R3QW21 last accessed: 2022-11-04

The Arabidopsis information resource (TAIR)
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:56.409468

tair
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:56.409468

Other names: TAIR, The Arabidopsis information resource (TAIR), tair

The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every week from the latest published research literature and community data submissions.

Webpage:

http://www.arabidopsis.org/

Licence:

Name: TAIR Terms of Use
URL: http://www.arabidopsis.org/doc/about/tair_terms_of_use/417

Publications: (6)

Publications
More detailed information about this field from each metasource.

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
PMID: 22140109
metasource: Fairsharing.org
version: FAIRsharing.org: TAIR; The Arabidopsis Information Resource; DOI: https://doi.org/10.25504/FAIRsharing.4dqw0; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:56.409468

The Arabidopsis Information Resource (TAIR): gene structure and function annotation
PMID: 17986450
metasource: Fairsharing.org
version: FAIRsharing.org: TAIR; The Arabidopsis Information Resource; DOI: https://doi.org/10.25504/FAIRsharing.4dqw0; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome
PMID: 26201819
metasource: Fairsharing.org
version: FAIRsharing.org: TAIR; The Arabidopsis Information Resource; DOI: https://doi.org/10.25504/FAIRsharing.4dqw0; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model
PMID: 26989150
metasource: Fairsharing.org
version: FAIRsharing.org: TAIR; The Arabidopsis Information Resource; DOI: https://doi.org/10.25504/FAIRsharing.4dqw0; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes
PMID: 29220077
metasource: Fairsharing.org
version: FAIRsharing.org: TAIR; The Arabidopsis Information Resource; DOI: https://doi.org/10.25504/FAIRsharing.4dqw0; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

Using the Arabidopsis information resource (TAIR) to find information about Arabidopsis genes
PMID: 20521243
metasource: Fairsharing.org
version: FAIRsharing.org: TAIR; The Arabidopsis Information Resource; DOI: https://doi.org/10.25504/FAIRsharing.4dqw0; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools PubMed citations: 917.

