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Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity

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Advanced Techniques in Omics Research in Relation to Heavy Metal/Metalloid Toxicity and Tolerance in Plants
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Molecular mechanisms of plant adaptive responses to heavy metals stress
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Epigenetic modifications preserve the hyperaccumulator Noccaea caerulescens from Ni geno‐toxicity
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Bottom‐up and top‐down proteomic approaches for the identification, characterization, and quantification of the low molecular weight proteome with focus on short open reading frame‐encoded peptides
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Systems biology for crop improvement
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Identification of Plant Protein–Metabolite Interactions by Limited Proteolysis-Coupled Mass Spectrometry (LiP-MS)
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Proteomics Approach to Uncover Key Signalling Pathways in Brassica juncea in Abiotic and Biotic Stress
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Biological Functions, Uptake and Transport of Essential Nutrients in Relation to Plant Growth
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Acute Lethal Toxicity of Heavy Metals to the Seeds of Plants of High Importance to Humans
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Prospects and challenges of multi-omics data integration in toxicology
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Metabolomics: a systems biology approach for enhancing heat stress tolerance in plants
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‘Omics’ approaches in developing combined drought and heat tolerance in food crops
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Transcriptomic and Metabolomic Reprogramming to Explore the High-Altitude Adaptation of Medicinal Plants: A Review
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Heavy metals pollution assessment and its associated human health risk evaluation of urban soils from Indian cities: a review
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Metabolomics analysis reveals different mechanisms of cadmium response and functions of reduced glutathione in cadmium detoxification in the Chinese cabbage
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Molecular mechanisms underpinning the silicon-selenium (Si-Se) interactome and cross-talk in stress-induced plant responses
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Evaluation of Selenium Influence on the Alleviation of Chromium Stress in Rapeseed by Physiological and Proteomic Approaches
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Cloning and functional identification of a strigolactone receptor gene MdD14 in apple
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Proteome and physiological analyses reveal tobacco (Nicotiana tabacum) peroxidase 7 (POD 7) functions in responses to copper stress
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A novel method for predicting cadmium concentration in rice grain using genetic algorithm and back-propagation neural network based on soil properties
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Nexus on climate change: agriculture and possible solution to cope future climate change stresses
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Transcriptomic analyses of sweet potato in response to Cd exposure and protective effects of K on Cd-induced physiological alterations
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Ionomics and metabolomics analysis reveal the molecular mechanism of metal tolerance of Pteris vittata L. dominating in a mining site in Thai Nguyen province, Vietnam
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Ascorbic acid and selenium nanoparticles synergistically interplay in chromium stress mitigation in rice seedlings by regulating oxidative stress indicators and antioxidant defense mechanism
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Proteomic and physiological analyses to elucidate nitric oxide-mediated adaptive responses of barley under cadmium stress
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Evolution-aided engineering of plant specialized metabolism
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Metal tolerance in plants: Molecular and physicochemical interface determines the “not so heavy effect” of heavy metals
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Probability of cultivating Se-rich maize in Se-poor farmland based on intensive field sampling and artificial neural network modelling
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The potential of remote sensing and artificial intelligence as tools to improve the resilience of agriculture production systems
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Omics approaches for understanding heavy metal responses and tolerance in plants
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Enhancing climate change resilience in agricultural crops
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Toxic effects of heavy metal Cd and Zn on chlorophyll, carotenoid metabolism and photosynthetic function in tobacco leaves revealed by physiological and proteomics analysis
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Comprehensive proteomic analysis of arsenic induced toxicity reveals the mechanism of multilevel coordination of efficient defense and energy metabolism in two Brassica napus cultivars
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Transcriptome analysis reveals the tolerant mechanisms to cobalt and copper in barley
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Proteomic analysis reveals the role of exogenous cysteine in alleviating chromium stress in maize seedlings
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Global proteome response to Pb(II) toxicity in poplar using SWATH-MS-based quantitative proteomics investigation
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Transcriptome characterization of candidate genes related to chromium uptake, transport and accumulation in Miscanthus sinensis
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Transcriptome analysis and physiological indicators reveal the role of sulfur in cadmium accumulation and transportation in water spinach (Ipomoea aquatica Forsk.)
