EZ-Root-VIS: A Software Pipeline for the Rapid Analysis and Visual Reconstruction of Root System Architecture
Zaigham Shahzad Fabian Kellermeier Emily M. Armstrong Simon Rogers Guillaume Lobet Anna Amtmann Adrian Hills
Plant Physiology, 2018-8
https://doi.org/10.1104/pp.18.00217
ZAIGHAM SHAHZAD
SHAHZAD ZAIGHAM
ORCID: 0000-0002-3953-3184
Aquaporins in plants 10.1152/physrev.00008.2015
Combating Mineral Malnutrition through Iron and Zinc Biofortification of Cereals 10.1111/1541-4337.12063
A Potassium-Dependent Oxygen Sensing Pathway Regulates Plant Root Hydraulics 10.1016/j.cell.2016.08.068
Food for thought: how nutrients regulate root system architecture 10.1016/j.pbi.2017.06.008
The five AHMTP1 zinc transporters undergo different evolutionary fates towards adaptive evolution to zinc tolerance in Arabidopsis halleri 10.1371/journal.pgen.1000911
Plant Defensin type 1 (PDF1): Protein promiscuity and expression variation within the Arabidopsis genus shed light on zinc tolerance acquisition in Arabidopsis halleri 10.1111/nph.12396
To respond or not to respond? Natural variation of root architectural responses to nutrient signals 10.1093/jxb/erx160
Phosphate and zinc transport and signalling in plants: Toward a better understanding of their homeostasis interaction 10.1093/jxb/eru314
Identification of three relationships linking cadmium accumulation to cadmium tolerance and zinc and citrate accumulation in lettuce 10.1016/j.jplph.2010.04.012
Estimation of Genetic Diversity in Rice (Oryza sativa L.) Genotypes using Simple Sequence Repeats 10.5376/mpb.2013.04.0036
An Assay to Test the Capacity of Arabidopsis Plant Defensin Type1 Protein to Induce Cellular Zinc (Zn) Tolerance in Yeast 10.21769/bioprotoc.1653
Adaptation conjointe des racines à l’inondation et aux nutriments du sol 10.1051/medsci/20173304005
EZ-Root-VIS: A Software Pipeline for the Rapid Analysis and Visual Reconstruction of Root System Architecture 10.1104/pp.18.00217
Natural variation at XND1 impacts root hydraulics and trade-off for stress responses in Arabidopsis 10.1038/s41467-018-06430-8
Anna Amtmann
Amtmann Anna
ORCID: 0000-0001-8533-121X
Potassium in Plants 10.1002/9780470015902.a0023737
Regulation of Ion Transporters 10.1002/9780470988862.ch6
Mechanisms of Na+ Uptake by Plant Cells 10.1016/s0065-2296(08)60310-9
Phenotyping Jasmonate Regulation of Root Growth 10.1007/978-1-62703-414-2_3
Nitrate reductase mutation alters potassium nutrition as well as nitric oxide-mediated control of guard cell ion channels in Arabidopsis 10.1111/nph.13714
Food for thought: how nutrients regulate root system architecture 10.1016/j.pbi.2017.06.008
Nutrient Sensing and Signalling in Plants: Potassium and Phosphorus 10.1016/S0065-2296(05)43005-0
Contrasting nutrient–disease relationships: Potassium gradients in barley leaves have opposite effects on two fungal pathogens with different sensitivities to jasmonic acid 10.1111/pce.13350
Stomatal clustering in Begonia associates with the kinetics of leaf gaseous exchange and influences water use efficiency 10.1093/jxb/erx072
Chromatin and epigenetics 10.1104/pp.15.01023
Pollen development and fertilization in Arabidopsis is dependent on the MALE GAMETOGENESIS IMPAIRED ANTHERS gene encoding a Type V P-type ATPase 10.1101/gad.357305
Thellungiella halophila, a salt-tolerant relative of Arabidopsis thaliana, has specific root ion-channel features supporting K+/Na+ homeostasis under salinity stress 10.1111/j.1365-313X.2006.02876.x
Na+transport in Acetabularia bypasses conductance of plasmalemma 10.1007/BF00232430
Electrophysiological characterization of pathways for K+ uptake into growing and non-growing leaf cells of barley 10.1111/j.1365-3040.2009.02034.x
Learning from evolution: Thellungiella generates new knowledge on essential and critical components of abiotic stress tolerance in plants 10.1093/mp/ssn094
Onguard, a computational platform for quantitative kinetic modeling of guard cell physiology 10.1104/pp.112.197244
Histone deacetylase Complex1 expression level titrates plant growth and abscisic acid sensitivity in Arabidopsis 10.1105/tpc.113.114835
Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome 10.1186/gb-2013-14-6-r59
Multilevel analysis of primary metabolism provides new insights into the role of potassium nutrition for glycolysis and nitrogen assimilation in arabidopsis roots1[W][OA] 10.1104/pp.108.133629
A minimal cysteine motif required to activate the SKOR K + channel of arabidopsis by the reactive oxygen species H 2 O 2 10.1074/jbc.M110.141176
Plant responses to abiotic stress: The chromatin context of transcriptional regulation 10.1016/j.bbagrm.2016.07.015
Effects of N, P, K and S on metabolism: new knowledge gained from multi-level analysis 10.1016/j.pbi.2009.04.014
Regulation of macronutrient transport 10.1111/j.1469-8137.2008.02666.x
Analysis of the root system architecture of Arabidopsis provides a quantitative readout of crosstalk between nutritional signals 10.1105/tpc.113.122101
Potassium deficiency induces the biosynthesis of oxylipins and glucosinolates in Arabidopsis thaliana 10.1186/1471-2229-10-172
Coronatine-insensitive 1 (COI1) mediates transcriptional responses of Arabidopsis thaliana to external potassium supply 10.1093/mp/ssq012
Biodesalination: an emerging technology for targeted removal of Na<sup>+</sup> and Cl<sup>−</sup> from seawater by cyanobacteria 10.1080/19443994.2014.940647
The twins K+ and Na+ in plants 10.1016/j.jplph.2013.10.014
EZ-Rhizo: Integrated software for the fast and accurate measurement of root system architecture 10.1111/j.1365-313X.2008.03739.x
The histone deacetylase complex 1 protein of Arabidopsis has the capacity to interact with multiple proteins including histone 3-binding proteins and histone 1 variants 10.1104/pp.15.01760
The role of calcium sensor-interacting protein kinases in plant adaptation to potassium-deficiency: New answers to old questions 10.1038/cr.2007.49
Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress 10.1046/j.1365-313X.2003.01839.x
Potassium channels in barley: Cloning, functional characterization and expression analyses in relation to leaf growth and development 10.1111/j.1365-3040.2009.02033.x
The potassium-dependent transcriptome of arabidopsis reveals a prominent role of jasmonic acid in nutrient signaling 10.1104/pp.104.046482
Low unidirectional sodium influx into root cells restricts net sodium accumulation in Thellungiella halophila, a salt-tolerant relative of Arabidopsis thaliana 10.1093/jxb/erj116
Engineering Mannitol Biosynthesis in Escherichia coli and Synechococcus sp. PCC 7002 Using a Green Algal Fusion Protein 10.1021/acssynbio.8b00238
N-glycan production in the endoplasmic reticulum of plants 10.1016/j.tplants.2008.11.008
Physiology and metabolism 10.1016/j.pbi.2011.04.008
The wheat cDNA LCT1 generates hypersensitivity to sodium in a salt-sensitive yeast strain 10.1104/pp.126.3.1061
Systems dynamic modeling of the stomatal guard cell predicts emergent behaviors in transport, signaling, and volume control 10.1104/pp.112.197350
Stomatal spacing safeguards stomatal dynamics by facilitating guard cell ion transport independent of the epidermal solute reservoir 10.1104/pp.16.00850
Vector analysis as a fast and easy method to compare gene expression responses between different experimental backgrounds 10.1186/1471-2105-6-181
EZ-root-VIS: A software pipeline for the rapid analysis and visual reconstruction of root system architecture 10.1104/pp.18.00217
Thellungiella halophila, a salt-tolerant relative of Arabidopsis thaliana, possesses effective mechanisms to discriminate between potassium and sodium 10.1046/j.0016-8025.2003.01116.x
The effect of potassium nutrition on pest and disease resistance in plants 10.1111/j.1399-3054.2008.01075.x
To respond or not to respond? Natural variation of root architectural responses to nutrient signals 10.1093/jxb/erx160
Abiotic stress and plant genome evolution. Search for new models 10.1104/pp.105.059972
Cytoplasmic free Ca+ in the marine alga acetabularia: Measurement with Ca+ -selective microelectrodes and kinetic analysis 10.1093/jxb/43.7.875
Arabidopsis thaliana Cyclic Nucleotide Gated Channel 3 forms a non-selective ion transporter involved in germination and cation transport 10.1093/jxb/erj064