917 articles citing: The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

Genome-wide identification and characterization of the bHLH gene family and analysis of their potential relevance to chlorophyll metabolism in Raphanus sativus L. PMID:35915410
LSAP: A Machine Learning Method for Leaf-Senescence-Associated Genes Prediction. PMID:35888183
The Plant V-ATPase. PMID:35845650
Keeping time in the dark: Potato diel and circadian rhythmic gene expression reveals tissue-specific circadian clocks. PMID:35844780
Genome-Wide Identification of PLATZ Transcription Factors in Ginkgo biloba L. and Their Expression Characteristics During Seed Development. PMID:35812908
Draft Genome of Tanacetum Coccineum: Genomic Comparison of Closely Related Tanacetum-Family Plants. PMID:35806039
The megabase-scale crossover landscape is largely independent of sequence divergence. PMID:35780220
Vacuoles in Bryophytes: Properties, Biogenesis, and Evolution. PMID:35747879
Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach. PMID:35709304
Gene fusion as an important mechanism to generate new genes in the genus Oryza. PMID:35706016
SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability. PMID:35664227
The hexokinase Gene Family in Cotton: Genome-Wide Characterization and Bioinformatics Analysis. PMID:35651774
Genome-Wide Analysis of C2H2 Zinc Finger Gene Family and Its Response to Cold and Drought Stress in Sorghum [Sorghum bicolor (L.) Moench]. PMID:35628380
Exogenous dsRNA Induces RNA Interference of a Chalcone Synthase Gene in Arabidopsis thaliana. PMID:35628133
Role of LOC_Os01g68450, Containing DUF2358, in Salt Tolerance Is Mediated via Adaptation of Absorbed Light Energy Dissipation. PMID:35567234
IQD1 Involvement in Hormonal Signaling and General Defense Responses Against Botrytis cinerea. PMID:35557724
Plants grown in Apollo lunar regolith present stress-associated transcriptomes that inform prospects for lunar exploration. PMID:35552509
Enzymes degraded under high light maintain proteostasis by transcriptional regulation in Arabidopsis. PMID:35549553
GURFAP: A Platform for Gene Function Analysis in Glycyrrhiza Uralensis. PMID:35495163
Sequence-based evaluation of promoter context for prediction of transcription start sites in Arabidopsis and rice. PMID:35484393
Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L. PMID:35457273
Identification of novel PHD-finger genes in pepper by genomic re-annotation and comparative analyses. PMID:35443608
Chromosome evolution and the genetic basis of agronomically important traits in greater yam. PMID:35422045
Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax. PMID:35393424
The Gastrodia menghaiensis (Orchidaceae) genome provides new insights of orchid mycorrhizal interactions. PMID:35392808
Loss of Plastid Developmental Genes Coincides With a Reversion to Monoplastidy in Hornworts. PMID:35360315
Genome-wide characterization and expression analysis of Erf gene family in cotton. PMID:35317739
Genome-wide analysis of AAAG and ACGT cis-elements in Arabidopsis thaliana reveals their involvement with genes downregulated under jasmonic acid response in an orientation independent manner. PMID:35302624
Phylogeny and evolution of plant Phytochrome Interacting Factors (PIFs) gene family and functional analyses of PIFs in Brachypodium distachyon. PMID:35218399
Genome-Wide Analysis of LBD Transcription Factor Genes in Dendrobiumcatenatum. PMID:35216201
iLoci: robust evaluation of genome content and organization for provisional and mature genome assemblies. PMID:35211671
'Nebbiolo' genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.). PMID:35209840
A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae. PMID:35205394
Histone demethylase IBM1-mediated meiocyte gene expression ensures meiotic chromosome synapsis and recombination. PMID:35192603
Local and global crosstalk among heterochromatin marks drives DNA methylome patterning in Arabidopsis. PMID:35165291
Differential gene expression associated with a floral scent polymorphism in the evening primrose Oenothera harringtonii (Onagraceae). PMID:35151274
Transcriptomic Landscape of Herbivore Oviposition in Arabidopsis: A Systematic Review. PMID:35126411
Subcellular Proteomics as a Unified Approach of Experimental Localizations and Computed Prediction Data for Arabidopsis and Crop Plants. PMID:35113396
Elongation factor TFIIS is essential for heat stress adaptation in plants. PMID:35100405
Long Non-Coding RNAs as Emerging Regulators of Pathogen Response in Plants. PMID:35076574
A complex network of interactions governs DNA methylation at telomeric regions. PMID:35061900
From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees. PMID:35055150
Nitrogen application and differences in leaf number retained after topping affect the tobacco (Nicotiana tabacum) transcriptome and metabolome. PMID:35045826
DeepLRR: An Online Webserver for Leucine-Rich-Repeat Containing Protein Characterization Based on Deep Learning. PMID:35009139
Recent Duplications Dominate VQ and WRKY Gene Expansions in Six Prunus Species. PMID:34961840
Systematic Characterization of MicroRNA Processing Modes in Plants With Parallel Amplification of RNA Ends. PMID:34950175
Submergence of the filamentous Zygnematophyceae Mougeotia induces differential gene expression patterns associated with core metabolism and photosynthesis. PMID:34939169
BrCNGC gene family in field mustard: genome-wide identification, characterization, comparative synteny, evolution and expression profiling. PMID:34921218
The mitochondrial copper chaperone COX11 has an additional role in cellular redox homeostasis. PMID:34919594
A multispecies amplicon sequencing approach for genetic diversity assessments in grassland plant species. PMID:34918474
Both Binding Strength and Evolutionary Accessibility Affect the Population Frequency of Transcription Factor Binding Sequences in Arabidopsis thaliana. PMID:34894231
Genome-Wide Identification and Expression Analysis of the MADS-Box Gene Family in Sweet Potato [Ipomoea batatas (L.) Lam]. PMID:34868221
Morus alba L. Leaves - Integration of Their Transcriptome and Metabolomics Dataset: Investigating Potential Genes Involved in Flavonoid Biosynthesis at Different Harvest Times. PMID:34868120
A rice gene encoding glycosyl hydrolase plays contrasting roles in immunity depending on the type of pathogens. PMID:34839574
Genome-Wide Identification and Functional Exploration of SBP-Box Gene Family in Black Pepper (Piper nigrum L.). PMID:34828347
Evolution Analyses of CAMTA Transcription Factor in Plants and Its Enhancing Effect on Cold-tolerance. PMID:34790215
Coordinated bacterial and plant sulfur metabolism in Enterobacter sp. SA187-induced plant salt stress tolerance. PMID:34772809
Dual activities of ACC synthase: Novel clues regarding the molecular evolution of ACS genes. PMID:34757795
Underwater CAM photosynthesis elucidated by Isoetes genome. PMID:34732722
Fungal genomes: suffering with functional annotation errors. PMID:34724975
qPTMplants: an integrative database of quantitative post-translational modifications in plants. PMID:34718741
"The PLCP gene family of grapevine (Vitis vinifera L.): characterization and differential expression in response to Plasmopara Viticola". PMID:34717550
Identification, expression, and functional analysis of Hsf and Hsp20 gene families in Brachypodium distachyon under heat stress. PMID:34703676
Transcriptome-wide characterization and functional analysis of Xyloglucan endo-transglycosylase/hydrolase (XTH) gene family of Salicornia europaea L. under salinity and drought stress. PMID:34696719
Arabidopsis MED18 Interaction With RNA Pol IV and V Subunit NRPD2a in Transcriptional Regulation of Plant Immune Responses. PMID:34691090
Genetic Mapping of the HLA1 Locus Causing Hybrid Lethality in Nicotiana Interspecific Hybrids. PMID:34685871
Sequence-Based Prediction of Plant Protein-Protein Interactions by Combining Discrete Sine Transformation With Rotation Forest. PMID:34671178
Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway. PMID:34654815
Global profiling of RNA-chromatin interactions reveals co-regulatory gene expression networks in Arabidopsis. PMID:34650265
Two plastid POLLUX ion channel-like proteins are required for stress-triggered stromal Ca2+release. PMID:34618095
Long-term acclimation to cadmium exposure reveals extensive phenotypic plasticity in Chlamydomonas. PMID:34618070
A BTB-TAZ protein is required for gene activation by Cauliflower mosaic virus 35S multimerized enhancers. PMID:34597402
Evolutionarily informed machine learning enhances the power of predictive gene-to-phenotype relationships. PMID:34561450
Genome-wide analysis of HSP70 gene superfamily in Pyropia yezoensis (Bangiales, Rhodophyta): identification, characterization and expression profiles in response to dehydration stress. PMID:34560838
PlantGSAD: a comprehensive gene set annotation database for plant species. PMID:34534340
Selection and Evaluation of a Thornless and HLB-Tolerant Bud-Sport of Pummelo Citrus With an Emphasis on Molecular Mechanisms. PMID:34531892
MedProDB: A database of Mediator proteins. PMID:34527190
A Comprehensive Phylogenetic Analysis of the MAP4K Family in the Green Lineage. PMID:34484252
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Conserved oligomeric Golgi (COG) complex genes functioning in defense are expressed in root cells undergoing a defense response to a pathogenic infection and exhibit regulation my MAPKs. PMID:34437620
Potential Arabidopsis thaliana glucosinolate genes identified from the co-expression modules using graph clustering approach. PMID:34430080
Exploring the evolutionary process of alkannin/shikonin O-acyltransferases by a reliable Lithospermum erythrorhizon genome. PMID:34424327
The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource. PMID:34411258
AtHDA6 functions as an H3K18ac eraser to maintain pericentromeric CHG methylation in Arabidopsis thaliana. PMID:34403482
Trans-species small RNAs move long distances in a parasitic plant complex. PMID:34393597
Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana. PMID:34381973
Growth Promotion or Osmotic Stress Response: How SNF1-Related Protein Kinase 2 (SnRK2) Kinases Are Activated and Manage Intracellular Signaling in Plants. PMID:34371646
Genome-Wide Identification and Evolutionary Analysis of Gossypium Tubby-Like Protein (TLP) Gene Family and Expression Analyses During Salt and Drought Stress. PMID:34367198
Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis. PMID:34362298
CRISPR/Cas9-mediated mutagenesis of WRKY3 and WRKY4 function decreases salt and Me-JA stress tolerance in Arabidopsis thaliana. PMID:34351541
Repression of CHROMOMETHYLASE 3 prevents epigenetic collateral damage in Arabidopsis. PMID:34296996
Comparative Label-Free Quantitative Proteomics Analysis Reveals the Essential Roles of N-Glycans in Salt Tolerance by Modulating Protein Abundance in Arabidopsis. PMID:34276718
The Taxus genome provides insights into paclitaxel biosynthesis. PMID:34267359
Analysis of genome variants in dwarf soybean lines obtained in F6 derived from cross of normal parents (cultivated and wild soybean). PMID:34261303
The sequenced genomes of nonflowering land plants reveal the innovative evolutionary history of peptide signaling. PMID:34240188
Databases for Protein-Protein Interactions. PMID:34236665
Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding. PMID:34226565
A genome wide transcriptional study of Populus alba x P. tremula var. glandulosa in response to nitrogen deficiency stress. PMID:34220043
Transcriptomic Analysis of Changes in Gene Expression During Flowering Induction in Sugarcane Under Controlled Photoperiodic Conditions. PMID:34211482
Gene-rich UV sex chromosomes harbor conserved regulators of sexual development. PMID:34193417
Molecular signatures of silencing suppression degeneracy from a complex RNA virus. PMID:34181647
Genome-Wide Comparative Analysis of Heat Shock Transcription Factors Provides Novel Insights for Evolutionary History and Expression Characterization in Cotton Diploid and Tetraploid Genomes. PMID:34168673
Genome-wide expression and network analyses of mutants in key brassinosteroid signaling genes. PMID:34157989
slim shady is a novel allele of PHYTOCHROME B present in the T-DNA line SALK_015201. PMID:34136747
Genome-wide characterization, evolution, and expression profiling of FBA gene family in response to light treatments and abiotic stress in Nicotiana tabacum. PMID:34120568
Genome-wide identification of the Capsicum bHLH transcription factor family: discovery of a candidate regulator involved in the regulation of species-specific bioactive metabolites. PMID:34098881
Genome Evolutionary Dynamics Meets Functional Genomics: A Case Story on the Identification of SLC25A44. PMID:34073512
Comparative Analysis of Re-Annotated Genes Provides Insight into Evolutionary Divergence and Expressions of Aquaporin Family in Pepper. PMID:34064088
TrancriptomeReconstructoR: data-driven annotation of complex transcriptomes. PMID:34058980
Genome-wide identification of the tea plant bHLH transcription factor family and discovery of candidate regulators of trichome formation. PMID:34031482
The Rhododendron Plant Genome Database (RPGD): a comprehensive online omics database for Rhododendron. PMID:34022814
Bioinformatics and Expression Analysis of IDA-Like Genes Reveal Their Potential Functions in Flower Abscission and Stress Response in Tobacco (Nicotiana tabacum L.). PMID:33986773
The tepary bean genome provides insight into evolution and domestication under heat stress. PMID:33976152
Comparative Genome Analyses Highlight Transposon-Mediated Genome Expansion and the Evolutionary Architecture of 3D Genomic Folding in Cotton. PMID:33973633
Identification of Candidate Susceptibility Genes to Puccinia graminis f. sp. tritici in Wheat. PMID:33968112
Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding. PMID:33964091
Evolution of pathogen response genes associated with increased disease susceptibility during adaptation to an extreme drought in a Brassica rapa plant population. PMID:33882815
Genome-wide identification and expression pattern of SnRK gene family under several hormone treatments and its role in floral scent emission in Hedychium coronarium. PMID:33854831
A multilayered cross-species analysis of GRAS transcription factors uncovered their functional networks in plant adaptation to the environment. PMID:33842016
Identification of potential candidate genes for lip and oral cavity cancer using network analysis. PMID:33840168
Identification and evolution analysis of the JAZ gene family in maize. PMID:33838665
Single-cell resolution of lineage trajectories in the Arabidopsis stomatal lineage and developing leaf. PMID:33823130
Insights into the Role of Transcriptional Gene Silencing in Response to Herbicide-Treatments in Arabidopsis thaliana. PMID:33804990
OsCBE1, a Substrate Receptor of Cullin4-Based E3 Ubiquitin Ligase, Functions as a Regulator of Abiotic Stress Response and Productivity in Rice. PMID:33801226
EIN2-directed histone acetylation requires EIN3-mediated positive feedback regulation in response to ethylene. PMID:33793786
Genomic analysis uncovers functional variation in the C-terminus of anthocyanin-activating MYB transcription factors. PMID:33790254
Multimerization variants as potential drivers of neofunctionalization. PMID:33771868
Genome-wide identification and expression pattern analysis of the ribonuclease T2 family in Eucommia ulmoides. PMID:33767357
Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture. PMID:33752605
Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species. PMID:33751107
Comparison of Brassica Genomes reveals asymmetrical gene retention between functional groups of genes in recurrent polyploidizations. PMID:33742369
Genome-wide identification of CLE gene family and their potential roles in bolting and fruit bearing in cucumber (Cucumis sativus L.). PMID:33740893
A Centrifuge-Based Method for Identifying Novel Genetic Traits That Affect Root-Substrate Adhesion in Arabidopsis thaliana. PMID:33732271
Alvis: a tool for contig and read ALignment VISualisation and chimera detection. PMID:33726674
Plant apocarotenoid metabolism utilizes defense mechanisms against reactive carbonyl species and xenobiotics. PMID:33721895
Pilot RNA-seq data from 24 species of vascular plants at Harvard Forest. PMID:33680580
Genome-wide analysis and expression profile of the bZIP gene family in poplar. PMID:33648455
Transcriptome analysis of the role of autophagy in plant response to heat stress. PMID:33635879
Evolutionary Comparison of the Developmental/Physiological Phenotype and the Molecular Behavior of SPIRRIG Between Arabidopsis thaliana and Arabis alpina. PMID:33584744
Tissue-specific transcriptome profiling of the Arabidopsis inflorescence stem reveals local cellular signatures. PMID:33582756
The expression of long non-coding RNAs is associated with H3Ac and H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex in Arabidopsis. PMID:33575615
Orthology and synteny analysis of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes. PMID:33568053
Transcriptomic analysis reveals key transcription factors associated to drought tolerance in a wild papaya (Carica papaya) genotype. PMID:33513158
Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. PMID:33505029
A candidate gene association analysis identifies SNPs potentially involved in drought tolerance in European beech (Fagus sylvatica L.). PMID:33504857
LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate. PMID:33504790
Convergence of sphingolipid desaturation across over 500 million years of plant evolution. PMID:33495556
Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis. PMID:33452249
Comparative Expression Analysis of Stress-Inducible Candidate Genes in Response to Cold and Drought in Tea Plant [Camellia sinensis (L.) Kuntze]. PMID:33424935
Arabidopsis mTERF9 protein promotes chloroplast ribosomal assembly and translation by establishing ribonucleoprotein interactions in vivo. PMID:33398331
Demographic Processes Linked to Genetic Diversity and Positive Selection across a Species' Range. PMID:33367266
Functional Interchangeability of Nucleotide Sugar Transporters URGT1 and URGT2 Reveals That urgt1 and urgt2 Cell Wall Chemotypes Depend on Their Spatio-Temporal Expression. PMID:33363558
SSRgenotyper: A simple sequence repeat genotyping application for whole-genome resequencing and reduced representational sequencing projects. PMID:33344093
RSD1 Is Essential for Stomatal Patterning and Files in Rice. PMID:33329664
Identification of chalcone synthase genes and their expression patterns reveal pollen abortion in cotton. PMID:33304181
Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus. PMID:33287721
The transcriptional repressors VAL1 and VAL2 recruit PRC2 for genome-wide Polycomb silencing in Arabidopsis. PMID:33270882
RNA interference-independent reprogramming of DNA methylation in Arabidopsis. PMID:33257860
Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation. PMID:33253423
The Evolutionary Dynamics of Genetic Incompatibilities Introduced by Duplicated Genes in Arabidopsis thaliana. PMID:33247726
A thorough analysis of the contribution of experimental, derived and sequence-based predicted protein-protein interactions for functional annotation of proteins. PMID:33237964
Effective characteristics on designing the information system of medicinal plants from users' perspective. PMID:33209937
Characterization of the Poplar R2R3-MYB Gene Family and Over-Expression of PsnMYB108 Confers Salt Tolerance in Transgenic Tobacco. PMID:33178243
Genome-wide identification, and phylogenetic and expression profiling analyses, of XTH gene families in Brassica rapa L. and Brassica oleracea L. PMID:33176678
Comparative Transcriptome Analysis of Rutabaga (Brassica napus) Cultivars Indicates Activation of Salicylic Acid and Ethylene-Mediated Defenses in Response to Plasmodiophora brassicae. PMID:33171675
Genome-Wide Identification and Functional Characterization of the Cation Proton Antiporter (CPA) Family Related to Salt Stress Response in Radish (Raphanus sativus L.). PMID:33158201
TREE1-EIN3-mediated transcriptional repression inhibits shoot growth in response to ethylene. PMID:33139535
Application of Genomic Big Data in Plant Breeding:Past, Present, and Future. PMID:33126607