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Silicon-enhanced tolerance to cadmium toxicity in soybean by enhancing antioxidant defense capacity and changing cadmium distribution and transport
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State-of-the-art OMICS strategies against toxic effects of heavy metals in plants: A review
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Metabolomics analysis reveal the molecular responses of high CO2 concentration improve resistance to Pb stress of Oryza sativa L. seedlings
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The regulatory metabolic networks of the Brassica campestris L. hairy roots in response to cadmium stress revealed from proteome studies combined with a transcriptome analysis
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Cadmium and arsenic affect root development in Oryza sativa L. negatively interacting with auxin
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Physiological responses and transcriptome analyses of upland rice following exposure to arsenite and arsenate
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NITRIC OXIDE ASSOCIATED PROTEIN1 (AtNOA1) is necessary for copper-induced lateral root elongation in Arabidopsis thaliana
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Physiological and DNA methylation analysis provides epigenetic insights into chromium tolerance in kenaf
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Genome-wide expression and variation in nucleotide sequences lead to differential response of Arabidopsis thaliana ecotypes towards arsenic stress under sulfur limiting condition
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Mechanisms for increased pH-mediated amelioration of copper toxicity in Citrus sinensis leaves using physiology, transcriptomics and metabolomics
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Ionomics, transcriptomics and untargeted metabolomics analyses provide new insights into the Cd response and accumulation mechanisms of mulberry
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Modelling bioaccumulation of heavy metals in soil-crop ecosystems and identifying its controlling factors using machine learning
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Integrated transcriptomic and metabolomic analysis the variation of rice cultivars response to arsenite stress
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Gas Chromatography Mass Spectrometry based metabolomic investigation on five different rice cutivars (Oryza sativa L.) under different induced Cadmium stress
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Transcriptomic and physiological analyses of Miscanthus lutarioriparius in response to plumbum stress
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ZEAMAP, a Comprehensive Database Adapted to the Maize Multi-Omics Era
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Mineral nutrient homeostasis, photosynthetic performance, and modulations of antioxidative defense components in two contrasting genotypes of Arachis hypogaea L. (peanut) for mitigation of nitrogen and/or phosphorus starvation
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Comparative transcriptomics provide new insights into the mechanisms by which foliar silicon alleviates the effects of cadmium exposure in rice
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Transcriptomics and physiological analyses reveal that sulfur alleviates mercury toxicity in rice (Oryza sativa L.)
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Oryza sativa class III peroxidase (OsPRX38) overexpression in Arabidopsis thaliana reduces arsenic accumulation due to apoplastic lignification
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Arsenic Stress-Related F-Box (ASRF) gene regulates arsenic stress tolerance in Arabidopsis thaliana
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Comparative cytology combined with transcriptomic and metabolomic analyses of Solanum nigrum L. in response to Cd toxicity
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Effects of polyester microfibers (PMFs) and cadmium on lettuce (Lactuca sativa) and the rhizospheric microbial communities: A study involving physio-biochemical properties and metabolomic profiles
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The potential role of plasma membrane proteins in response to Zn stress in rice roots based on iTRAQ and PRM under low Cd condition
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Integrated physiological, transcriptomic and metabolomic analysis of the response of Trifolium pratense L. to Pb toxicity
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Mechanism exploration of Solanum nigrum L. hyperaccumulating Cd compared to Zn from the perspective of metabolic pathways based on differentially expressed proteins using iTRAQ
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GWAS-assisted genomic prediction of cadmium accumulation in maize kernel with machine learning and linear statistical methods
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Integrated transcriptome and metabolome analysis reveals the mechanism of tolerance to manganese and cadmium toxicity in the Mn/Cd hyperaccumulator Celosia argentea Linn
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Morphophysiological, proteomic and metabolomic analyses reveal cadmium tolerance mechanism in common wheat (Triticum aestivum L.)
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Phenotypic and transcriptomic shifts in roots and leaves of rice under the joint stress from microplastic and arsenic
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Proteomic analysis reveals differential responsive mechanisms in Solanum nigrum exposed to low and high dose of cadmium
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Physiological and transcriptome analysis of response of soybean (Glycine max) to cadmium stress under elevated CO2 concentration
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Comprehensive mechanisms of heavy metal toxicity in plants, detoxification, and remediation
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Integrated transcriptomics and metabolomics reveal key metabolic pathway responses in Pistia stratiotes under Cd stress
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Integrated physio-biochemical and transcriptomic analysis revealed mechanism underlying of Si-mediated alleviation to cadmium toxicity in wheat
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Metabolomics and transcriptomics reveal the toxic mechanism of Cd and nano TiO2 coexposure on rice (Oryza sativa L.)