Lotus tenuis tolerates combined salinity and waterlogging: Maintaining O2 transport to roots and expression of an NHX1-like gene contribute to regulation of Na+ transport 10.1111/j.1399-3054.2010.01373.x
Graph-based iterative group analysis enhances microarray interpretation 10.1186/1471-2105-5-100
K+-selective inward-rectifying channels and apoplastic pH in barley roots 10.1104/pp.120.1.331
Phylogenetic relationships within cation transporter families of Arabidopsis 10.1104/pp.126.4.1646
K+ nutrition and Na+ toxicity: The basis of cellular K+/Na+ ratios 10.1006/anbo.1999.0912
Natural variation of Arabidopsis root architecture reveals complementing adaptive strategies to potassium starvation 10.1104/pp.112.211144
Rank products: A simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments 10.1016/j.febslet.2004.07.055
Iterative Group Analysis (iGA): A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments 10.1186/1471-2105-5-34
Biodesalination: A case study for applications of photosynthetic bacteria in water treatment 10.1104/pp.113.233973
Cryptic variation in RNA-directed DNA-methylation controls lateral root development when auxin signalling is perturbed 10.1038/s41467-019-13927-3
Cotranslational recruitment of ribosomes in protocells recreates a translocon-independent mechanism of proteorhodopsin biogenesis 10.1016/j.isci.2021.102429
Positive Selection and Heat-Response Transcriptomes Reveal Adaptive Features of the Arabidopsis Desert Relative, Anastatica hierochuntica 10.1101/2021.05.23.445339
Simon Rogers
Rogers Simon
ORCID: 0000-0003-3578-4477
An Optimal Frequency in Ca2+ Oscillations for Stomatal Closure Is an Emergent Property of Ion Transport in Guard Cells 10.1104/pp.15.01607
Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets. 10.1093/bioinformatics/btv072
MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach. 10.1093/bioinformatics/btu370
Probabilistic assignment of formulas to mass peaks in metabolomics experiments. 10.1093/bioinformatics/btn642
Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models. 10.1093/bioinformatics/btn553
Bayesian model-based inference of transcription factor activity. 10.1186/1471-2105-8-S2-S2
Identification of prognostic signatures in breast cancer microarray data using Bayesian techniques. 10.1098/rsif.2005.0093
A Bayesian regression approach to the inference of regulatory networks from gene expression data. 10.1093/bioinformatics/bti487
The latent process decomposition of cDNA microarray data sets. 10.1109/TCBB.2005.29
HDP-Align: Hierarchical Dirichlet Process Clustering for Multiple Peak Alignment of Liquid Chromatography Mass Spectrometry Data 10.1101/074831
Topic modeling for untargeted substructure exploration in metabolomics 10.1073/pnas.1608041113
Global Sensitivity Analysis of OnGuard Models Identifies Key Hubs for Transport Interaction in Stomatal Dynamics 10.1104/pp.17.00170
Unexpected Connections between Humidity and Ion Transport Discovered Using a Model to Bridge Guard Cell-to-Leaf Scales 10.1105/tpc.17.00694
Minimally-destructive atmospheric ionisation mass spectrometry authenticates authorship of historical manuscripts 10.1038/s41598-018-28810-2
Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra 10.1101/491506
Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra 10.1039/C8FD00235E
MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools 10.1101/654459
EZ-Root-VIS: A Software Pipeline for the Rapid Analysis and Visual Reconstruction of Root System Architecture 10.1104/pp.18.00217
MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools 10.3390/metabo9070144
In-silico Optimisation of Mass Spectrometry Fragmentation Strategies in Metabolomics 10.1101/744227
In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics 10.3390/metabo9100219
Gestational-age-dependent development of the neonatal metabolome 10.1101/2020.03.27.20045534
Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service 10.1101/2020.05.09.086066
Predicting host taxonomic information from viral genomes: A comparison of feature representations 10.1371/journal.pcbi.1007894
Decomposing metabolite set activity levels with PALS 10.1101/2020.06.07.138974