Drought-Tolerance Gene Identification Using Genome Comparison and Co-Expression Network Analysis of Chromosome Substitution Lines in Rice. PMID:33066648
TERMINAL FLOWER 1-FD complex target genes and competition with FLOWERING LOCUS T. PMID:33046692
The reuse of public datasets in the life sciences: potential risks and rewards. PMID:33024631
Transcriptome and phytohormone changes associated with ethylene-induced onion bulb dormancy. PMID:33012993
Biased Gene Retention in the Face of Introgression Obscures Species Relationships. PMID:33011798
Unusual DNA-binding properties of the Arabidopsis thaliana WRKY50 transcription factor at target gene promoters. PMID:33006643
Characteristics and Expression Analyses of Trehalose-6-Phosphate Synthase Family in Prunus mume Reveal Genes Involved in Trehalose Biosynthesis and Drought Response. PMID:32977584
Genome-Wide Identification and Expression Analysis of the NHX (Sodium/Hydrogen Antiporter) Gene Family in Cotton. PMID:32973884
Genomic signatures of convergent adaptation to Alpine environments in three Brassicaceae species. PMID:32969558
Construction of a chromosome-scale long-read reference genome assembly for potato. PMID:32964225
Genome-Wide Identification and Characterization of the SHI-Related Sequence Gene Family in Rice. PMID:32963469
Exploring genomic variation associated with drought stress in Picea mariana populations. PMID:32953060
Chromatin regulates expression of small RNAs to help maintain transposon methylome homeostasis in Arabidopsis. PMID:32943088
Molecular Characterization, Expression Pattern and Function Analysis of Glycine-Rich Protein Genes Under Stresses in Chinese Cabbage (Brassica rapa L. ssp. pekinensis). PMID:32849790
The Brassica napus wall-associated kinase-like (WAKL) gene Rlm9 provides race-specific blackleg resistance. PMID:32794614
Genome-Wide Identification of Apple Ubiquitin SINA E3 Ligase and Functional Characterization of MdSINA2. PMID:32793265
Identification of Players Controlling Meristem Arrest Downstream of the FRUITFULL-APETALA2 Pathway. PMID:32778534
The composition and turnover of the Arabidopsis thaliana 80S cytosolic ribosome. PMID:32744327
The Genome of Microthlaspi erraticum (Brassicaceae) Provides Insights Into the Adaptation to Highly Calcareous Soils. PMID:32719698
Calmodulin-binding transcription activator (CAMTA) genes family: Genome-wide survey and phylogenetic analysis in flax (Linum usitatissimum). PMID:32702710
Regulation of Cell Type-Specific Immunity Networks in Arabidopsis Roots. PMID:32699170
The oilseed rape developmental expression resource: a resource for the investigation of gene expression dynamics during the floral transition in oilseed rape. PMID:32693783
Long-Read cDNA Sequencing Enables a "Gene-Like" Transcript Annotation of Transposable Elements. PMID:32647069
Computational identification of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes. PMID:32620079
Computational analysis of microarray data of Arabidopsis thaliana challenged with Alternaria brassicicola for identification of key genes in Brassica. PMID:32607787
Structural and Functional Heat Stress Responses of Chloroplasts of Arabidopsis thaliana. PMID:32545654
Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants. PMID:32541953
The cohesin loader SCC2 contains a PHD finger that is required for meiosis in land plants. PMID:32516352
What Can Long Terminal Repeats Tell Us About the Age of LTR Retrotransposons, Gene Conversion and Ectopic Recombination? PMID:32508870
NATpare: a pipeline for high-throughput prediction and functional analysis of nat-siRNAs. PMID:32463462
Spaceflight induces novel regulatory responses in Arabidopsis seedling as revealed by combined proteomic and transcriptomic analyses. PMID:32460700
Heavy Metal Stress-Associated Proteins in Rice and Arabidopsis: Genome-Wide Identification, Phylogenetics, Duplication, and Expression Profiles Analysis. PMID:32457808
Genome-Wide Identification of Peanut KCS Genes Reveals That AhKCS1 and AhKCS28 Are Involved in Regulating VLCFA Contents in Seeds. PMID:32457765
Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants. PMID:32427841
Identification of nodulation-related genes in Medicago truncatula using genome-wide association studies and co-expression networks. PMID:32426691
Biased Gene Conversion Constrains Adaptation in Arabidopsis thaliana. PMID:32414868
Dynamic Expansion and Functional Evolutionary Profiles of Plant Conservative Gene Family SBP-Box in Twenty Two Flowering Plants and the Origin of miR156. PMID:32414086
Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation. PMID:32404413
Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PMID:32384671
Cellular Plasticity in Response to Suppression of Storage Proteins in the Brassica napus Embryo. PMID:32358071
REPIC: a database for exploring the N6-methyladenosine methylome. PMID:32345346
Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis. PMID:32302366
Full-length transcriptome sequencing provides insights into the evolution of apocarotenoid biosynthesis in Crocus sativus. PMID:32280432
Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments. PMID:32265943
A Collection of Pre-mRNA Splicing Mutants in Arabidopsis thaliana. PMID:32265287
Emerging Technologies in Algal Biotechnology: Toward the Establishment of a Sustainable, Algae-Based Bioeconomy. PMID:32256509
Performance of Mapping Approaches for Whole-Genome Bisulfite Sequencing Data in Crop Plants. PMID:32256504
Comparison of Read Mapping and Variant Calling Tools for the Analysis of Plant NGS Data. PMID:32252268
Interspecific Signaling Between the Parasitic Plant and the Host Plants Regulate Xylem Vessel Cell Differentiation in Haustoria of Cuscuta campestris. PMID:32231674
Arabidopsis DNA Replication Initiates in Intergenic, AT-Rich Open Chromatin. PMID:32205451
Biological and Cellular Functions of the Microdomain-Associated FWL/CNR Protein Family in Plants. PMID:32204387
Portal of Juglandaceae: A comprehensive platform for Juglandaceae study. PMID:32194971
Root Skewing-Associated Genes Impact the Spaceflight Response of Arabidopsis thaliana. PMID:32194611
Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions. PMID:32184350
Genome-wide identification and expression analysis of WRKY transcription factors in pearl millet (Pennisetum glaucum) under dehydration and salinity stress. PMID:32171257
COST1 regulates autophagy to control plant drought tolerance. PMID:32170020
Pathogen Genetic Control of Transcriptome Variation in the Arabidopsis thaliana - Botrytis cinerea Pathosystem. PMID:32165442
Mutagenesis of a Quintuple Mutant Impaired in Environmental Responses Reveals Roles for CHROMATIN REMODELING4 in the Arabidopsis Floral Transition. PMID:32132131
Comprehensive Sequence Analysis of IQD Gene Family and their Expression Profiling in Grapevine (Vitis vinifera). PMID:32102395
PlaPPISite: a comprehensive resource for plant protein-protein interaction sites. PMID:32028878
A population genomics appraisal suggests independent dispersals for bitter and sweet manioc in Brazilian Amazonia. PMID:31993081
MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets. PMID:31956905
Plasticity of Phymatotrichopsis omnivora infection strategies is dependent on host and nonhost plant responses. PMID:31930733
Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study. PMID:31871489
Mutant analysis in the nonlegume Parasponia andersonii identifies NIN and NF-YA1 transcription factors as a core genetic network in nitrogen-fixing nodule symbioses. PMID:31863481
Identifying Early Warning Signals for the Sudden Transition from Mild to Severe Tobacco Etch Disease by Dynamical Network Biomarkers. PMID:31861938
Transcriptome assembly from long-read RNA-seq alignments with StringTie2. PMID:31842956
miR824/AGAMOUS-LIKE16 Module Integrates Recurring Environmental Heat Stress Changes to Fine-Tune Poststress Development. PMID:31824525
Draft genome of Tanacetum cinerariifolium, the natural source of mosquito coil. PMID:31796833
HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis. PMID:31787073
Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in A. thaliana. PMID:31766757
ORCAE-AOCC: A Centralized Portal for the Annotation of African Orphan Crop Genomes. PMID:31757073
Arabidopsis TRM5 encodes a nuclear-localised bifunctional tRNA guanine and inosine-N1-methyltransferase that is important for growth. PMID:31756231
The effector GpRbp-1 of Globodera pallida targets a nuclear HECT E3 ubiquitin ligase to modulate gene expression in the host. PMID:31756029
Analysis of Arabidopsis thaliana Redox Gene Network Indicates Evolutionary Expansion of Class III Peroxidase in Plants. PMID:31673065
Suppression of abscisic acid biosynthesis at the early infection stage of Verticillium longisporum in oilseed rape (Brassica napus). PMID:31603283
MicroRNA Dynamics and Functions During Arabidopsis Embryogenesis. PMID:31562217
MUR1-mediated cell-wall fucosylation is required for freezing tolerance in Arabidopsis thaliana. PMID:31549420
Genetic Diversity Linked to Haplotype Variation in the World Core Collection of Trifolium subterraneum for Boron Toxicity Tolerance Provides Valuable Markers for Pasture Breeding. PMID:31543883
Analysis of Orthologous SECONDARY WALL-ASSOCIATED NAC DOMAIN1 (SND1) Promotor Activity in Herbaceous and Woody Angiosperms. PMID:31540430
An Ultra High-Density Arabidopsis thaliana Crossover Map That Refines the Influences of Structural Variation and Epigenetic Features. PMID:31527048
Genome-wide identification and characterization of the Hsp70 gene family in allopolyploid rapeseed (Brassica napus L.) compared with its diploid progenitors. PMID:31497395
Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing of Spirodela. PMID:31484765
Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency. PMID:31481099
A Role for Pre-mRNA-PROCESSING PROTEIN 40C in the Control of Growth, Development, and Stress Tolerance in Arabidopsis thaliana. PMID:31456814
A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana. PMID:31442410
Metabolomic and transcriptomic profiling of three types of litchi pericarps reveals that changes in the hormone balance constitute the molecular basis of the fruit cracking susceptibility of Litchi chinensis cv. Baitangying. PMID:31440876
Resolving subcellular plant metabolism. PMID:31361942
An 'eFP-Seq Browser' for visualizing and exploring RNA sequencing data. PMID:31350781
Enhanced Maps of Transcription Factor Binding Sites Improve Regulatory Networks Learned from Accessible Chromatin Data. PMID:31345953
Genomics analysis of genes encoding respiratory burst oxidase homologs (RBOHs) in jatropha and the comparison with castor bean. PMID:31338257
Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT. PMID:31324144
Genome-Wide Identification and Characterization of Xyloglucan Endotransglycosylase/Hydrolase in Ananas comosus during Development. PMID:31315260
The Transcriptome Landscape of Walnut Interspecies Hybrid (Juglans hindsii × Juglans regia) and Regulation of Cambial Activity in Relation to Grafting. PMID:31293615
SRAssembler: Selective Recursive local Assembly of homologous genomic regions. PMID:31266441
PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation. PMID:31258543
Many rice genes are differentially spliced between roots and shoots but cytokinin has minimal effect on splicing. PMID:31245776
Genome-wide occupancy of histone H3K27 methyltransferases CURLY LEAF and SWINGER in Arabidopsis seedlings. PMID:31245749
Dark period transcriptomic and metabolic profiling of two diverse Eutrema salsugineum accessions. PMID:31245703
RedoxiBase: A database for ROS homeostasis regulated proteins. PMID:31228650
Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album. PMID:31199791
The Class III Peroxidase (POD) Gene Family in Cassava: Identification, Phylogeny, Duplication, and Expression. PMID:31163686
Integrating Molecular Biology and Bioinformatics Education. PMID:31145692
Genome-Wide Identification of Na+/H+ Antiporter (NHX) Genes in Sugar Beet (Beta vulgaris L.) and Their Regulated Expression under Salt Stress. PMID:31137880
Loss of function mutation of the Rapid Alkalinization Factor (RALF1)-like peptide in the dandelion Taraxacum koksaghyz entails a high-biomass taproot phenotype. PMID:31125376
Plant-necrotroph co-transcriptome networks illuminate a metabolic battlefield. PMID:31081752
Agrobacterium-mediated plant transformation: biology and applications. PMID:31068763
Regulation of Parent-of-Origin Allelic Expression in the Endosperm. PMID:31064812
Enhancement of vitamin B6 levels in rice expressing Arabidopsis vitamin B6 biosynthesis de novo genes. PMID:31063672
Phylogenetic Analyses and GAGA-Motif Binding Studies of BBR/BPC Proteins Lend to Clues in GAGA-Motif Recognition and a Regulatory Role in Brassinosteroid Signaling. PMID:31057577
CEP-CEPR1 signalling inhibits the sucrose-dependent enhancement of lateral root growth. PMID:31056646
The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. PMID:31043757
Evolution Analysis of the Fasciclin-Like Arabinogalactan Proteins in Plants Shows Variable Fasciclin-AGP Domain Constitutions. PMID:31010036
Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction. PMID:30971226
GCR1 and GPA1 coupling regulates nitrate, cell wall, immunity and light responses in Arabidopsis. PMID:30967583
The architecture of intra-organism mutation rate variation in plants. PMID:30964866
An Overview of Methodologies in Studying lncRNAs in the High-Throughput Era: When Acronyms ATTACK! PMID:30945176
Transcription is a major driving force for plastid genome instability in Arabidopsis. PMID:30943245
The Ethylene Signaling Pathway Negatively Impacts CBF/DREB-Regulated Cold Response in Soybean (Glycine max). PMID:30853961
The evolution of gene regulatory networks controlling Arabidopsis thaliana L. trichome development. PMID:30813891
Origin and evolution of the octoploid strawberry genome. PMID:30804557
Unraveling the complex genome of Saccharum spontaneum using Polyploid Gene Assembler. PMID:30768175
QTL Underlying Circadian Clock Parameters Under Seasonally Variable Field Settings in Arabidopsis thaliana. PMID:30755409
Comparative transcriptome analysis reveals new molecular pathways for cucumber genes related to sex determination. PMID:30719568
Genome-wide association analysis of stalk biomass and anatomical traits in maize. PMID:30704393
Induction of desiccation tolerance in desiccation sensitive Citrus limon seeds. PMID:30697936
Identification and Characterization of Mitogen-Activated Protein Kinase (MAPK) Genes in Sunflower (Helianthus annuus L.). PMID:30678298
Nitrogen Supply Drives Senescence-Related Seed Storage Protein Expression in Rapeseed Leaves. PMID:30678241
High Levels of Variation Within Gene Sequences of Olea europaea L. PMID:30671076
Extracellular ATP Shapes a Defense-Related Transcriptome Both Independently and along with Other Defense Signaling Pathways. PMID:30630869
Comprehensive analysis of Lon proteases in plants highlights independent gene duplication events. PMID:30590727
Computational and Experimental Tools to Monitor the Changes in Translation Efficiency of Plant mRNA on a Genome-Wide Scale: Advantages, Limitations, and Solutions. PMID:30577638
PhytoTypeDB: a database of plant protein inter-cultivar variability and function. PMID:30576486
Redundancy, Feedback, and Robustness in the Arabidopsis thaliana BZR/BEH Gene Family. PMID:30542366
An updated gene atlas for maize reveals organ-specific and stress-induced genes. PMID:30537259
Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function. PMID:30520727
Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA. PMID:30498193
Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies. PMID:30497373
The BioGRID interaction database: 2019 update. PMID:30476227
The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain. PMID:30443017
New insights into the evolution and functional divergence of the SWEET family in Saccharum based on comparative genomics. PMID:30404601
Long-Read Annotation: Automated Eukaryotic Genome Annotation Based on Long-Read cDNA Sequencing. PMID:30401722
Combined multivariate analysis and machine learning reveals a predictive module of metabolic stress response in Arabidopsis thaliana. PMID:30387490
Desiccation Tolerance Evolved through Gene Duplication and Network Rewiring in Lindernia. PMID:30361236
NanoPARE: parallel analysis of RNA 5' ends from low-input RNA. PMID:30355603
Translational genomics and multi-omics integrated approaches as a useful strategy for crop breeding. PMID:30353370
De novo assembly of haplotype-resolved genomes with trio binning. PMID:30346939
Recovery of novel association loci in Arabidopsis thaliana and Drosophila melanogaster through leveraging INDELs association and integrated burden test. PMID:30325920
Dissecting the functional domains of the Arabidopsis thaliana nonhost resistance 2B (AtNHR2B) protein. PMID:30325257
Regulation of Root Angle and Gravitropism. PMID:30322904
Assessment of flux through oleoresin biosynthesis in epithelial cells of loblolly pine resin ducts. PMID:30312429
PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System. PMID:30266409
Proteomics dataset containing proteins that obscure identification of TOPLESS interactors in Arabidopsis. PMID:30225301
Discovery and characterization of conserved binding of eIF4E 1 (CBE1), a eukaryotic translation initiation factor 4E-binding plant protein. PMID:30213859
HeteroMeth: A Database of Cell-to-cell Heterogeneity in DNA Methylation. PMID:30196115
Comparative transcriptome analysis to identify putative genes involved in thymol biosynthesis pathway in medicinal plant Trachyspermum ammi L. PMID:30194320
Genome-wide identification and characterization of LRR-RLKs reveal functional conservation of the SIF subfamily in cotton (Gossypium hirsutum). PMID:30189845
Mediator of tolerance to abiotic stress ERF6 regulates susceptibility of Arabidopsis to Meloidogyne incognita. PMID:30160354
Birth and Death of LTR-Retrotransposons in Aegilops tauschii. PMID:30158124
The intertwined metabolism during symbiotic nitrogen fixation elucidated by metabolic modelling. PMID:30131500
The Arabidopsis LDL1/2-HDA6 histone modification complex is functionally associated with CCA1/LHY in regulation of circadian clock genes. PMID:30124938
Transcriptional regulation of osmotic stress tolerance in wheat (Triticum aestivum L.). PMID:30109563
A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome. PMID:30107523
Genome-Wide Association Study and Selection Signatures Detect Genomic Regions Associated with Seed Yield and Oil Quality in Flax. PMID:30082613
Investigating the NAD-ME biochemical pathway within C4 grasses using transcript and amino acid variation in C4 photosynthetic genes. PMID:30078073
RNA-seq assistant: machine learning based methods to identify more transcriptional regulated genes. PMID:30029596
Gene expression drives the evolution of dominance. PMID:30013096
A comprehensive review of web-based resources of non-coding RNAs for plant science research. PMID:29989090
A genome-wide scan for correlated mutations detects macromolecular and chromatin interactions in Arabidopsis thaliana. PMID:29986106
Editing of Chloroplast rps14 by PPR Editing Factor EMB2261 Is Essential for Arabidopsis Development. PMID:29973946
A gene-phenotype relationship extraction pipeline from the biomedical literature using a representation learning approach. PMID:29950017
High V-PPase activity is beneficial under high salt loads, but detrimental without salinity. PMID:29938800
The Direct Involvement of Dark-Induced Tic55 Protein in Chlorophyll Catabolism and Its Indirect Role in the MYB108-NAC Signaling Pathway during Leaf Senescence in Arabidopsis thaliana. PMID:29937503
Phenotypic characterization of an Arabidopsis T-DNA insertion line SALK_063500. PMID:29900258
Improved de novo genome assembly and analysis of the Chinese cucurbit Siraitia grosvenorii, also known as monk fruit or luo-han-guo. PMID:29893829
Genome-wide identification and characterization of the RIO atypical kinase family in plants. PMID:29892951
MU-LOC: A Machine-Learning Method for Predicting Mitochondrially Localized Proteins in Plants. PMID:29875778
Cytokinins: Their Impact on Molecular and Growth Responses to Drought Stress and Recovery in Arabidopsis. PMID:29872444
Genome-Wide Identification and Expression Analysis of the UGlcAE Gene Family in Tomato. PMID:29861481
Genome-wide association study reveals novel players in defense hormone crosstalk in Arabidopsis. PMID:29852537