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Multi-omics analysis reveals differential molecular responses to cadmium toxicity in rice root tip and mature zone
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Metabolomics combined with physiology and transcriptomics reveal key metabolic pathway responses in apple plants exposure to different selenium concentrations
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Physiology and proteomics reveal Fulvic acid mitigates Cadmium adverse effects on growth and photosynthetic properties of lettuce
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The phytochelatin synthase from Nitella mucronata (Charophyta) plays a role in the homeostatic control of iron(II)/(III)
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Nitric oxide alleviates cadmium- but not arsenic-induced damages in rice roots
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Pseudomonas citronellolis alleviates arsenic toxicity and maintains cellular homeostasis in chickpea (Cicer arietinum L.)
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Metabolomic analysis reveals the molecular responses to copper toxicity in rice (Oryza sativa)
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Nickel, cadmium and lead phytotoxicity and potential of halophytic plants in heavy metal extraction
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Alteration of antioxidant gene expression in response to heavy metal stress in Trigonella foenum-graecum L.
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Exogenous cysteine alleviates chromium stress via reducing its uptake and regulating proteome in roots of Brassica napus L. seedlings
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Heavy metals and metalloids: Sources, risks and strategies to reduce their accumulation in horticultural crops
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Identification of heavy metal-responsive genes in radish (Raphanus sativus L.) through RNA-Seq meta-analysis
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Concentration is not enough to evaluate accumulation of heavy metals and nutrients in plants
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Low-level arsenite boosts rhizospheric exudation of low-molecular-weight organic acids from mangrove seedlings (Avicennia marina): Arsenic phytoextraction, removal, and detoxification
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Artificial intelligence (AI) applications in adsorption of heavy metals using modified biochar
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Integrated transcriptomic and metabolomic analysis reveals the potential mechanisms underlying indium-induced inhibition of root elongation in wheat plants
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Liquid chromatography-mass spectrometry (LC-MS) based metabolomic fingerprinting in contrasting rice varieties for iron (Fe) excess.
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Accelerating Climate Resilient Plant Breeding by Applying Next-Generation Artificial Intelligence
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Global Warming, Climate Change, and Environmental Pollution: Recipe for a Multifactorial Stress Combination Disaster
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Designing Future Crops: Genomics-Assisted Breeding Comes of Age
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Machine learning bridges omics sciences and plant breeding
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Charting plant gene functions in the multi-omics and single-cell era
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Single-cell and spatial multi-omics in the plant sciences: Technical advances, applications, and perspectives
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Copper Oxide Nanomaterial Fate in Plant Tissue: Nanoscale Impacts on Reproductive Tissues
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Nanoscale Sulfur Improves Plant Growth and Reduces Arsenic Toxicity and Accumulation in Rice (Oryza sativa L.)
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A Metabolic Activation-Based Chemoproteomic Platform to Profile Adducted Proteins Derived from Furan-Containing Compounds
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The molecular basis of phosphate discrimination in arsenate-rich environments
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Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander
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Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics
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Histone post-translational modifications — cause and consequence of genome function
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Method of the Year: spatially resolved transcriptomics
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Spatially resolved transcriptomics adds a new dimension to genomics
inferredcites →https://doi.org/10.1038/s41598-017-18263-4openalex-snapshot
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inferredcites →https://doi.org/10.1038/s41598-019-56847-4openalex-snapshot
Re-epithelialization and immune cell behaviour in an ex vivo human skin model
inferredcites →https://doi.org/10.1038/s41598-020-61745-1openalex-snapshot
Metabolomics-based study reveals the effect of lead (Pb) in the culture environment on Whitmania pigra
inferredcites →https://doi.org/10.1038/s41598-021-04388-0openalex-snapshot
Stage specific comparative transcriptomic analysis to reveal gene networks regulating iron and zinc content in pearl millet [Pennisetum glaucum (L.) R. Br.]