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions 10.1101/2020.06.12.148205
matchms - processing and similarity evaluation of mass spectrometry data 10.1101/2020.08.06.239244
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships 10.1101/2020.08.11.245928
Probabilistic Framework for Integration of Mass Spectrum and Retention Time Information in Small Molecule Identification 10.1101/2020.08.19.255653
matchms - processing and similarity evaluation of mass spectrometry data. 10.21105/joss.02411
Rapid Development of Improved Data-dependent Acquisition Strategies 10.1101/2020.09.11.293092
User guide to the red blood cell model (RCM), a multiplatform JAVA-based model of human red blood cell homeostasis 10.1101/2020.03.07.981779
Probabilistic framework for integration of mass spectrum and retention time information in small molecule identification 10.1093/bioinformatics/btaa998
Comparative Metabologenomics Analysis of Polar Actinomycetes 10.3390/md19020103
Ranking Metabolite Sets by Their Activity Levels 10.3390/metabo11020103
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships 10.1371/journal.pcbi.1008724
Up-down biphasic volume response of human red blood cells to PIEZO1 activation during capillary transits 10.1371/journal.pcbi.1008706
PIEZO1 and the mechanism of the long circulatory longevity of human red blood cells 10.1371/journal.pcbi.1008496
Rapid Development of Improved Data-Dependent Acquisition Strategies 10.1021/acs.analchem.0c03895
Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches 10.1039/D1NP00023C
Using topic modeling to detect cellular crosstalk in scRNA-seq 10.1101/2021.07.26.453767
Guillaume Lobet
Lobet Guillaume / Guillaume Lobet
ORCID: 0000-0002-5883-4572
Plant Water Uptake in Drying Soils 10.​1104/​pp.​113.​233486
Root system markup language: Toward a unified root architecture description language 10.1104/pp.114.253625
"Rhizoponics": A novel hydroponic rhizotron for root system analyses on mature Arabidopsis thaliana plants 10.1186/s13007-015-0046-x
Inflorescence development in tomato: Gene functions within a zigzag model 10.3389/fpls.2014.00121
A modeling approach to determine the importance of dynamic regulation of plant hydraulic conductivities on the water uptake dynamics in the soil-plant-atmosphere system 10.1016/j.ecolmodel.2013.11.025
Root systems biology: Integrative modeling across scales, from gene regulatory networks to the rhizosphere 10.1104/pp.113.227215
Novel scanning procedure enabling the vectorization of entire rhizotron-grown root systems 10.1186/1746-4811-9-1
Comparative analysis of Cd and Zn impacts on root distribution and morphology of Lolium Perenne and Trifolium repens: Implications for phytostabilization 10.1007/s11104-013-1975-7
An online database for plant image analysis software tools 10.1186/1746-4811-9-38
A novel image-analysis toolbox enabling quantitative analysis of root system architecture 10.1104/pp.111.179895
Model-assisted integration of physiological and environmental constraints affecting the dynamic and spatial patterns of root water uptake from soils 10.1093/jxb/erq077
archiDART: an R package for the automated computation of plant root architectural traits 10.1007/s11104-015-2673-4
GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems 10.7554/eLife.07597
FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana 10.1093/nar/gkv1054
Environmental Control of Root System Biology 10.1146/annurev-arplant-043015-111848
Water relations in the soil-plant system: what can we learn from functional-structural plant models 10.6084/M9.FIGSHARE.1257741
A modeling approach to determine the contribution of plant hydraulic conductivities on the water uptake dynamics in the soil-plant-atmosphere system 10.6084/M9.FIGSHARE.97203.V2
Inflorescence development in tomato: gene functions within a zigzag model 10.6084/M9.FIGSHARE.976039.V1
Introducing Root System Markup Language, a new toolbox to link experimental data with simulation 10.6084/M9.FIGSHARE.1379862
Science Valorisation 10.6084/M9.FIGSHARE.1057995.V3
Open Science: A view from the Bench 10.6084/M9.FIGSHARE.3020170.V4