Genome-Wide Screening and Characterization of the Dof Gene Family in Physic Nut (Jatropha curcas L.). PMID:29844264
Comparative analysis of plant MKK gene family reveals novel expansion mechanism of the members and sheds new light on functional conservation. PMID:29843611
Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi. PMID:29843602
The Late Embryogenesis Abundant Protein Family in Cassava (Manihot esculenta Crantz): Genome-Wide Characterization and Expression during Abiotic Stress. PMID:29772750
Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions. PMID:29766351
Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli. PMID:29764390
The m6A Reader ECT2 Controls Trichome Morphology by Affecting mRNA Stability in Arabidopsis. PMID:29716990
Multiplex confounding factor correction for genomic association mapping with squared sparse linear mixed model. PMID:29705210
OMGene: mutual improvement of gene models through optimisation of evolutionary conservation. PMID:29703150
Towards annotating the plant epigenome: the Arabidopsis thaliana small RNA locus map. PMID:29679055
A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants. PMID:29661190
Present Scenario of Long Non-Coding RNAs in Plants. PMID:29657289
An Updated Functional Annotation of Protein-Coding Genes in the Cucumber Genome. PMID:29599790
Genome-Wide Analyses of the NAC Transcription Factor Gene Family in Pepper (Capsicum annuum L.): Chromosome Location, Phylogeny, Structure, Expression Patterns, Cis-Elements in the Promoter, and Interaction Network. PMID:29596349
Embryophyte stress signaling evolved in the algal progenitors of land plants. PMID:29581286
Characterization of the basic helix-loop-helix gene family and its tissue-differential expression in response to salt stress in poplar. PMID:29576971
Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host's Transcriptome: The Tobacco Etch Potyvirus-Tobacco Case Study. PMID:29562354
A stable tRNA-like molecule is generated from the long noncoding RNA GUT15 in Arabidopsis. PMID:29561243
Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach. PMID:29560823
CRISPR/Cas9-Mediated Mutagenesis of Four Putative Symbiosis Genes of the Tropical Tree Parasponia andersonii Reveals Novel Phenotypes. PMID:29559988
The CLAVATA receptor FASCIATED EAR2 responds to distinct CLE peptides by signaling through two downstream effectors. PMID:29543153
Malate transported from chloroplast to mitochondrion triggers production of ROS and PCD in Arabidopsis thaliana. PMID:29540758
Predicted Arabidopsis Interactome Resource and Gene Set Linkage Analysis: A Transcriptomic Analysis Resource. PMID:29530937
Comprehensive analysis of small RNAs expressed in developing male strobili of Cryptomeria japonica. PMID:29529051
Trust but Verify: A Lesson in Technology Limitations and Error Propagation. PMID:29519895
Subcellular Compartmentation of Alternatively Spliced Transcripts Defines SERINE/ARGININE-RICH PROTEIN30 Expression. PMID:29496883
Synopsis of the SOFL Plant-Specific Gene Family. PMID:29467189
Divergent N Deficiency-Dependent Senescence and Transcriptome Response in Developmentally Old and Young Brassica napus Leaves. PMID:29449851
araGWAB: Network-based boosting of genome-wide association studies in Arabidopsis thaliana. PMID:29440686
The genomes of two Eutrema species provide insight into plant adaptation to high altitudes. PMID:29394339
A Poly(A) Ribonuclease Controls the Cellotriose-Based Interaction between Piriformospora indica and Its Host Arabidopsis. PMID:29371249
Identification of Gossypium hirsutum long non-coding RNAs (lncRNAs) under salt stress. PMID:29370759
RFAthM6A: a new tool for predicting m6A sites in Arabidopsis thaliana. PMID:29340952
Genome-wide comparative analysis of papain-like cysteine protease family genes in castor bean and physic nut. PMID:29321580
Computational exploration of cis-regulatory modules in rhythmic expression data using the "Exploration of Distinctive CREs and CRMs" (EDCC) and "CRM Network Generator" (CNG) programs. PMID:29298348
Arabidopsis thaliana rapid alkalinization factor 1-mediated root growth inhibition is dependent on calmodulin-like protein 38. PMID:29282286
An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench). PMID:29273003
TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information. PMID:29272447
Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population. PMID:29259624
Unravelling Protein-Protein Interaction Networks Linked to Aliphatic and Indole Glucosinolate Biosynthetic Pathways in Arabidopsis. PMID:29238354
N-linked Glycan Micro-heterogeneity in Glycoproteins of Arabidopsis. PMID:29237727
Genome Assembly and Annotation of the Medicinal Plant Calotropis gigantea, a Producer of Anticancer and Antimalarial Cardenolides. PMID:29237703
funRiceGenes dataset for comprehensive understanding and application of rice functional genes. PMID:29220485
eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality. PMID:29220476
EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species. PMID:29220468
Cell-Type Transcriptomes of the Multicellular Green Alga Volvox carteri Yield Insights into the Evolutionary Origins of Germ and Somatic Differentiation Programs. PMID:29208647
The phenotypic and molecular assessment of the non-conserved Arabidopsis MICRORNA163/S-ADENOSYL-METHYLTRANSFERASE regulatory module during biotic stress. PMID:29196849
ALKBH10B Is an RNA N6-Methyladenosine Demethylase Affecting Arabidopsis Floral Transition. PMID:29180595
Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq. PMID:29176847
Nucleotide patterns aiding in prediction of eukaryotic promoters. PMID:29141011
Transcription Factors VND1-VND3 Contribute to Cotyledon Xylem Vessel Formation. PMID:29133368
Comprehensive genomic analysis of the CNGC gene family in Brassica oleracea: novel insights into synteny, structures, and transcript profiles. PMID:29132315
Reference-guided de novo assembly approach improves genome reconstruction for related species. PMID:29126390
Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts. PMID:29048540
Plastic Transcriptomes Stabilize Immunity to Pathogen Diversity: The Jasmonic Acid and Salicylic Acid Networks within the Arabidopsis/Botrytis Pathosystem. PMID:29042403
Synteny analysis of genes and distribution of loci controlling oil content and fatty acid profile based on QTL alignment map in Brassica napus. PMID:29025408
Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples. PMID:29024340
Dissecting the 'bacon and eggs' phenotype: transcriptomics of post-anthesis colour change in Lotus. PMID:28981620
qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms. PMID:28977518
Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species. PMID:28973974
Framework for gradual progression of cell ontogeny in the Arabidopsis root meristem. PMID:28973915
A uORF Represses the Transcription Factor AtHB1 in Aerial Tissues to Avoid a Deleterious Phenotype. PMID:28956754
Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination. PMID:28927400
EIN2 mediates direct regulation of histone acetylation in the ethylene response. PMID:28874528
Vitamin B1 diversity and characterization of biosynthesis genes in cassava. PMID:28859374
Comprehensive transcriptome analyses reveal tomato plant responses to tobacco rattle virus-based gene silencing vectors. PMID:28852064
Genome-wide analysis of DUF221 domain-containing gene family in Oryza species and identification of its salinity stress-responsive members in rice. PMID:28846681
Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation. PMID:28831143
Automated identification of reference genes based on RNA-seq data. PMID:28830520
Brassinosteroid signaling-dependent root responses to prolonged elevated ambient temperature. PMID:28827608
Field-based species identification of closely-related plants using real-time nanopore sequencing. PMID:28827531
Long Noncoding RNAs in Plants. PMID:28815539
Transcriptomic analysis of the response of Acropora millepora to hypo-osmotic stress provides insights into DMSP biosynthesis by corals. PMID:28806970
Repliscan: a tool for classifying replication timing regions. PMID:28784090
Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response. PMID:28764653
T-DNA-genome junctions form early after infection and are influenced by the chromatin state of the host genome. PMID:28742090
Deficient glutamate biosynthesis triggers a concerted upregulation of ribosomal protein genes in Arabidopsis. PMID:28733652
Systematic Analysis of Hsf Family Genes in the Brassica napus Genome Reveals Novel Responses to Heat, Drought and High CO2 Stresses. PMID:28729874
Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls. PMID:28720072
Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation. PMID:28717205
Ethylene induces combinatorial effects of histone H3 acetylation in gene expression in Arabidopsis. PMID:28716006
Evolution, gene expression profiling and 3D modeling of CSLD proteins in cotton. PMID:28693426
Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum. PMID:28662642
Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments. PMID:28652936
Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction. PMID:28651538
Analysis of MAP kinase MPK4/MEKK1/MKK genes of Carica papaya L. comparative to other plant homologues. PMID:28642634
Evidence for Adaptive Introgression of Disease Resistance Genes Among Closely Related Arabidopsis Species. PMID:28630104
A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency. PMID:28625162
Main and epistatic loci studies in soybean for Sclerotinia sclerotiorum resistance reveal multiple modes of resistance in multi-environments. PMID:28620159
Network Analysis Reveals a Common Host-Pathogen Interaction Pattern in Arabidopsis Immune Responses. PMID:28611808
Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY-DNA (W-Box) Complex Interaction in Tomato (Solanum lycopersicum L.). A Computational Approach. PMID:28611792
Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem. PMID:28611454
In silico analysis reveals widespread presence of three gene families, MAPK, MAPKK and MAPKKK, of the MAPK cascade from crop plants of Solanaceae in comparison to the distantly-related syntenic species from Rubiaceae, coffee. PMID:28603666
Insertion of a solo LTR retrotransposon associates with spur mutations in 'Red Delicious' apple (Malus × domestica). PMID:28577237
Genome-Wide Comparative Analysis of Miniature Inverted Repeat Transposable Elements in 19 Arabidopsis thaliana Ecotype Accessions. PMID:28572566
Evolinc: A Tool for the Identification and Evolutionary Comparison of Long Intergenic Non-coding RNAs. PMID:28536600
Seqping: gene prediction pipeline for plant genomes using self-training gene models and transcriptomic data. PMID:28466793
Systems biology study of transcriptional and post-transcriptional co-regulatory network sheds light on key regulators involved in important biological processes in Citrus sinensis. PMID:28461722
The genetic architecture of UV floral patterning in sunflower. PMID:28459939
Identification and allelic dissection uncover roles of lncRNAs in secondary growth of Populus tomentosa. PMID:28453813
N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana. PMID:28432195
Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis. PMID:28431015
ELF18-INDUCED LONG-NONCODING RNA Associates with Mediator to Enhance Expression of Innate Immune Response Genes in Arabidopsis. PMID:28400491
The elaborate route for UDP-arabinose delivery into the Golgi of plants. PMID:28373556
Positional bias in variant calls against draft reference assemblies. PMID:28351369
Gene Expression, Protein Function and Pathways of Arabidopsis thaliana Responding to Silver Nanoparticles in Comparison to Silver Ions, Cold, Salt, Drought, and Heat. PMID:28347022
Epigenetic Regulation of Intronic Transgenes in Arabidopsis. PMID:28338020
Comprehensive Transcriptome Analyses Reveal that Potato Spindle Tuber Viroid Triggers Genome-Wide Changes in Alternative Splicing, Inducible trans-Acting Activity of Phased Secondary Small Interfering RNAs, and Immune Responses. PMID:28331096
Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes. PMID:28327990
Electromagnetic Field Seems to Not Influence Transcription via CTCT Motif in Three Plant Promoters. PMID:28326086
The plant cell cycle: Pre-Replication complex formation and controls. PMID:28304073
Gene Mining for Proline Based Signaling Proteins in Cell Wall of Arabidopsis thaliana. PMID:28289422
Bioinformatics Study of Structural Patterns in Plant MicroRNA Precursors. PMID:28280737
Root morphogenic pathways in Eucalyptus grandis are modified by the activity of protein arginine methyltransferases. PMID:28279165
Accumulation of high OPDA level correlates with reduced ROS and elevated GSH benefiting white cell survival in variegated leaves. PMID:28276518
RXLR Effector AVR2 Up-Regulates a Brassinosteroid-Responsive bHLH Transcription Factor to Suppress Immunity. PMID:28270626
PAPE (Prefractionation-Assisted Phosphoprotein Enrichment): A Novel Approach for Phosphoproteomic Analysis of Green Tissues from Plants. PMID:28250405
Comparative "Golgi" Proteome Study of Lolium multiflorum and Populus trichocarpa. PMID:28248233
Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana. PMID:28175342
Survey of the rubber tree genome reveals a high number of cysteine protease-encoding genes homologous to Arabidopsis SAG12. PMID:28166280
Genomics and evolutionary aspect of calcium signaling event in calmodulin and calmodulin-like proteins in plants. PMID:28158973
TEA: the epigenome platform for Arabidopsis methylome study. PMID:28155665
Function of the Plant DNA Polymerase Epsilon in Replicative Stress Sensing, a Genetic Analysis. PMID:28153919
Protein Bioinformatics Databases and Resources. PMID:28150231
Skewing in Arabidopsis roots involves disparate environmental signaling pathways. PMID:28143395
Protein Degradation Rate in Arabidopsis thaliana Leaf Growth and Development. PMID:28138016
An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts. PMID:28135269
Towards new sources of resistance to the currant-lettuce aphid (Nasonovia ribisnigri). PMID:28111522
TOMATOMICS: A Web Database for Integrated Omics Information in Tomato. PMID:28111364
ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana. PMID:28095775
Nicotiana attenuata Data Hub (NaDH): an integrative platform for exploring genomic, transcriptomic and metabolomic data in wild tobacco. PMID:28086860
Estimating genomic diversity and population differentiation - an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri. PMID:28077077
Transcriptome-Wide Mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and Noncoding RNAs. PMID:28062751
Plant genome and transcriptome annotations: from misconceptions to simple solutions. PMID:28062412
PceRBase: a database of plant competing endogenous RNA. PMID:28053167
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Genome sequence and genetic diversity of European ash trees. PMID:28024298
Developing integrated crop knowledge networks to advance candidate gene discovery. PMID:28018846
Identification and Network-Enabled Characterization of Auxin Response Factor Genes in Medicago truncatula. PMID:28018393
myGenomeBrowser: building and sharing your own genome browser. PMID:28011789
Genome-Wide Survey of Flavonoid Biosynthesis Genes and Gene Expression Analysis between Black- and Yellow-Seeded Brassica napus. PMID:27999578
Utility and Limitations of Using Gene Expression Data to Identify Functional Associations. PMID:27935950
Light Regulation of Alternative Pre-mRNA Splicing in Plants. PMID:27925216
PlaMoM: a comprehensive database compiles plant mobile macromolecules. PMID:27924044
PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. PMID:27924042
Co-expression network analyses identify functional modules associated with development and stress response in Gossypium arboreum. PMID:27922095
AtPID: a genome-scale resource for genotype-phenotype associations in Arabidopsis. PMID:27899679
The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms. PMID:27899657
SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations. PMID:27899614
Novel Genomic and Evolutionary Insight of WRKY Transcription Factors in Plant Lineage. PMID:27853303
Gain-of-function in Arabidopsis (GAINA) for identifying functional genes in Hevea brasiliensis. PMID:27818891
Primer on the Gene Ontology. PMID:27812933
A transcription factor hierarchy defines an environmental stress response network. PMID:27811239
Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. PMID:27803309
Transcriptional Analysis of serk1 and serk3 Coreceptor Mutants. PMID:27803191
Plant Reactome: a resource for plant pathways and comparative analysis. PMID:27799469
Transcriptomic resources and marker validation for diploid and polyploid Veronica (Plantaginaceae) from New Zealand and Europe. PMID:27785388
RAP2.4a Is Transported through the Phloem to Regulate Cold and Heat Tolerance in Papaya Tree (Carica papaya cv. Maradol): Implications for Protection Against Abiotic Stress. PMID:27764197
The Minimum Open Reading Frame, AUG-Stop, Induces Boron-Dependent Ribosome Stalling and mRNA Degradation. PMID:27760805
Retention and Molecular Evolution of Lipoxygenase Genes in Modern Rosid Plants. PMID:27746812
A De Novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny. PMID:27711162
CeNDR, the Caenorhabditis elegans natural diversity resource. PMID:27701074
A transcriptomic resource for Douglas-fir seed development and analysis of transcription during late megagametophyte development. PMID:27699505
Transcriptome Profiling of Petal Abscission Zone and Functional Analysis of an Aux/IAA Family Gene RhIAA16 Involved in Petal Shedding in Rose. PMID:27695465
Tomato phyE Is Required for Shade Avoidance in the Absence of phyB1 and phyB2. PMID:27695458
Survey of Genes Involved in Biosynthesis, Transport, and Signaling of Phytohormones with Focus on Solanum lycopersicum. PMID:27695302
EIN2-dependent regulation of acetylation of histone H3K14 and non-canonical histone H3K23 in ethylene signalling. PMID:27694846
Genome-wide identification of multifunctional laccase gene family in cotton (Gossypium spp.); expression and biochemical analysis during fiber development. PMID:27679939
Phosphate uptake kinetics and tissue-specific transporter expression profiles in poplar (Populus × canescens) at different phosphorus availabilities. PMID:27663513
Unveiling the functional diversity of the alpha/beta hydrolase superfamily in the plant kingdom. PMID:27662376
Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development. PMID:27660483
Genomewide analysis of the lateral organ boundaries domain gene family in Vitis vinifera. PMID:27659322
Plant Carbonic Anhydrases: Structures, Locations, Evolution, and Physiological Roles. PMID:27646307
Development of a prediction system for tail-anchored proteins. PMID:27634135
Genetic basis of nitrogen use efficiency and yield stability across environments in winter rapeseed. PMID:27628849
Genome-wide analysis of long intergenic non-coding RNAs in chickpea and their potential role in flower development. PMID:27628568
Phylogeny and Expression Analyses Reveal Important Roles for Plant PKS III Family during the Conquest of Land by Plants and Angiosperm Diversification. PMID:27625671
MYB107 and MYB9 Homologs Regulate Suberin Deposition in Angiosperms. PMID:27604696
Mining for Candidate Genes in an Introgression Line by Using RNA Sequencing: The Anthocyanin Overaccumulation Phenotype in Brassica. PMID:27597857
The antifungal plant defensin AtPDF2.3 from Arabidopsis thaliana blocks potassium channels. PMID:27573545
Origination, Expansion, Evolutionary Trajectory, and Expression Bias of AP2/ERF Superfamily in Brassica napus. PMID:27570529
Altered Transcription and Neofunctionalization of Duplicated Genes Rescue the Harmful Effects of a Chimeric Gene in Brassica napus. PMID:27559024
RNALocate: a resource for RNA subcellular localizations. PMID:27543076
Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana. PMID:27538394
De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure. PMID:27527578
Exocyst SEC3 and Phosphoinositides Define Sites of Exocytosis in Pollen Tube Initiation and Growth. PMID:27516531
Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation. PMID:27506905
SoyNet: a database of co-functional networks for soybean Glycine max. PMID:27492285
