exploit this wealth of technology available for humans also for
A Holistic Approach to Analyze Systemic Jasmonate Accumulation in Individual Leaves of Arabidopsis Rosettes Upon Wounding.
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Phytohormones, especially jasmonates, are known to be mediators of the plant responses to wounding and herbivore feeding. Their role in such stress responses has been largely studied locally in treated leaves. However, less is known about the induced systemic distribution of phytohormone signals
N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence.
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Myristoylation by the myristoyl-CoA:protein N-myristoyltransferase (NMT) is an important lipid anchor modification of eukaryotic and viral proteins. Automated prediction of N-terminal N-myristoylation from the substrate protein sequence alone is necessary for large-scale sequence annotation projects
Utilization of single-image normalized difference vegetation index (SI-NDVI) for early plant stress detection.
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UNASSIGNED
An imaging system was refined to monitor the health of vegetation grown in controlled conditions using spectral reflectance patterns. To measure plant health, the single-image normalized difference vegetation index (SI-NDVI) compares leaf reflectance in visible and near-infrared light
Arabidopsis galactinol synthase AtGolS2 improves drought tolerance in the monocot model Brachypodium distachyon.
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Brachypodium distachyon (purple false brome) is a herbaceous species belonging to the grass subfamily Pooideae, which also includes major crops like wheat, barley, oat and rye. The species has been established as experimental model organism for understanding and improving cereal crops and temperate
Os-GIGANTEA confers robust diurnal rhythms on the global transcriptome of rice in the field.
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The circadian clock controls physiological traits such as flowering time, photosynthesis, and growth in plants under laboratory conditions. Under natural field conditions, however, little is known about the significance of the circadian clock in plants. By time-course transcriptome analyses of rice
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