Structural Root Modelling 10.6084/M9.FIGSHARE.1594792.V3
Rhizotrons blueprints 10.6084/M9.FIGSHARE.97204.V5
SmartRoot gets topological 10.6084/M9.FIGSHARE.94095.V2
Integrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana 10.1038/srep29042
Using a structural root system model for an in-depth assessment of root image analysis pipeline 10.1101/074922
Using structural model to validate and improve root image analysis pipelines 10.6084/M9.FIGSHARE.4311848.V1
Presentation of plant-image-analysis.org 10.6084/M9.FIGSHARE.3826488.V2
Water flow in the soil-plant domain. New tools and methods 10.6084/M9.FIGSHARE.2009226.V1
How to deal with the complexity of plants: a modelling vision 10.6084/M9.FIGSHARE.4239140.V3
Social Media in Research: a beginner's guide 10.6084/M9.FIGSHARE.4263308.V2
Inflorescence development in tomato: gene functions within a zigzag model 10.6084/M9.FIGSHARE.976039
Maize root emergence 10.6084/M9.FIGSHARE.1411214.V1
Research Project UCL-FZJ 10.6084/M9.FIGSHARE.2069911.V10
Modelling water relations in the soil-plant-atmosphere system 10.6084/M9.FIGSHARE.1091425.V9
Plant image analysis tools: current trends and future challenges 10.6084/M9.FIGSHARE.1169928.V4
An evaluation of inexpensive methods for root image acquisition when using rhizotrons 10.1186/s13007-017-0160-z
Image Analysis in Plant Sciences: Publish Then Perish 10.1016/j.tplants.2017.05.002
Novel multiscale insights into the composite nature of water transport in roots 10.1101/147314
Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large scale genetic studies 10.1101/152702
Alternative plants, why we need models to understand the complexity of plants 10.6084/M9.FIGSHARE.5089900
Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large scale genetic studies. 10.1093/gigascience/gix084
archiDART v3.0: A new data analysis pipeline allowing the topological analysis of plant root systems 10.12688/f1000research.13541.1
CRootBox: a structural–functional modelling framework for root systems 10.1093/aob/mcx221
Measuring root system traits of wheat in 2D images to parameterize 3D root architecture models 10.1007/s11104-018-3595-8
A new phenotyping pipeline reveals three types of lateral roots and a random branching pattern in two cereals 10.1104/pp.17.01648
Alternative plants: why do we need models to understand the complexity of plants. 10.6084/M9.FIGSHARE.6188372
Connecting the dots between computational tools to analyse soil-root water relations 10.6084/M9.FIGSHARE.6890744
Demystifying roots: A need for clarification and extended concepts in root phenotyping 10.1016/j.plantsci.2018.09.015
Going with the Flow: Multiscale Insights into the Composite Nature of Water Transport in Roots 10.1104/pp.18.01006
Connecting the dots between computational tools to analyse soil–root water relations 10.1093/jxb/ery361
EZ-Root-VIS: A Software Pipeline for the Rapid Analysis and Visual Reconstruction of Root System Architecture 10.1104/pp.18.00217
Impact of crop residue management on crop production and soil chemistry after seven years of crop rotation in temperate climate, loamy soils 10.7717/peerj.4836
CPlantBox, a whole plant modelling framework for the simulation of water and carbon related processes 10.1101/810507
Call for participation: Collaborative benchmarking of functional-structural root architecture models. The case of root water uptake 10.1101/808972
Lateral Roots: Random Diversity in Adversity 10.1016/j.tplants.2019.05.011
MARSHAL, a novel tool for virtual phenotyping of maize root system hydraulic architectures 10.1093/insilicoplants/diz012
GRANAR, a computational tool to better understand the functional importance of monocotyledon root anatomy 10.1104/pp.19.00617
Summary of the Sussex-Huawei locomotion-transportation recognition challenge
Observation of a manifold in the chaotic phase space of an asymmetric optical microcavity
Localized temporal variation of Earth's inner-core boundary from high-quality waveform doublets
Off-axis multi-wavelength dispersion controlling metalens for multi-color imaging
Impact of United States political sanctions on international collaborations and research in Iran