CicerTransDB 1.0: a resource for expression and functional study of chickpea transcription factors. PMID:27472917
IGDD: a database of intronless genes in dicots. PMID:27465544
Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease. PMID:27465111
A Clade-Specific Arabidopsis Gene Connects Primary Metabolism and Senescence. PMID:27462324
Agroinfiltration contributes to VP1 recombinant protein degradation. PMID:27459147
The phylogeny of C/S1 bZIP transcription factors reveals a shared algal ancestry and the pre-angiosperm translational regulation of S1 transcripts. PMID:27457880
Low-coverage, whole-genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery. PMID:27437173
Indel Group in Genomes (IGG) Molecular Genetic Markers. PMID:27436831
Origin and Functional Prediction of Pollen Allergens in Plants. PMID:27436829
The activity of HYDROPEROXIDE LYASE 1 regulates accumulation of galactolipids containing 12-oxo-phytodienoic acid in Arabidopsis. PMID:27422994
Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the Allotetraploid Arabidopsis kamchatica. PMID:27413047
The Arabidopsis Golgi-localized GDP-L-fucose transporter is required for plant development. PMID:27381418
Divergent Evolutionary Pattern of Sugar Transporter Genes is Associated with the Difference in Sugar Accumulation between Grasses and Eudicots. PMID:27356489
Integrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana. PMID:27352932
Gibberellin deficiency is responsible for shy-flowering nature of Epipremnum aureum. PMID:27345283
AraPPISite: a database of fine-grained protein-protein interaction site annotations for Arabidopsis thaliana. PMID:27338257
cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing. PMID:27327613
A Genome-wide Study of "Non-3UTR" Polyadenylation Sites in Arabidopsis thaliana. PMID:27301740
Bioinformatics resources for pollen. PMID:27271281
tRNA-Related Sequences Trigger Systemic mRNA Transport in Plants. PMID:27268430
A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants. PMID:27261064
Systematic analysis of plant mitochondrial and chloroplast small RNAs suggests organelle-specific mRNA stabilization mechanisms. PMID:27235415
OGRO: The Overview of functionally characterized Genes in Rice online database. PMID:27234245
High light intensity plays a major role in emergence of population level variation in Arabidopsis thaliana along an altitudinal gradient. PMID:27211014
The Second Subunit of DNA Polymerase Delta Is Required for Genomic Stability and Epigenetic Regulation. PMID:27208288
Venus flytrap carnivorous lifestyle builds on herbivore defense strategies. PMID:27197216
Role of the Polymerase ϵ sub-unit DPB2 in DNA replication, cell cycle regulation and DNA damage response in Arabidopsis. PMID:27193996
Theobroma cacao L. pathogenesis-related gene tandem array members show diverse expression dynamics in response to pathogen colonization. PMID:27189060
Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy. PMID:27177130
A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. PMID:27158781
Arbuscular mycorrhiza Symbiosis Induces a Major Transcriptional Reprogramming of the Potato SWEET Sugar Transporter Family. PMID:27148312
Cassava (Manihot esculenta) transcriptome analysis in response to infection by the fungus Colletotrichum gloeosporioides using an oligonucleotide-DNA microarray. PMID:27138000
RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data. PMID:27137891
Response of Arabidopsis thaliana Roots with Altered Lipid Transfer Protein (LTP) Gene Expression to the Clubroot Disease and Salt Stress. PMID:27135222
Tobacco mosaic virus-directed reprogramming of auxin/indole acetic acid protein transcriptional responses enhances virus phloem loading. PMID:27118842
Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis. PMID:27111034
Learning from Co-expression Networks: Possibilities and Challenges. PMID:27092161
Expansion Mechanisms and Evolutionary History on Genes Encoding DNA Glycosylases and Their Involvement in Stress and Hormone Signaling. PMID:27026054
Analyses of Old "Prokaryotic" Proteins Indicate Functional Diversification in Arabidopsis and Oryza sativa. PMID:27014324
Deciphering the transcriptional regulation and spatiotemporal distribution of immunity response in barley to Pyrenophora graminea fungal invasion. PMID:27004551
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model. PMID:26989150
Transcriptomic Signature of the SHATTERPROOF2 Expression Domain Reveals the Meristematic Nature of Arabidopsis Gynoecial Medial Domain. PMID:26983993
An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry. PMID:26982336
Proteome distribution between nucleoplasm and nucleolus and its relation to ribosome biogenesis in Arabidopsis thaliana. PMID:26980300
Programming of Plant Leaf Senescence with Temporal and Inter-Organellar Coordination of Transcriptome in Arabidopsis. PMID:26966169
Genome-Wide Identification and Expression Analysis of WRKY Gene Family in Capsicum annuum L. PMID:26941768
Genome-Wide Identification of Mitogen-Activated Protein Kinase Gene Family across Fungal Lineage Shows Presence of Novel and Diverse Activation Loop Motifs. PMID:26918378
MGFD: the maize gene families database. PMID:26896848
Comprehensive Phylogenetic Analysis Sheds Light on the Diversity and Origin of the MLO Family of Integral Membrane Proteins. PMID:26893454
Transcriptome comparisons shed light on the pre-condition and potential barrier for C4 photosynthesis evolution in eudicots. PMID:26893123
LEAFDATA: a literature-curated database for Arabidopsis leaf development. PMID:26884807
Transcriptome Profiling of Beach Morning Glory (Ipomoea imperati) under Salinity and Its Comparative Analysis with Sweetpotato. PMID:26848754
PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis. PMID:26839287
A cis-regulatory sequence from a short intergenic region gives rise to a strong microbe-associated molecular pattern-responsive synthetic promoter. PMID:26833485
One Step Forward, Two Steps Back; Xeno-MicroRNAs Reported in Breast Milk Are Artifacts. PMID:26824347
Structural and functional annotation of the MADS-box transcription factor family in grapevine. PMID:26818751
pATsi: Paralogs and Singleton Genes from Arabidopsis thaliana. PMID:26792975
Mobile small RNAs regulate genome-wide DNA methylation. PMID:26787884
Identification, duplication, evolution and expression analyses of caleosins in Brassica plants and Arabidopsis subspecies. PMID:26786939
Network-Based Comparative Analysis of Arabidopsis Immune Responses to Golovinomyces orontii and Botrytis cinerea Infections. PMID:26750561
Genome-Wide Identification of Calcium Dependent Protein Kinase Gene Family in Plant Lineage Shows Presence of Novel D-x-D and D-E-L Motifs in EF-Hand Domain. PMID:26734045
The Arabidopsis COX11 Homolog is Essential for Cytochrome c Oxidase Activity. PMID:26734017
Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome. PMID:26731733
BioGRID: A Resource for Studying Biological Interactions in Yeast. PMID:26729913
Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions. PMID:26729909
Functional Analysis of Cellulose and Xyloglucan in the Walls of Stomatal Guard Cells of Arabidopsis. PMID:26729799
Biocuration with insufficient resources and fixed timelines. PMID:26708987
Novel Genes Affecting the Interaction between the Cabbage Whitefly and Arabidopsis Uncovered by Genome-Wide Association Mapping. PMID:26699853
Integration of a Decrescent Transcriptome and Metabolomics Dataset of Peucedanum praeruptorum to Investigate the CYP450 and MDR Genes Involved in Coumarins Biosynthesis and Transport. PMID:26697023
De Novo Assembly of Coding Sequences of the Mangrove Palm (Nypa fruticans) Using RNA-Seq and Discovery of Whole-Genome Duplications in the Ancestor of Palms. PMID:26684618
The European Bioinformatics Institute in 2016: Data growth and integration. PMID:26673705
Repeated Whole-Genome Duplication, Karyotype Reshuffling, and Biased Retention of Stress-Responding Genes in Buckler Mustard. PMID:26668305
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics. PMID:26656885
ALCOdb: Gene Coexpression Database for Microalgae. PMID:26644461
Removal of redundant contigs from de novo RNA-Seq assemblies via homology search improves accurate detection of differentially expressed genes. PMID:26637306
De novo and comparative transcriptome analysis of cultivated and wild spinach. PMID:26635144
Differential abundance analysis of mesocarp protein from high- and low-yielding oil palms associates non-oil biosynthetic enzymes to lipid biosynthesis. PMID:26617468
Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana. PMID:26607788
Genome-wide identification and phylogenetic analysis of plant RNA binding proteins comprising both RNA recognition motifs and contiguous glycine residues. PMID:26589419
GREENC: a Wiki-based database of plant lncRNAs. PMID:26578586
Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos. PMID:26572793
Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes. PMID:26560341
miRA: adaptable novel miRNA identification in plants using small RNA sequencing data. PMID:26542525
AIP1 is a novel Agenet/Tudor domain protein from Arabidopsis that interacts with regulators of DNA replication, transcription and chromatin remodeling. PMID:26538092
Target Enrichment Improves Mapping of Complex Traits by Deep Sequencing. PMID:26530422
Exploring potential new floral organ morphogenesis genes of Arabidopsis thaliana using systems biology approach. PMID:26528302
A Glimpse to Background and Characteristics of Major Molecular Biological Networks. PMID:26491677
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. PMID:26476450
FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana. PMID:26476447
Developmental and Reproductive Effects of Iron Oxide Nanoparticles in Arabidopsis thaliana. PMID:26473847
Gene expression profiling during adventitious root formation in carnation stem cuttings. PMID:26467528
FlyBase: establishing a Gene Group resource for Drosophila melanogaster. PMID:26467478
Get the jump - Do 3'UTRs protect transposable elements from silencing? PMID:26442184
Genome-wide analysis and expression profiling under heat and drought treatments of HSP70 gene family in soybean (Glycine max L.). PMID:26442082
Tissue specific and abiotic stress regulated transcription of histidine kinases in plants is also influenced by diurnal rhythm. PMID:26442025
Genome-Wide Comparative Analysis of Flowering-Related Genes in Arabidopsis, Wheat, and Barley. PMID:26435710
SUVH1, a Su(var)3-9 family member, promotes the expression of genes targeted by DNA methylation. PMID:26400170
PlantDHS: a database for DNase I hypersensitive sites in plants. PMID:26400163
Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling. PMID:26394049
Identification of 4CL Genes in Desert Poplars and Their Changes in Expression in Response to Salt Stress. PMID:26393655
Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data. PMID:26382944
Molecular marker development from transcript sequences and germplasm evaluation for cultivated peanut (Arachis hypogaea L.). PMID:26362763
Cytokinin-induced promotion of root meristem size in the fern Azolla supports a shoot-like origin of euphyllophyte roots. PMID:26358624
G-protein α-subunit (GPA1) regulates stress, nitrate and phosphate response, flavonoid biosynthesis, fruit/seed development and substantially shares GCR1 regulation in A. thaliana. PMID:26346778
ReprOlive: a database with linked data for the olive tree (Olea europaea L.) reproductive transcriptome. PMID:26322066
Overaccumulation of γ-Glutamylcysteine in a Jasmonate-Hypersensitive Arabidopsis Mutant Causes Jasmonate-Dependent Growth Inhibition. PMID:26282239
Conservation of tRNA and rRNA 5-methylcytosine in the kingdom Plantae. PMID:26268215
Large-Scale Transcriptome Analysis in Faba Bean (Vicia faba L.) under Ascochyta fabae Infection. PMID:26267359
Spt-Ada-Gcn5-Acetyltransferase (SAGA) Complex in Plants: Genome Wide Identification, Evolutionary Conservation and Functional Determination. PMID:26263547
Overexpression of Arabidopsis thaliana ERI, the homolog of C. elegans Enhancer of RNAinterference, leads to enhanced growth. PMID:26257748
Transcriptional transitions in Nicotiana benthamiana leaves upon induction of oil synthesis by WRINKLED1 homologs from diverse species and tissues. PMID:26253704
Whole transcriptome profiling of the vernalization process in Lilium longiflorum (cultivar White Heaven) bulbs. PMID:26216467
The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome. PMID:26201819
The Glycine max cv. Enrei Genome for Improvement of Japanese Soybean Cultivars. PMID:26199933
Genome-wide annotation and characterization of CLAVATA/ESR (CLE) peptide hormones of soybean (Glycine max) and common bean (Phaseolus vulgaris), and their orthologues of Arabidopsis thaliana. PMID:26188205
Integrating Phosphoproteomics and Bioinformatics to Study Brassinosteroid-Regulated Phosphorylation Dynamics in Arabidopsis. PMID:26187819
Genome-Wide Survey and Expression Profile Analysis of the Mitogen-Activated Protein Kinase (MAPK) Gene Family in Brassica rapa. PMID:26173020
Genome-wide identification and Phylogenic analysis of kelch motif containing ACBP in Brassica napus. PMID:26156054
AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana. PMID:26111100
Proteasome targeting of proteins in Arabidopsis leaf mesophyll, epidermal and vascular tissues. PMID:26074939
A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda. PMID:26068575
Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures. PMID:26067253
microProtein Prediction Program (miP3): A Software for Predicting microProteins and Their Target Transcription Factors. PMID:26060811
The distribution and evolution of Arabidopsis thaliana cis natural antisense transcripts. PMID:26054753
A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads. PMID:26052341
De Novo Assembly of Bitter Gourd Transcriptomes: Gene Expression and Sequence Variations in Gynoecious and Monoecious Lines. PMID:26047102
Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice. PMID:26045464
The Arabidopsis KH-Domain RNA-Binding Protein ESR1 Functions in Components of Jasmonate Signalling, Unlinking Growth Restraint and Resistance to Stress. PMID:25985302
Catastrophic chromosomal restructuring during genome elimination in plants. PMID:25977984
Long-read, whole-genome shotgun sequence data for five model organisms. PMID:25977796
Comparative Transcriptomics of Sijung and Jumli Marshi Rice during Early Chilling Stress Imply Multiple Protective Mechanisms. PMID:25973918
AtmiRNET: a web-based resource for reconstructing regulatory networks of Arabidopsis microRNAs. PMID:25972521
Comprehensive analysis of transcriptome response to salinity stress in the halophytic turf grass Sporobolus virginicus. PMID:25954282
CNL Disease Resistance Genes in Soybean and Their Evolutionary Divergence. PMID:25922568
Transcript abundance patterns of Populus C-repeat binding factor2 orthologs and genetic association of PsCBF2 allelic variation with physiological and biochemical traits in response to abiotic stress. PMID:25916311
MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes. PMID:25909041
Genome-wide negative feedback drives transgenerational DNA methylation dynamics in Arabidopsis. PMID:25902052
Mongolian Almond (Prunus mongolica Maxim): The Morpho-Physiological, Biochemical and Transcriptomic Response to Drought Stress. PMID:25893685
Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants. PMID:25888265
NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss. PMID:25886915
Measuring semantic similarities by combining gene ontology annotations and gene co-function networks. PMID:25886899
Standard flow liquid chromatography for shotgun proteomics in bioenergy research. PMID:25883932
Genome wide comparative analysis of the effects of PRMT5 and PRMT4/CARM1 arginine methyltransferases on the Arabidopsis thaliana transcriptome. PMID:25880665
Biochemical functional predictions for protein structures of unknown or uncertain function. PMID:25848497
Identification and Characterization of a Golgi-Localized UDP-Xylose Transporter Family from Arabidopsis. PMID:25804536
Network analysis of postharvest senescence process in citrus fruits revealed by transcriptomic and metabolomic profiling. PMID:25802366
Transcriptome analysis of thermogenic Arum concinnatum reveals the molecular components of floral scent production. PMID:25736477
Coordinated rates of evolution between interacting plastid and nuclear genes in Geraniaceae. PMID:25724640
Biological databases for human research. PMID:25712261
EXPath: a database of comparative expression analysis inferring metabolic pathways for plants. PMID:25708775
A systems biology approach toward understanding seed composition in soybean. PMID:25708381
Web resources for model organism studies. PMID:25707592
Extracellular peptidase hunting for improvement of protein production in plant cells and roots. PMID:25705212
Techniques for transferring host-pathogen protein interactions knowledge to new tasks. PMID:25699028
Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis using a genome-scale metabolic network. PMID:25670818
Transcriptome analysis of Arabidopsis GCR1 mutant reveals its roles in stress, hormones, secondary metabolism and phosphate starvation. PMID:25668726
FlowerNet: a gene expression correlation network for anther and pollen development. PMID:25667314
A recently evolved isoform of the transcription factor BES1 promotes brassinosteroid signaling and development in Arabidopsis thaliana. PMID:25649439
Duplicate gene divergence by changes in microRNA binding sites in Arabidopsis and Brassica. PMID:25644246
The Arabidopsis SWI2/SNF2 chromatin Remodeler BRAHMA regulates polycomb function during vegetative development and directly activates the flowering repressor gene SVP. PMID:25615622
Gene families as soft cliques with backbones: Amborella contrasted with other flowering plants. PMID:25572777
Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network. PMID:25563969
Allele Workbench: transcriptome pipeline and interactive graphics for allele-specific expression. PMID:25541944
Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty. PMID:25534030
An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes. PMID:25521792
Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. PMID:25517485
Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems. PMID:25511303
Plant Omics Data Center: an integrated web repository for interspecies gene expression networks with NLP-based curation. PMID:25505034
The exosome and trans-acting small interfering RNAs regulate cuticular wax biosynthesis during Arabidopsis inflorescence stem development. PMID:25502190
Molecular effects of resistance elicitors from biological origin and their potential for crop protection. PMID:25484886
Association genetics and expression patterns of a CBF4 homolog in Populus under abiotic stress. PMID:25481715
The grapevine gene nomenclature system. PMID:25481684
AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants. PMID:25480687
LAILAPS: the plant science search engine. PMID:25480116
Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case. PMID:25476999
Plant-PrAS: a database of physicochemical and structural properties and novel functional regions in plant proteomes. PMID:25435546
Unique features of the m6A methylome in Arabidopsis thaliana. PMID:25430002
Promotion of testa rupture during garden cress germination involves seed compartment-specific expression and activity of pectin methylesterases. PMID:25429110
The BioGRID interaction database: 2015 update. PMID:25428363
Araport: the Arabidopsis information portal. PMID:25414324
TE-Tracker: systematic identification of transposition events through whole-genome resequencing. PMID:25408240
Proteome analysis of cytoplasmatic and plastidic β-carotene lipid droplets in Dunaliella bardawil. PMID:25404729
PNRD: a plant non-coding RNA database. PMID:25398903
Comparative analysis of predicted plastid-targeted proteomes of sequenced higher plant genomes. PMID:25393533
The coffee genome hub: a resource for coffee genomes. PMID:25392413
GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response. PMID:25392409
AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species. PMID:25355510
De novo sequencing and analysis of the lily pollen transcriptome: an open access data source for an orphan plant species. PMID:25341867
