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
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