inferredcites →https://doi.org/10.1038/s43016-020-0043-8openalex-snapshot
Impacts of ozone and climate change on yields of perennial crops in California
inferredcites →https://doi.org/10.1038/s43705-023-00213-zopenalex-snapshot
Metagenomic and machine learning-aided identification of biomarkers driving distinctive Cd accumulation features in the root-associated microbiome of two rice cultivars
inferredcites →https://doi.org/10.1039/c3mb70072kopenalex-snapshot
Comparative analyses of stress-responsive genes in Arabidopsis thaliana : insight from genomic data mining, functional enrichment, pathway analysis and phenomics
inferredcites →https://doi.org/10.1071/cp21387openalex-snapshot
Digital applications and artificial intelligence in agriculture toward next-generation plant phenotyping
inferredcites →https://doi.org/10.1071/fp21258openalex-snapshot
Investigating Phragmites australis response to copper exposure using physiologic, Fourier Transform Infrared and metabolomic approaches†
inferredcites →https://doi.org/10.1080/10937404.2019.1654422openalex-snapshot
Environmental health effects attributed to toxic and infectious agents following hurricanes, cyclones, flash floods and major hydrometeorological events
inferredcites →https://doi.org/10.1080/13102818.2021.1950566openalex-snapshot
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inferredcites →https://doi.org/10.1089/omi.2014.0061openalex-snapshot
MOPED 2.5—An Integrated Multi-Omics Resource: Multi-Omics Profiling Expression Database Now Includes Transcriptomics Data
inferredcites →https://doi.org/10.1093/bib/bbac485openalex-snapshot
From single- to multi-omics: future research trends in medicinal plants
inferredcites →https://doi.org/10.1093/bioinformatics/bty534openalex-snapshot
SLIDE – a web-based tool for interactive visualization of large-scale – omics data
inferredcites →https://doi.org/10.1093/database/baw117openalex-snapshot
MODEM: multi-omics data envelopment and mining in maize
inferredcites →https://doi.org/10.1093/gigascience/giaa097openalex-snapshot
Machado: Open source genomics data integration framework
inferredcites →https://doi.org/10.1093/jxb/erx333openalex-snapshot
Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants
inferredcites →https://doi.org/10.1093/nar/gkac917openalex-snapshot
PlantExp: a platform for exploration of gene expression and alternative splicing based on public plant RNA-seq samples
inferredcites →https://doi.org/10.1093/nar/gkq989openalex-snapshot
KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data
inferredcites →https://doi.org/10.1093/nar/gkr1004openalex-snapshot
MetaCrop 2.0: managing and exploring information about crop plant metabolism
inferredcites →https://doi.org/10.1093/nar/gkv1164openalex-snapshot
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
inferredcites →https://doi.org/10.1093/nar/gkx372openalex-snapshot
Pathview Web: user friendly pathway visualization and data integration
inferredcites →https://doi.org/10.1093/nar/gky310openalex-snapshot
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis
inferredcites →https://doi.org/10.1093/nar/gky466openalex-snapshot
PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data
inferredcites →https://doi.org/10.1093/nar/gky962openalex-snapshot
New approach for understanding genome variations in KEGG
inferredcites →https://doi.org/10.1104/pp.105.073635openalex-snapshot
A Reassessment of Substrate Specificity and Activation of Phytochelatin Synthases from Model Plants by Physiologically Relevant Metals
inferredcites →https://doi.org/10.1104/pp.108.127472openalex-snapshot
Phytochelatin Synthesis Is Essential for the Detoxification of Excess Zinc and Contributes Significantly to the Accumulation of Zinc
inferredcites →https://doi.org/10.1111/j.1744-7909.2008.00737.xopenalex-snapshot
How Plants Cope with Cadmium: Staking All on Metabolism and Gene Expression
inferredcites →https://doi.org/10.1111/nph.13557openalex-snapshot
The Plant Genome Integrative Explorer Resource: PlantGen IE .org
inferredcites →https://doi.org/10.1111/pce.12706openalex-snapshot
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inferredcites →https://doi.org/10.1111/pce.13670openalex-snapshot
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inferredcites →https://doi.org/10.1111/pce.13821openalex-snapshot
Evolution of the metal hyperaccumulation and hypertolerance traits
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Single cell gene regulatory networks in plants: Opportunities for enhancing climate change stress resilience