Transcriptome sequencing of rhizome tissue of Sinopodophyllum hexandrum at two temperatures. PMID:25287271
Constitutive overexpression of the pollen specific gene SKS13 in leaves reduces aphid performance on Arabidopsis thaliana. PMID:25267093
Plant protein peptidase inhibitors: an evolutionary overview based on comparative genomics. PMID:25253557
A root-expressed L-phenylalanine:4-hydroxyphenylpyruvate aminotransferase is required for tropane alkaloid biosynthesis in Atropa belladonna. PMID:25228340
Evolutionary conserved function of barley and Arabidopsis 3-KETOACYL-CoA SYNTHASES in providing wax signals for germination of powdery mildew fungi. PMID:25201879
NPEST: a nonparametric method and a database for transcription start site prediction. PMID:25197613
Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome. PMID:25189238
The RNA helicases AtMTR4 and HEN2 target specific subsets of nuclear transcripts for degradation by the nuclear exosome in Arabidopsis thaliana. PMID:25144737
Bioinformatic indications that COPI- and clathrin-based transport systems are not present in chloroplasts: an Arabidopsis model. PMID:25137124
Digital inventory of Arabidopsis transcripts revealed by 61 RNA sequencing samples. PMID:25118256
Genome-wide comparative analysis of tonoplast intrinsic protein (TIP) genes in plants. PMID:25095751
Prediction and functional analysis of the sweet orange protein-protein interaction network. PMID:25091279
Proteins with high turnover rate in barley leaves estimated by proteome analysis combined with in planta isotope labeling. PMID:25082890
Comparative genomic and transcriptomic analysis of terpene synthases in Arabidopsis and Medicago. PMID:25075527
The draft genome and transcriptome of Amaranthus hypochondriacus: a C4 dicot producing high-lysine edible pseudo-cereal. PMID:25071079
Transcriptome analysis reveals the same 17 S-locus F-box genes in two haplotypes of the self-incompatibility locus of Petunia inflata. PMID:25070642
The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. PMID:25064006
A role for SUV39H1-mediated H3K9 trimethylation in the control of genome stability and senescence in WI38 human diploid lung fibroblasts. PMID:25063769
Broad-range glycosidase activity profiling. PMID:25056938
A genome-scale resource for the functional characterization of Arabidopsis transcription factors. PMID:25043187
FANCM-associated proteins MHF1 and MHF2, but not the other Fanconi anemia factors, limit meiotic crossovers. PMID:25038251
Characterization of MORE AXILLARY GROWTH genes in Populus. PMID:25036388
Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures. PMID:25035402
Functional analysis of COP1 and SPA orthologs from Physcomitrella and rice during photomorphogenesis of transgenic Arabidopsis reveals distinct evolutionary conservation. PMID:24985152
Adaptive evolution and divergent expression of heat stress transcription factors in grasses. PMID:24974883
Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population. PMID:24972714
Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping. PMID:24958856
Cross-species outlier detection reveals different evolutionary pressures between sister species. PMID:24942459
Mapping-by-sequencing accelerates forward genetics in barley. PMID:24917130
Association mapping of germination traits in Arabidopsis thaliana under light and nutrient treatments: searching for G×E effects. PMID:24902604
DUF581 is plant specific FCS-like zinc finger involved in protein-protein interaction. PMID:24901469
Sustainable harvest: managing plasticity for resilient crops. PMID:24891039
Expression-based network biology identifies immune-related functional modules involved in plant defense. PMID:24888606
Overexpression of UCP1 in tobacco induces mitochondrial biogenesis and amplifies a broad stress response. PMID:24886177
Dehydration stress memory genes of Zea mays; comparison with Arabidopsis thaliana. PMID:24885787
BioCreative-IV virtual issue. PMID:24852177
Extending the model of Arabidopsis telomere length and composition across Brassicaceae. PMID:24846723
MiRNAting control of DNA methylation. PMID:24845501
Genomewide analysis of LATERAL ORGAN BOUNDARIES Domain gene family in Zea mays. PMID:24840825
Metabolomic Characterization of Knockout Mutants in Arabidopsis: Development of a Metabolite Profiling Database for Knockout Mutants in Arabidopsis. PMID:24828308
Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production. PMID:24808102
A functional TOC complex contributes to gravity signal transduction in Arabidopsis. PMID:24795735
Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes. PMID:24773781
RNA sequencing analysis reveals transcriptomic variations in tobacco (Nicotiana tabacum) leaves affected by climate, soil, and tillage factors. PMID:24733065
Protein abundance changes and ubiquitylation targets identified after inhibition of the proteasome with syringolin A. PMID:24732913
Dissecting a hidden gene duplication: the Arabidopsis thaliana SEC10 locus. PMID:24728280
'In silico expression analysis', a novel PathoPlant web tool to identify abiotic and biotic stress conditions associated with specific cis-regulatory sequences. PMID:24727366
Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs. PMID:24722185
SysPTM 2.0: an updated systematic resource for post-translational modification. PMID:24705204
Integrative study of Arabidopsis thaliana metabolomic and transcriptomic data with the interactive MarVis-Graph software. PMID:24688832
Improved transcript isoform discovery using ORF graphs. PMID:24659106
Genomics and bioinformatics resources for translational science in Rosaceae. PMID:24634697
Tetrahymena thermophila: a divergent perspective on membrane traffic. PMID:24634411
Arabidopsis thaliana RALF1 opposes brassinosteroid effects on root cell elongation and lateral root formation. PMID:24620000
Arabidopsis VASCULAR-RELATED UNKNOWN PROTEIN1 regulates xylem development and growth by a conserved mechanism that modulates hormone signaling. PMID:24567189
Functional approach to high-throughput plant growth analysis. PMID:24565437
The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. PMID:24548928
ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa. PMID:24498971
Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome. PMID:24489955
Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress. PMID:24489928
Antagonistic regulation of growth and immunity by the Arabidopsis basic helix-loop-helix transcription factor homolog of brassinosteroid enhanced expression2 interacting with increased leaf inclination1 binding bHLH1. PMID:24443525
Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis. PMID:24423873
Genome scale transcriptional response diversity among ten ecotypes of Arabidopsis thaliana during heat stress. PMID:24409190
Reconstruction and analysis of nutrient-induced phosphorylation networks in Arabidopsis thaliana. PMID:24400017
Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. PMID:24377444
An extensive evaluation of read trimming effects on Illumina NGS data analysis. PMID:24376861
Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing. PMID:24373163
POMO--Plotting Omics analysis results for Multiple Organisms. PMID:24365393
Plant Genome DataBase Japan (PGDBj): a portal website for the integration of plant genome-related databases. PMID:24363285
Insertion of a specific fungal 3'-phosphoadenosine-5'-phosphatase motif into a plant homologue improves halotolerance and drought tolerance of plants. PMID:24349144
The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana. PMID:24347547
Characterization of cytokinin signaling and homeostasis gene families in two hardwood tree species: Populus trichocarpa and Prunus persica. PMID:24341635
POGs2: a web portal to facilitate cross-species inferences about protein architecture and function in plants. PMID:24340041
ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants. PMID:24334350
Identification of Cassava MicroRNAs under Abiotic Stress. PMID:24328029
De novo assembly of the transcriptome of the non-model plant Streptocarpus rexii employing a novel heuristic to recover locus-specific transcript clusters. PMID:24324652
MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. PMID:24306534
eggNOG v4.0: nested orthology inference across 3686 organisms. PMID:24297252
Selected reaction monitoring to determine protein abundance in Arabidopsis using the Arabidopsis proteotypic predictor. PMID:24296071
Genome-wide identification and expression analysis of the mitogen-activated protein kinase gene family from banana suggest involvement of specific members in different stages of fruit ripening. PMID:24275941
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. PMID:24275491
RARGE II: an integrated phenotype database of Arabidopsis mutant traits using a controlled vocabulary. PMID:24272250
Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture. PMID:24267747
Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application). PMID:24256031
MEGANTE: a web-based system for integrated plant genome annotation. PMID:24253915
Validation of SNP allele frequencies determined by pooled next-generation sequencing in natural populations of a non-model plant species. PMID:24244686
P³DB 3.0: From plant phosphorylation sites to protein networks. PMID:24243849
The Genome Database for Rosaceae (GDR): year 10 update. PMID:24225320
DNASU plasmid and PSI:Biology-Materials repositories: resources to accelerate biological research. PMID:24225319
Manually curated database of rice proteins. PMID:24214963
CottonGen: a genomics, genetics and breeding database for cotton research. PMID:24203703
ppdb: plant promoter database version 3.0. PMID:24194597
Differential expression of CPKs and cytosolic Ca2+ variation in resistant and susceptible apple cultivars (Malus x domestica) in response to the pathogen Erwinia amylovora and mechanical wounding. PMID:24192013
Characterization and transcript profiling of the pectin methylesterase (PME) and pectin methylesterase inhibitor (PMEI) gene families in flax (Linum usitatissimum). PMID:24168262
MASCP gator: an overview of the Arabidopsis proteomic aggregation portal. PMID:24167507
Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes. PMID:24148294
Transcriptome-mining for single-copy nuclear markers in ferns. PMID:24116189
Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps. PMID:24102711
High-throughput RNA sequencing of pseudomonas-infected Arabidopsis reveals hidden transcriptome complexity and novel splice variants. PMID:24098335
Use of MSAP markers to analyse the effects of salt stress on DNA methylation in rapeseed (Brassica napus var. oleifera). PMID:24086583
Gene regulatory networks elucidating huanglongbing disease mechanisms. PMID:24086326
Development of a next-generation NIL library in Arabidopsis thaliana for dissecting complex traits. PMID:24063355
Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits. PMID:24048646
Genome-wide discovery and information resource development of DNA polymorphisms in cassava. PMID:24040164
Vacuolar transport of abscisic acid glucosyl ester is mediated by ATP-binding cassette and proton-antiport mechanisms in Arabidopsis. PMID:24028845
Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS. PMID:24015873
Web Apollo: a web-based genomic annotation editing platform. PMID:24000942
RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions. PMID:23984645
GnpIS: an information system to integrate genetic and genomic data from plants and fungi. PMID:23959375
Controlled vocabularies for plant anatomical parts optimized for use in data analysis tools and for cross-species studies. PMID:23958387
Overexpression of IRM1 enhances resistance to aphids in Arabidopsis thaliana. PMID:23951039
Predicting gene function from uncontrolled expression variation among individual wild-type Arabidopsis plants. PMID:23943861
Genome-wide identification and analysis of membrane-bound O-acyltransferase (MBOAT) gene family in plants. PMID:23928653
The GreenCut: re-evaluation of physiological role of previously studied proteins and potential novel protein functions. PMID:23873414
An integrative, translational approach to understanding rare and orphan genetically based diseases. PMID:23853703
CoLIde: a bioinformatics tool for CO-expression-based small RNA Loci Identification using high-throughput sequencing data. PMID:23851377
Common and distinct functions of Arabidopsis class A1 and A2 heat shock factors in diverse abiotic stress responses and development. PMID:23832625
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. PMID:23817568
De novo assembly of the pennycress (Thlaspi arvense) transcriptome provides tools for the development of a winter cover crop and biodiesel feedstock. PMID:23786378
Getting to the roots of it: Genetic and hormonal control of root architecture. PMID:23785372
Genome-wide survey of DNA-binding proteins in Arabidopsis thaliana: analysis of distribution and functions. PMID:23775796
PromoterCAD: Data-driven design of plant regulatory DNA. PMID:23766287
PosMed: Ranking genes and bioresources based on Semantic Web Association Study. PMID:23761449
SVGenes: a library for rendering genomic features in scalable vector graphic format. PMID:23749959
Transcriptome and proteome data reveal candidate genes for pollinator attraction in sexually deceptive orchids. PMID:23734209
Profiling protein kinases and other ATP binding proteins in Arabidopsis using Acyl-ATP probes. PMID:23722185
Genomic and expression analysis of the flax (Linum usitatissimum) family of glycosyl hydrolase 35 genes. PMID:23701735
WebAUGUSTUS--a web service for training AUGUSTUS and predicting genes in eukaryotes. PMID:23700307
Identification of ta-siRNAs and cis-nat-siRNAs in cassava and their roles in response to cassava bacterial blight. PMID:23665476
dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts. PMID:23660284
Simultaneous transcriptome analysis of Sorghum and Bipolaris sorghicola by using RNA-seq in combination with de novo transcriptome assembly. PMID:23638091
The Tomato Yellow Leaf Curl Virus resistance genes Ty-1 and Ty-3 are allelic and code for DFDGD-class RNA-dependent RNA polymerases. PMID:23555305
Molecular signatures in Arabidopsis thaliana in response to insect attack and bacterial infection. PMID:23536844
Transcriptome Profiling Identifies Candidate Genes Associated with the Accumulation of Distinct Sulfur γ-Glutamyl Dipeptides in Phaseolus vulgaris and Vigna mungo Seeds. PMID:23532826
Computational predictions provide insights into the biology of TAL effector target sites. PMID:23526890
Coupling deep transcriptome analysis with untargeted metabolic profiling in Ophiorrhiza pumila to further the understanding of the biosynthesis of the anti-cancer alkaloid camptothecin and anthraquinones. PMID:23503598
Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas. PMID:23497159
Flying saucer1 is a transmembrane RING E3 ubiquitin ligase that regulates the degree of pectin methylesterification in Arabidopsis seed mucilage. PMID:23482858
A temporal switch model for estimating transcriptional activity in gene expression. PMID:23479351
Transcriptome responses to combinations of stresses in Arabidopsis. PMID:23447525
Global approaches for telling time: omics and the Arabidopsis circadian clock. PMID:23435351
Defining the core proteome of the chloroplast envelope membranes. PMID:23390424
Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly. PMID:23382244
Repeat-encoded poly-Q tracts show statistical commonalities across species. PMID:23374135
Orchidstra: an integrated orchid functional genomics database. PMID:23324169
STIFDB2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in Arabidopsis and rice. PMID:23314754
Novel thylakoid membrane GreenCut protein CPLD38 impacts accumulation of the cytochrome b6f complex and associated regulatory processes. PMID:23303190
Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. PMID:23299411
Inferring the Brassica rapa Interactome Using Protein-Protein Interaction Data from Arabidopsis thaliana. PMID:23293649
PRIMe Update: innovative content for plant metabolomics and integration of gene expression and metabolite accumulation. PMID:23292601
Identification of RNA targets for the nuclear multidomain cyclophilin atCyp59 and their effect on PPIase activity. PMID:23248006
Give It AGO: The Search for miRNA-Argonaute Sorting Signals in Arabidopsis thaliana Indicates a Relevance of Sequence Positions Other than the 5'-Position Alone. PMID:23233858
Early cone setting in Picea abies acrocona is associated with increased transcriptional activity of a MADS box transcription factor. PMID:23221834
Building an efficient curation workflow for the Arabidopsis literature corpus. PMID:23221298
The plant ontology as a tool for comparative plant anatomy and genomic analyses. PMID:23220694
Proteomic analysis of the Cyanophora paradoxa muroplast provides clues on early events in plastid endosymbiosis. PMID:23212214
The BioGRID interaction database: 2013 update. PMID:23203989
OrysPSSP: a comparative platform for small secreted proteins from rice and other plants. PMID:23203890
Finding microRNA targets in plants: current status and perspectives. PMID:23200136
The tomato RLK superfamily: phylogeny and functional predictions about the role of the LRRII-RLK subfamily in antiviral defense. PMID:23198823
Transcriptome analysis of symptomatic and recovered leaves of geminivirus-infected pepper (Capsicum annuum). PMID:23185982
PGDD: a database of gene and genome duplication in plants. PMID:23180799
SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis. PMID:23180787
PeroxiBase: a database for large-scale evolutionary analysis of peroxidases. PMID:23180785
Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars. PMID:23171001
PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants. PMID:23161682
Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts. PMID:23160414
Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR. PMID:23160413
Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis). PMID:23112803
Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. PMID:23110892
Selaginella Genome Analysis - Entering the "Homoplasy Heaven" of the MADS World. PMID:23049534
Common and specific protein accumulation patterns in different albino/pale-green mutants reveals regulon organization at the proteome level. PMID:23027667
Conserved non-coding regulatory signatures in Arabidopsis co-expressed gene modules. PMID:23024789
Aldehyde dehydrogenase (ALDH) superfamily in plants: gene nomenclature and comparative genomics. PMID:23007552
Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints. PMID:22992304
Online tools for bioinformatics analyses in nutrition sciences. PMID:22983844
Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit. PMID:22929616
Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics. PMID:22923678
Evolution of flux control in the glucosinolate pathway in Arabidopsis thaliana. PMID:22923463
Evolution of the land plant exocyst complexes. PMID:22826714
A proteogenomic survey of the Medicago truncatula genome. PMID:22774004
The Choice between MapMan and Gene Ontology for Automated Gene Function Prediction in Plant Science. PMID:22754563
Uncovering Arabidopsis membrane protein interactome enriched in transporters using mating-based split ubiquitin assays and classification models. PMID:22737156
Current status of the plant phosphorylation site database PhosPhAt and its use as a resource for molecular plant physiology. PMID:22723801
De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus. PMID:22721448
pep2pro: the high-throughput proteomics data processing, analysis, and visualization tool. PMID:22701464
PsRobot: a web-based plant small RNA meta-analysis toolbox. PMID:22693224
Genome-Wide Characterization of ISR Induced in Arabidopsis thaliana by Trichoderma hamatum T382 Against Botrytis cinerea Infection. PMID:22661981
RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats. PMID:22647529
Illuminating the wall: using click chemistry to image pectins in Arabidopsis cell walls. PMID:22580708
Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum. PMID:22570076
SAVoR: a server for sequencing annotation and visualization of RNA structures. PMID:22492627
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:22144685
The Arabidopsis Information Resource (TAIR): gene structure and function annotation PubMed citations: 472.

472 articles citing: The Arabidopsis Information Resource (TAIR): gene structure and function annotation

Cassava (Manihot esculenta) Slow Anion Channel (MeSLAH4) Gene Overexpression Enhances Nitrogen Assimilation, Growth, and Yield in Rice. PMID:35832225
Comparative Genomic Analysis of SAUR Gene Family, Cloning and Functional Characterization of Two Genes (PbrSAUR13 and PbrSAUR52) in Pyrus bretschneideri. PMID:35806062
PbrCalS5, a callose synthase protein, is involved in pollen tube growth in Pyrus bretschneideri. PMID:35767158
Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach. PMID:35709304
Genetic Diversity in Nitrogen Fertiliser Responses and N Gas Emission in Modern Wheat. PMID:35646002
A successful hybrid deep learning model aiming at promoter identification. PMID:35641900
Genome-Wide Analysis of Invertase Gene Family, and Expression Profiling under Abiotic Stress Conditions in Potato. PMID:35453738
Using Transcriptome Analysis to Explore Gray Mold Resistance-Related Genes in Onion (Alliumcepa L.). PMID:35328095
Genome-Wide Identification of Cotton (Gossypium spp.) Glycerol-3-Phosphate Dehydrogenase (GPDH) Family Members and the Role of GhGPDH5 in Response to Drought Stress. PMID:35270062
Genome-wide identification and expression profiling analysis of maize AP2/ERF superfamily genes reveal essential roles in abiotic stress tolerance. PMID:35151253
Stress Conditions Modulate the Chromatin Interactions Network in Arabidopsis. PMID:35069698
Chromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication Signature. PMID:34899800
Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance. PMID:34880890
In silico analysis and expression profiling of S-domain receptor-like kinases (SD-RLKs) under different abiotic stresses in Arabidopsis thaliana. PMID:34772363
Expression Elements Derived From Plant Sequences Provide Effective Gene Expression Regulation and New Opportunities for Plant Biotechnology Traits. PMID:34745155
A consensus-based ensemble approach to improve transcriptome assembly. PMID:34674629
Genome-Wide Identification and Expression Profiling of 2OGD Superfamily Genes from Three Brassica Plants. PMID:34573381
Promoter analysis of the SPATULA (FvSPT) and SPIRAL (FvSPR) genes in the woodland diploid strawberry (Fragaria vesca L.). PMID:34554560
Can functional genomic diversity provide novel insights into mechanisms of community assembly? A pilot study from an invaded alpine streambed. PMID:34522362
Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome. PMID:34465761
Transcriptome-Wide Identification and Quantification of Caffeoylquinic Acid Biosynthesis Pathway and Prediction of Its Putative BAHDs Gene Complex in A. spathulifolius. PMID:34199260
Genome-wide identification of auxin response factor (ARF) family in kiwifruit (Actinidia chinensis) and analysis of their inducible involvements in abiotic stresses. PMID:34177147
Characterization of the pectin methylesterase inhibitor gene family in Rosaceae and role of PbrPMEI23/39/41 in methylesterified pectin distribution in pear pollen tube. PMID:33961146
Identification and Expression Analysis of SLAC/SLAH Gene Family in Brassica napus L. PMID:33925116
Transcriptome analysis of gynoecium morphogenesis uncovers the chronology of gene regulatory network activity. PMID:33793890
Comparing de novo transcriptome assembly tools in di- and autotetraploid non-model plant species. PMID:33752598
Evolutionary Divergence and Biased Expression of NAC Transcription Factors in Hexaploid Bread Wheat (Triticum aestivum L.). PMID:33671285
Genome-Wide Association Mapping Unravels the Genetic Control of Seed Vigor under Low-Temperature Conditions in Rapeseed (Brassica napus L.). PMID:33668258
Characterization of novel pollen-expressed transcripts reveals their potential roles in pollen heat stress response in Arabidopsis thaliana. PMID:33459869
Global View on the Cytokinin Regulatory System in Potato. PMID:33408733
Sugar Signaling and Post-transcriptional Regulation in Plants: An Overlooked or an Emerging Topic? PMID:33224165
m6A RNA Methylation in Marine Plants: First Insights and Relevance for Biological Rhythms. PMID:33053767
Dwarfism of high-monolignol Arabidopsis plants is rescued by ectopic LACCASE overexpression. PMID:33005856
NGS_SNPAnalyzer: a desktop software supporting genome projects by identifying and visualizing sequence variations from next-generation sequencing data. PMID:32980993
Data-mining bioinformatics: suggesting Arabidopsis thaliana L-type lectin receptor kinase IX.2 (LecRK-IX.2) modulate metabolites and abiotic stress responses. PMID:32924779
An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton. PMID:32894064
The Brittle Rachis Trait in Species Belonging to the Triticeae and Its Controlling Genes Btr1 and Btr2. PMID:32793251
Mining ancient microbiomes using selective enrichment of damaged DNA molecules. PMID:32586278
Expression regulation of MALATE SYNTHASE involved in glyoxylate cycle during protocorm development in Phalaenopsis aphrodite (Orchidaceae). PMID:32572104
Dissecting the genome of star fruit (Averrhoa carambola L.). PMID:32528706
Spaceflight induces novel regulatory responses in Arabidopsis seedling as revealed by combined proteomic and transcriptomic analyses. PMID:32460700
FluentDNA: Nucleotide Visualization of Whole Genomes, Annotations, and Alignments. PMID:32425967
PbMC1a/1b regulates lignification during stone cell development in pear (Pyrus bretschneideri) fruit. PMID:32377350
A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies. PMID:32191846
Genome-Wide Identification and Expression Analysis of Sugar Transporter (ST) Gene Family in Longan (Dimocarpus longan L.). PMID:32182715
A Small RNA-Mediated Regulatory Network in Arabidopsis thaliana Demonstrates Connectivity Between phasiRNA Regulatory Modules and Extensive Co-Regulation of Transcription by miRNAs and phasiRNAs. PMID:32082334
Identification of eukaryotic translation initiation factors and the temperature-dependent nature of Turnip mosaic virus epidemics in allopolyploid Brassica juncea. PMID:32051808
High-resolution expression profiling of selected gene sets during plant immune activation. PMID:31916350
Genome-wide analysis of polygalacturonase gene family from pear genome and identification of the member involved in pear softening. PMID:31881836
A PXY-Mediated Transcriptional Network Integrates Signaling Mechanisms to Control Vascular Development in Arabidopsis. PMID:31806676
Evolution of C4 photosynthesis predicted by constraint-based modelling. PMID:31799932
Pheophorbide a May Regulate Jasmonate Signaling during Dark-Induced Senescence. PMID:31753845
Evolution of the Cell Wall Gene Families of Grasses. PMID:31681352
CsBZIP40, a BZIP transcription factor in sweet orange, plays a positive regulatory role in citrus bacterial canker response and tolerance. PMID:31584990
Identification of genes encoding ALMT and MATE transporters as candidate aluminum tolerance genes from a typical acid soil plant, Psychotria rubra (Rubiaceae). PMID:31579611
Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes. PMID:31455637
A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana. PMID:31442410
OryzaGP: rice gene and protein dataset for named-entity recognition. PMID:31307132
Interactome Analysis and Docking Sites of MutS Homologs Reveal New Physiological Roles in Arabidopsis thaliana. PMID:31288414
Site-specific cleavage of bacterial MucD by secreted proteases mediates antibacterial resistance in Arabidopsis. PMID:31253808
Identification of gene expression logical invariants in Arabidopsis. PMID:31245766
Alternative Splicing and Protein Diversity: Plants Versus Animals. PMID:31244866
The Copper Amine Oxidase AtCuAOδ Participates in Abscisic Acid-Induced Stomatal Closure in Arabidopsis. PMID:31226798
Agrobacterium-mediated plant transformation: biology and applications. PMID:31068763
Classification and Interactions of LRR Receptors and Co-receptors Within the Arabidopsis Plasma Membrane - An Overview. PMID:31057579
Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri). PMID:31023218
Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear (Pyrus bretschneideri). PMID:30941270
Genome-wide characterization and expression analyses of the MYB superfamily genes during developmental stages in Chinese jujube. PMID:30697496
Genome sequence of Malania oleifera, a tree with great value for nervonic acid production. PMID:30689848
NPR1 paralogs of Arabidopsis and their role in salicylic acid perception. PMID:30592744
Distinct Patterns of PPARγ Promoter Usage, Lipid Degradation Activity, and Gene Expression in Subcutaneous Adipose Tissue of Lean and Obese Swine. PMID:30563100
PlantEAR: Functional Analysis Platform for Plant EAR Motif-Containing Proteins. PMID:30555515
Redundancy, Feedback, and Robustness in the Arabidopsis thaliana BZR/BEH Gene Family. PMID:30542366
Landscape genomics provides evidence of climate-associated genetic variation in Mexican populations of Quercus rugosa. PMID:30459833
Efficient and accurate detection of splice junctions from RNA-seq with Portcullis. PMID:30418570
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
sppIDer: A Species Identification Tool to Investigate Hybrid Genomes with High-Throughput Sequencing. PMID:30184140
Assessing genome assembly quality using the LTR Assembly Index (LAI). PMID:30107434
Fast Maximum Likelihood Estimation via Equilibrium Expectation for Large Network Data. PMID:30065311
A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16). PMID:30041596
Comparative Genomics, Whole-Genome Re-sequencing and Expression Profile Analysis of Nucleobase:Cation Symporter 2 (NCS2) Genes in Maize. PMID:30002663
Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events. PMID:29945224
GEsture: an online hand-drawing tool for gene expression pattern search. PMID:29942676
The Direct Involvement of Dark-Induced Tic55 Protein in Chlorophyll Catabolism and Its Indirect Role in the MYB108-NAC Signaling Pathway during Leaf Senescence in Arabidopsis thaliana. PMID:29937503
Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. PMID:29884752
Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses. PMID:29717040
Towards annotating the plant epigenome: the Arabidopsis thaliana small RNA locus map. PMID:29679055
Genetic Loci Governing Androgenic Capacity in Perennial Ryegrass (Lolium perenne L.). PMID:29626084
LARP7 in papillary thyroid carcinoma induces NIS expression through suppression of the SHH signaling pathway. PMID:29620212
An Updated Functional Annotation of Protein-Coding Genes in the Cucumber Genome. PMID:29599790
Evaluating the adaptive evolutionary convergence of carnivorous plant taxa through functional genomics. PMID:29404217
Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant Transcriptomes. PMID:29346292
Transcript Profiling Identifies Gene Cohorts Controlled by Each Signal Regulating Trans-Differentiation of Epidermal Cells of Vicia faba Cotyledons to a Transfer Cell Phenotype. PMID:29234338
Dissection of Resistance Genes to Pseudomonas syringae pv. phaseolicola in UI3 Common Bean Cultivar. PMID:29168746
Genome-wide identification and characterization of GRAS transcription factors in tomato (Solanum lycopersicum). PMID:29134140
Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton. PMID:29104824
Transcription Factors Responding to Pb Stress in Maize. PMID:28927013
Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis. PMID:28902852
Evidence-based gene models for structural and functional annotations of the oil palm genome. PMID:28886750
Genome-wide analysis and expression profiling of zinc finger homeodomain (ZHD) family genes reveal likely roles in organ development and stress responses in tomato. PMID:28874115
Genome-wide identification and characterization of TCP transcription factor genes in upland cotton (Gossypium hirsutum). PMID:28860559
Functional Profiling of Transcription Factor Genes in Neurospora crassa. PMID:28696922
Identification and characterization of miRNAs in two closely related C4 and C3 species of Cleome by high-throughput sequencing. PMID:28422166
Succinct colored de Bruijn graphs. PMID:28200001
Global transcriptome analysis reveals extensive gene remodeling, alternative splicing and differential transcription profiles in non-seed vascular plant Selaginella moellendorffii. PMID:28198676
Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana. PMID:28175342
Genome-wide analysis of auxin transport genes identifies the hormone responsive patterns associated with leafy head formation in Chinese cabbage. PMID:28169368
Nicotiana attenuata Data Hub (NaDH): an integrative platform for exploring genomic, transcriptomic and metabolomic data in wild tobacco. PMID:28086860
Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes. PMID:28069893
Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation. PMID:28031032
Mining the Cicer arietinum genome for the mildew locus O (Mlo) gene family and comparative evolutionary analysis of the Mlo genes from Medicago truncatula and some other plant species. PMID:27900493
Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana). PMID:27799338
De novo Sequencing and Transcriptome Analysis of Pinellia ternata Identify the Candidate Genes Involved in the Biosynthesis of Benzoic Acid and Ephedrine. PMID:27579029
Bioinformatics Approach in Plant Genomic Research. PMID:27499685
The emergence of molecular profiling and omics techniques in seagrass biology; furthering our understanding of seagrasses. PMID:27443314
Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens. PMID:27429780
Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum. PMID:27287040
Large-Scale Gene Relocations following an Ancient Genome Triplication Associated with the Diversification of Core Eudicots. PMID:27195960
Deciphering the transcriptional regulation and spatiotemporal distribution of immunity response in barley to Pyrenophora graminea fungal invasion. PMID:27004551
Transcriptome and Biochemical Analysis of a Flower Color Polymorphism in Silene littorea (Caryophyllaceae). PMID:26973662
Comparative analysis of genome-wide Mlo gene family in Cajanus cajan and Phaseolus vulgaris. PMID:26961357
CURLY LEAF Regulates Gene Sets Coordinating Seed Size and Lipid Biosynthesis. PMID:26945048
Genome-Wide Identification and Characterization of Long Non-Coding RNAs from Mulberry (Morus notabilis) RNA-seq Data. PMID:26938562
Late Embryogenesis Abundant (LEA) Constitutes a Large and Diverse Family of Proteins Involved in Development and Abiotic Stress Responses in Sweet Orange (Citrus sinensis L. Osb.). PMID:26700652
Pipecolic Acid Orchestrates Plant Systemic Acquired Resistance and Defense Priming via Salicylic Acid-Dependent and -Independent Pathways. PMID:26672068
Transcriptional dynamics of the developing sweet cherry (Prunus avium L.) fruit: sequencing, annotation and expression profiling of exocarp-associated genes. PMID:26504533
Get the jump - Do 3'UTRs protect transposable elements from silencing? PMID:26442184
Genome-Wide Identification of the Invertase Gene Family in Populus. PMID:26393355
The Amborella vacuolar processing enzyme family. PMID:26347753
Implications of ethylene biosynthesis and signaling in soybean drought stress tolerance. PMID:26335593
Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks. PMID:26215102
The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome. PMID:26201819
Computational approaches for the classification of seed storage proteins. PMID:26139889
Transcriptome sequencing reveals the roles of transcription factors in modulating genotype by nitrogen interaction in maize. PMID:26116219
Efficient Detection of Novel Nuclear Markers for Brassicaceae by Transcriptome Sequencing. PMID:26061739
Large-Scale Evolutionary Analysis of Genes and Supergene Clusters from Terpenoid Modular Pathways Provides Insights into Metabolic Diversification in Flowering Plants. PMID:26046541
Long non-coding RNAs and their biological roles in plants. PMID:25936895
Transcriptome and genome size analysis of the Venus flytrap. PMID:25886597
The Apoplastic Copper AMINE OXIDASE1 Mediates Jasmonic Acid-Induced Protoxylem Differentiation in Arabidopsis Roots. PMID:25883242
Oriented cell division shapes carnivorous pitcher leaves of Sarracenia purpurea. PMID:25774486
The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. PMID:25765701
A classification of basic helix-loop-helix transcription factors of soybean. PMID:25763382
Fine-mapping of a major QTL controlling angular leaf spot resistance in common bean (Phaseolus vulgaris L.). PMID:25740562
Data Interpretation in the Digital Age. PMID:25729262
A whole-genome microarray study of Arabidopsis thaliana semisolid callus cultures exposed to microgravity and nonmicrogravity related spaceflight conditions for 5 days on board of Shenzhou 8. PMID:25654111
The draft genome of Primula veris yields insights into the molecular basis of heterostyly. PMID:25651398
A complex interplay of tandem- and whole-genome duplication drives expansion of the L-type lectin receptor kinase gene family in the brassicaceae. PMID:25635042
Genome-wide identification and comparative analysis of the heat shock transcription factor family in Chinese white pear (Pyrus bretschneideri) and five other Rosaceae species. PMID:25604453
Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis. PMID:25566309
Patterns of evolutionary conservation of ascorbic acid-related genes following whole-genome triplication in Brassica rapa. PMID:25552535
The chickpea genomic web resource: visualization and analysis of the desi-type Cicer arietinum nuclear genome for comparative exploration of legumes. PMID:25518738
System-level insights into the cellular interactome of a non-model organism: inferring, modelling and analysing functional gene network of soybean (Glycine max). PMID:25423109
Transcriptome sequencing of two wild barley (Hordeum spontaneum L.) ecotypes differentially adapted to drought stress reveals ecotype-specific transcripts. PMID:25408241
Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization. PMID:25393550
A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants. PMID:25380807
Genome-wide analysis of Cyclophilin gene family in soybean (Glycine max). PMID:25348509
Genome-wide analysis of the GRAS gene family in Prunus mume. PMID:25245166
Transcriptome analysis of a petal anthocyanin polymorphism in the arctic mustard, Parrya nudicaulis. PMID:25033465
The Arabidopsis Kinome: phylogeny and evolutionary insights into functional diversification. PMID:24984858
Inductive matrix completion for predicting gene-disease associations. PMID:24932006
Mapping-by-sequencing accelerates forward genetics in barley. PMID:24917130
De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification. PMID:24912738
Identification and functional characterization of bidirectional gene pairs and their intergenic regions in maize. PMID:24886269
Plant systems biology: insights, advances and challenges. PMID:24671625
MAGI: Methylation analysis using genome information. PMID:24589664
Analyses of hypomethylated oil palm gene space. PMID:24497974
In vivo mapping of arabidopsis scaffold/matrix attachment regions reveals link to nucleosome-disfavoring poly(dA:dT) tracts. PMID:24488963
The non-JAZ TIFY protein TIFY8 from Arabidopsis thaliana is a transcriptional repressor. PMID:24416306
Correlations between predicted protein disorder and post-translational modifications in plants. PMID:24403539
Genome-wide identification, phylogenetic analysis, expression profiling, and protein-protein interaction properties of TOPLESS gene family members in tomato. PMID:24399174
The temporal foliar transcriptome of the perennial C3 desert plant Rhazya stricta in its natural environment. PMID:24387666
A predicted protein interactome for rice. PMID:24279740
Optimized probe masking for comparative transcriptomics of closely related species. PMID:24260119
Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network. PMID:24228871
Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs. PMID:24204767
MASCP gator: an overview of the Arabidopsis proteomic aggregation portal. PMID:24167507
Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases. PMID:24163125
Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis. PMID:24147765
Comprehensive analysis of expressed sequence tags from cultivated and wild radish (Raphanus spp.). PMID:24144082
Importance of gene duplication in the evolution of genomic imprinting revealed by molecular evolutionary analysis of the type I MADS-box gene family in Arabidopsis species. PMID:24039992
gff2sequence, a new user friendly tool for the generation of genomic sequences. PMID:24020993
Rapid speciation with gene flow following the formation of Mt. Etna. PMID:23973865
Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. PMID:23879659
GoSynthetic database tool to analyse natural and engineered molecular processes. PMID:23813641
Detailed analysis of putative genes encoding small proteins in legume genomes. PMID:23802007
Prediction of gene-phenotype associations in humans, mice, and plants using phenologs. PMID:23800157
Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana with tiling microarray. PMID:23776682
Transcriptome analyses of Arabidopsis thaliana seedlings grown in space: implications for gravity-responsive genes. PMID:23771594
Revealing the hidden relationship by sparse modules in complex networks with a large-scale analysis. PMID:23762457
Expansion of the pseudo-autosomal region and ongoing recombination suppression in the Silene latifolia sex chromosomes. PMID:23733786
Evaluation of higher plant virus resistance genes in the green alga, Chlorella variabilis NC64A, during the early phase of infection with Paramecium bursaria chlorella virus-1. PMID:23701839
Genomic and expression analysis of the flax (Linum usitatissimum) family of glycosyl hydrolase 35 genes. PMID:23701735
Conserved Non-Coding Sequences are Associated with Rates of mRNA Decay in Arabidopsis. PMID:23675377
Prediction and validation of gene-disease associations using methods inspired by social network analyses. PMID:23650495
PlantGSEA: a gene set enrichment analysis toolkit for plant community. PMID:23632162
Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases. PMID:23586394