inferredcites →https://doi.org/10.1111/plb.13175openalex-snapshot
Responses of Phragmites australis to copper stress: A combined analysis of plant morphology, physiology and proteomics
inferredcites →https://doi.org/10.1111/ppl.13433openalex-snapshot
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inferredcites →https://doi.org/10.1111/tpj.15772openalex-snapshot
Advances and applications of single‐cell omics technologies in plant research
inferredcites →https://doi.org/10.1111/tpj.16350openalex-snapshot
GERDH : an interactive multi‐omics database for cross‐species data mining in horticultural crops
inferredcites →https://doi.org/10.1111/tpj.16497openalex-snapshot
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inferredcites →https://doi.org/10.1111/tpj.16557openalex-snapshot
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Identifying Signal‐Crosstalk Mechanism in Maize Plants during Combined Salinity and Boron Stress Using Integrative Systems Biology Approaches
inferredcites →https://doi.org/10.1177/1177932219899051openalex-snapshot
Multi-omics Data Integration, Interpretation, and Its Application
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Pan-transcriptomic Profiling Demarcates Serendipita Indica-Phosphorus Mediated Tolerance Mechanisms in Rice Exposed to Arsenic Toxicity
inferredcites →https://doi.org/10.1186/s12864-020-07017-8openalex-snapshot
Comparative transcriptome combined with metabolome analyses revealed key factors involved in nitric oxide (NO)-regulated cadmium stress adaptation in tall fescue
inferredcites →https://doi.org/10.1186/s12864-020-6716-8openalex-snapshot
Differential expression pattern of the proteome in response to cadmium stress based on proteomics analysis of wheat roots
inferredcites →https://doi.org/10.1186/s12870-021-03145-9openalex-snapshot
Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice
inferredcites →https://doi.org/10.1186/s12870-022-03569-xopenalex-snapshot
Identification and functional analysis of cation-efflux transporter 1 from Brassica juncea L.
inferredcites →https://doi.org/10.1186/s12951-022-01509-3openalex-snapshot
Comparative physiological and metabolomic analyses reveal that Fe3O4 and ZnO nanoparticles alleviate Cd toxicity in tobacco
inferredcites →https://doi.org/10.1186/s13007-019-0515-8openalex-snapshot
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inferredcites →https://doi.org/10.1186/s13062-016-0112-yopenalex-snapshot
MONGKIE: an integrated tool for network analysis and visualization for multi-omics data
inferredcites →https://doi.org/10.1371/journal.pcbi.1005752openalex-snapshot
mixOmics: An R package for ‘omics feature selection and multiple data integration
inferredcites →https://doi.org/10.1371/journal.pone.0272750openalex-snapshot
Analysis of the mechanism of Ricinus communis L. tolerance to Cd metal based on proteomics and metabolomics
inferredcites →https://doi.org/10.1515/jib-2011-160openalex-snapshot
MADMAX – Management and analysis database for multiple ~omics experiments
inferredcites →https://doi.org/10.1515/jib-2023-0012openalex-snapshot
Integrating omics databases for enhanced crop breeding
inferredcites →https://doi.org/10.1530/jme-18-0055openalex-snapshot
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inferredcites →https://doi.org/10.21203/rs.3.rs-1589675/v1openalex-snapshot
Transcriptome analysis Cladophora rupestris absorption and response to Pb stress
inferredcites →https://doi.org/10.2139/ssrn.4206689openalex-snapshot
The Mechanism of Solanum Nigrum L. Only Hyperaccumulating Cadmium Explored Through the Differential Expression Protein Comparation Associated with Copper Accumulation Based on Itraq Proteomics
inferredcites →https://doi.org/10.32615/bp.2022.016openalex-snapshot
LC-MS/MS shotgun proteomics reveals biochemical mechanisms of Paspalum fasciculatum tolerance to Pb-stress
inferredcites →https://doi.org/10.3389/fgene.2021.652974openalex-snapshot
A Sight on Single-Cell Transcriptomics in Plants Through the Prism of Cell-Based Computational Modeling Approaches: Benefits and Challenges for Data Analysis
inferredcites →https://doi.org/10.3389/fgene.2021.655885openalex-snapshot
Use of Comparative Transcriptomics Combined With Physiological Analyses to Identify Key Factors Underlying Cadmium Accumulation in Brassica juncea L.
inferredcites →https://doi.org/10.3389/fgene.2021.713224openalex-snapshot
Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress
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