WOX4 and WOX14 act downstream of the PXY receptor kinase to regulate plant vascular proliferation independently of any role in vascular organisation. PMID:23578929
The Arabidopsis stress responsive gene database. PMID:23573074
NUCLEAR FACTOR Y transcription factors have both opposing and additive roles in ABA-mediated seed germination. PMID:23527203
PLncDB: plant long non-coding RNA database. PMID:23476021
A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation. PMID:23445355
The protein chaperone HSP90 can facilitate the divergence of gene duplicates. PMID:23410833
Regulation of the S-locus receptor kinase and self-incompatibility in Arabidopsis thaliana. PMID:23390607
Impact of whole-genome and tandem duplications in the expansion and functional diversification of the F-box family in legumes (Fabaceae). PMID:23390519
An allele of Arabidopsis COI1 with hypo- and hypermorphic phenotypes in plant growth, defence and fertility. PMID:23383073
Genome-wide identification and analysis of the B3 superfamily of transcription factors in Brassicaceae and major crop plants. PMID:23377560
Locally duplicated ohnologs evolve faster than nonlocally duplicated ohnologs in Arabidopsis and rice. PMID:23362157
TreeTFDB: an integrative database of the transcription factors from six economically important tree crops for functional predictions and comparative and functional genomics. PMID:23284086
OPTIMAS-DW: a comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize. PMID:23272737
Signalling network construction for modelling plant defence response. PMID:23272172
Toward a comprehensive phylogenetic reconstruction of the evolutionary history of mitogen-activated protein kinases in the plant kingdom. PMID:23230446
Building an efficient curation workflow for the Arabidopsis literature corpus. PMID:23221298
A catalogue of putative unique transcripts from Douglas-fir (Pseudotsuga menziesii) based on 454 transcriptome sequencing of genetically diverse, drought stressed seedlings. PMID:23190494
The plant short-chain dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns. PMID:23167570
Plant vascular cell division is maintained by an interaction between PXY and ethylene signalling. PMID:23166504
PMRD: a curated database for genes and mutants involved in plant male reproduction. PMID:23153247
Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. PMID:23136377
Comparative evaluation of intron prediction methods and detection of plant genome annotation using intron length distributions. PMID:23105930
Genome-wide identification and analysis of late embryogenesis abundant (LEA) genes in Prunus mume. PMID:23086279
Microbial virus genome annotation-mustering the troops to fight the sequence onslaught. PMID:23084289
MetNet Online: a novel integrated resource for plant systems biology. PMID:23066841
Non-recognition-of-BTH4, an Arabidopsis mediator subunit homolog, is necessary for development and response to salicylic acid. PMID:23064321
A novel approach to dissect the abscission process in Arabidopsis. PMID:22992509
Analysis of tiling array expression studies with flexible designs in Bioconductor (waveTiling). PMID:22974078
A gene family derived from transposable elements during early angiosperm evolution has reproductive fitness benefits in Arabidopsis thaliana. PMID:22969437
Modelling and simulating generic RNA-Seq experiments with the flux simulator. PMID:22962361
Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells. PMID:22938179
Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective. PMID:22900718
Identification of Late Embryogenesis Abundant (LEA) protein putative interactors using phage display. PMID:22837651
Role of the G-box element in regulation of chlorophyll biosynthesis in Arabidopsis roots. PMID:22827944
Transcript profiling of cytokinin action in Arabidopsis roots and shoots discovers largely similar but also organ-specific responses. PMID:22824128
Chips and tags suggest plant-environment interactions differ for two alpine Pachycladon species. PMID:22812500
AP2/ERF Transcription Factor in Rice: Genome-Wide Canvas and Syntenic Relationships between Monocots and Eudicots. PMID:22807623
'MicroRNA Targets', a new AthaMap web-tool for genome-wide identification of miRNA targets in Arabidopsis thaliana. PMID:22800758
The core of chloroplast nucleoids contains architectural SWIB domain proteins. PMID:22797472
POWRS: position-sensitive motif discovery. PMID:22792292
GFam: a platform for automatic annotation of gene families. PMID:22790981
A transcriptional dynamic network during Arabidopsis thaliana pollen development. PMID:22784627
Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. PMID:22773751
Transcriptional and metabolic analysis of senescence induced by preventing pollination in maize. PMID:22732243
Lycopene cyclase paralog CruP protects against reactive oxygen species in oxygenic photosynthetic organisms. PMID:22706644
Frequency-based time-series gene expression recomposition using PRIISM. PMID:22703599
Horizontal transfer of expressed genes in a parasitic flowering plant. PMID:22681756
Interactions of an Arabidopsis RanBPM homologue with LisH-CTLH domain proteins revealed high conservation of CTLH complexes in eukaryotes. PMID:22676313
Evolutionary and structural perspectives of plant cyclic nucleotide-gated cation channels. PMID:22661976
Gene regulation by cytokinin in Arabidopsis. PMID:22639635
Detecting functional groups of Arabidopsis mutants by metabolic profiling and evaluation of pleiotropic responses. PMID:22639613
Directly e-mailing authors of newly published papers encourages community curation. PMID:22554788
A pair of partially overlapping Arabidopsis genes with antagonistic circadian expression. PMID:22548050
Characterization and evolution of microRNA genes derived from repetitive elements and duplication events in plants. PMID:22523544
Truncation of class IV chitinases from Arabidopsis by secreted fungal proteases. PMID:22512872
Long identical multispecies elements in plant and animal genomes. PMID:22496592
LARP7 is a potential tumor suppressor gene in gastric cancer. PMID:22488152
ArraySearch: A Web-Based Genomic Search Engine. PMID:22474412
PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing. PMID:22467211
Molecular convergence of the parasitic plant species Cuscuta reflexa and Phelipanche aegyptiaca. PMID:22460777
Low relative humidity triggers RNA-directed de novo DNA methylation and suppression of genes controlling stomatal development. PMID:22442411
Tetrahymena Genome Database Wiki: a community-maintained model organism database. PMID:22434841
Biocurators and biocuration: surveying the 21st century challenges. PMID:22434828
Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report. PMID:22434826
Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants. PMID:22417298
AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana. PMID:22397531
A role for nonsense-mediated mRNA decay in plants: pathogen responses are induced in Arabidopsis thaliana NMD mutants. PMID:22384098
GrameneMart: the BioMart data portal for the Gramene project. PMID:22374386
An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin. PMID:22355196
Nucleotide and RNA metabolism prime translational initiation in the earliest events of mitochondrial biogenesis during Arabidopsis germination. PMID:22345507
Gaining confidence in cross-species annotation transfer: from simple molecular function to complex phenotypic traits. PMID:22319070
Web-based Arabidopsis functional and structural genomics resources. PMID:22303243
Chloroplast biogenesis: control of plastid development, protein import, division and inheritance. PMID:22303235
SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data. PMID:22293517
Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms. PMID:22264329
Transcriptome-based differentiation of closely-related Miscanthus lines. PMID:22253803
Ecotype dependent expression and alternative splicing of epithiospecifier protein (ESP) in Arabidopsis thaliana. PMID:22228407
Evolution and functional diversification of the small heat shock protein/α-crystallin family in higher plants. PMID:22210597
Functional characterisation of metal(loid) processes in planta through the integration of synchrotron techniques and plant molecular biology. PMID:22200921
Comprehensive analysis of tandem amino acid repeats from ten angiosperm genomes. PMID:22195734
Systems analysis of a maize leaf developmental gradient redefines the current C4 model and provides candidates for regulation. PMID:22186372
Identification of cis-acting promoter elements in cold- and dehydration-induced transcriptional pathways in Arabidopsis, rice, and soybean. PMID:22184637
Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana. PMID:22168340
Transcriptional regulation of ribosome components are determined by stress according to cellular compartments in Arabidopsis thaliana. PMID:22164228
Advances in omics and bioinformatics tools for systems analyses of plant functions. PMID:22156726
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. PMID:22140109
MetaBase--the wiki-database of biological databases. PMID:22139927
Evolution of plant nucleotide-sugar interconversion enzymes. PMID:22125650
Phytozome: a comparative platform for green plant genomics. PMID:22110026
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. PMID:22096231
PLEXdb: gene expression resources for plants and plant pathogens. PMID:22084198
Transcriptomic resilience to global warming in the seagrass Zostera marina, a marine foundation species. PMID:22084086
GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database. PMID:22080561
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. PMID:22067447
Nitrate and ammonium lead to distinct global dynamic phosphorylation patterns when resupplied to nitrogen-starved Arabidopsis seedlings. PMID:22060019
Selection for higher gene copy number after different types of plant gene duplications. PMID:22056313
Comprehensive network analysis of anther-expressed genes in rice by the combination of 33 laser microdissection and 143 spatiotemporal microarrays. PMID:22046259
Genetic dissection of the biotic stress response using a genome-scale gene network for rice. PMID:22042862
Assembly, gene annotation and marker development using 454 floral transcriptome sequences in Ziziphus celata (Rhamnaceae), a highly endangered, Florida endemic plant. PMID:22039173
Identification, utilisation and mapping of novel transcriptome-based markers from blackcurrant (Ribes nigrum). PMID:22035129
Apoplastic reactive oxygen species transiently decrease auxin signaling and cause stress-induced morphogenic response in Arabidopsis. PMID:22007024
Computing gene expression data with a knowledge-based gene clustering approach. PMID:21968910
CastorDB: a comprehensive knowledge base for Ricinus communis. PMID:21914200
Targeted identification of short interspersed nuclear element families shows their widespread existence and extreme heterogeneity in plant genomes. PMID:21908723
AtPTR4 and AtPTR6 are differentially expressed, tonoplast-localized members of the peptide transporter/nitrate transporter 1 (PTR/NRT1) family. PMID:21904872
Perspectives on Systematic Analyses of Gene Function in Arabidopsis thaliana: New Tools, Topics and Trends. PMID:21886450
MaizeGDB becomes 'sequence-centric'. PMID:21847242
Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds. PMID:21838868
Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing. PMID:21813626
Genome-wide comparison of nucleotide-binding site-leucine-rich repeat-encoding genes in Arabidopsis. PMID:21810963
Gene discovery using next-generation pyrosequencing to develop ESTs for Phalaenopsis orchids. PMID:21749684
Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. PMID:21746925
In silico analysis of transcription factor repertoires and prediction of stress-responsive transcription factors from six major gramineae plants. PMID:21729923
Improved haplotype-based detection of ongoing selective sweeps towards an application in Arabidopsis thaliana. PMID:21729283
Analysis of Arabidopsis JAZ gene expression during Pseudomonas syringae pathogenesis. PMID:21726394
Single nucleotide polymorphism discovery in elite North American potato germplasm. PMID:21658273
De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants. PMID:21649902
Gene coexpression clusters and putative regulatory elements underlying seed storage reserve accumulation in Arabidopsis. PMID:21635767
Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases. PMID:21632604
A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure. PMID:21619600
Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. PMID:21615673
Differential phylogenetic expansions in BAHD acyltransferases across five angiosperm taxa and evidence of divergent expression among Populus paralogues. PMID:21569431
Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing. PMID:21569327
The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video. PMID:21565781
Multi-source and ontology-based retrieval engine for maize mutant phenotypes. PMID:21558151
Common and unique elements of the ABA-regulated transcriptome of Arabidopsis guard cells. PMID:21554708
RNA 3' processing functions of Arabidopsis FCA and FPA limit intergenic transcription. PMID:21536901
The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage. PMID:21515685
miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. PMID:21515631
PR-10, defensin and cold dehydrin genes are among those over expressed in Oxytropis (Fabaceae) species adapted to the arctic. PMID:21499864
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. PMID:21478890
The predicted Arabidopsis interactome resource and network topology-based systems biology analyses. PMID:21441435
Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops. PMID:21441235
Mass-balanced randomization of metabolic networks. PMID:21436128
PSI:Biology-materials repository: a biologist's resource for protein expression plasmids. PMID:21360289
The chloroplast permease PIC1 regulates plant growth and development by directing homeostasis and transport of iron. PMID:21343424
Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays. PMID:21324185
Sense and antisense transcripts of convergent gene pairs in Arabidopsis thaliana can share a common polyadenylation region. PMID:21311762
Transcription reprogramming during root nodule development in Medicago truncatula. PMID:21304580
ZFNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organisms. PMID:21276248
The transcription factor PHR1 plays a key role in the regulation of sulfate shoot-to-root flux upon phosphate starvation in Arabidopsis. PMID:21261953
ARTADE2DB: improved statistical inferences for Arabidopsis gene functions and structure predictions by dynamic structure-based dynamic expression (DSDE) analyses. PMID:21227933
ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. PMID:21217125
RiceFOX: a database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function. PMID:21186176
AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana. PMID:21177332
Distribution of short interstitial telomere motifs in two plant genomes: putative origin and function. PMID:21171996
MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis. PMID:21123653
Mining the bitter melon (momordica charantia l.) seed transcriptome by 454 analysis of non-normalized and normalized cDNA populations for conjugated fatty acid metabolism-related genes. PMID:21080948
Gramene database in 2010: updates and extensions. PMID:21076153
MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data. PMID:21075962
Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes. PMID:21073700
The BioGRID Interaction Database: 2011 update. PMID:21071413
AGRIS: the Arabidopsis Gene Regulatory Information Server, an update. PMID:21059685
Ongoing and future developments at the Universal Protein Resource. PMID:21051339
Dynamic changes in genome-wide histone H3 lysine 4 methylation patterns in response to dehydration stress in Arabidopsis thaliana. PMID:21050490
AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis. PMID:21036873
MAPK machinery in plants: recognition and response to different stresses through multiple signal transduction pathways. PMID:20980831
PAIR: the predicted Arabidopsis interactome resource. PMID:20952401
Evolutionary history of the poly(ADP-ribose) polymerase gene family in eukaryotes. PMID:20942953
The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. PMID:20935049
Substrates of the Arabidopsis thaliana protein isoaspartyl methyltransferase 1 identified using phage display and biopanning. PMID:20870712
GreenPhylDB v2.0: comparative and functional genomics in plants. PMID:20864446
A Brassica exon array for whole-transcript gene expression profiling. PMID:20862292
RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles. PMID:20860998
SNPs discovery and CAPS marker conversion in soybean. PMID:20859693
Sustainable digital infrastructure. Although databases and other online resources have become a central tool for biological research, their long-term support and maintenance is far from secure. PMID:20847740
Investigating the validity of current network analysis on static conglomerate networks by protein network stratification. PMID:20846443
Molecular and physiological analysis of drought stress in Arabidopsis reveals early responses leading to acclimation in plant growth. PMID:20807999
Tethering factors required for cytokinesis in Arabidopsis. PMID:20713617
Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. PMID:20706207
baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. PMID:20698981
Efficient plant gene identification based on interspecies mapping of full-length cDNAs. PMID:20668003
Diversification and Specialization of Plant RBR Ubiquitin Ligases. PMID:20644651
Choosing a genome browser for a Model Organism Database: surveying the maize community. PMID:20627860
Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana. PMID:20594336
Comparative genomic sequence analysis of strawberry and other rosids reveals significant microsynteny. PMID:20565715
Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state. PMID:20548960
An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 species. PMID:20543093
Deciphering the Arabidopsis floral transition process by integrating a protein-protein interaction network and gene expression data. PMID:20530214
Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. PMID:20522724
Analysis of antisense expression by whole genome tiling microarrays and siRNAs suggests mis-annotation of Arabidopsis orphan protein-coding genes. PMID:20520764
Nucleotide diversity in Silene latifolia autosomal and sex-linked genes. PMID:20519224
High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. PMID:20508152
Transcriptional regulation of the CRK/DUF26 group of receptor-like protein kinases by ozone and plant hormones in Arabidopsis. PMID:20500828
GOAL: a software tool for assessing biological significance of genes groups. PMID:20459620
Two closely related genes of Arabidopsis encode plastidial cytidinediphosphate diacylglycerol synthases essential for photoautotrophic growth. PMID:20442275
Towards reliable isoform quantification using RNA-SEQ data. PMID:20438653
agriGO: a GO analysis toolkit for the agricultural community. PMID:20435677
Meeting report: a workshop on Best Practices in Genome Annotation. PMID:20428316
Artificial selection for determinate growth habit in soybean. PMID:20421496
AP2/EREBP transcription factors are part of gene regulatory networks and integrate metabolic, hormonal and environmental signals in stress acclimation and retrograde signalling. PMID:20411284
MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. PMID:20407027
Transcriptional profiles underlying parent-of-origin effects in seeds of Arabidopsis thaliana. PMID:20406451
Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways. PMID:20383554
A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series. PMID:20377450
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. PMID:20369061
NINJA connects the co-repressor TOPLESS to jasmonate signalling. PMID:20360743
Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. PMID:20233449
Co-expression of neighbouring genes in Arabidopsis: separating chromatin effects from direct interactions. PMID:20233415
The structure, organization and radiation of Sadhu non-long terminal repeat retroelements in Arabidopsis species. PMID:20226007
A MOD(ern) perspective on literature curation. PMID:20221640
Genomics and bioinformatics resources for crop improvement. PMID:20208064
Shewregdb: database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1. PMID:20198195
RNase T2 genes from rice and the evolution of secretory ribonucleases in plants. PMID:20182746
The PPH1 phosphatase is specifically involved in LHCII dephosphorylation and state transitions in Arabidopsis. PMID:20176943
Genome-wide identification of intron fragment insertion mutations and their potential use as SCAR molecular markers in the soybean. PMID:20162255
Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana. PMID:20152032
Transcriptome analysis of secondary-wall-enriched seed coat tissues of canola (Brassica napus L.). PMID:20145934
Stt7-dependent phosphorylation during state transitions in the green alga Chlamydomonas reinhardtii. PMID:20124224
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. PMID:20118918
The RAD23 family provides an essential connection between the 26S proteasome and ubiquitylated proteins in Arabidopsis. PMID:20086187
Dynamic networks from hierarchical bayesian graph clustering. PMID:20084108
OLS dialog: an open-source front end to the ontology lookup service. PMID:20078892
A markov classification model for metabolic pathways. PMID:20047667
Laser microdissection of Arabidopsis cells at the powdery mildew infection site reveals site-specific processes and regulators. PMID:20018666
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. PMID:20015972
deepBase: a database for deeply annotating and mining deep sequencing data. PMID:19966272
Quantitative proteomics by metabolic labeling of model organisms. PMID:19955089
Cloning of Glucuronokinase from Arabidopsis thaliana, the last missing enzyme of the myo-inositol oxygenase pathway to nucleotide sugars. PMID:19951951
A genome-wide characterization of microRNA genes in maize. PMID:19936050
Recurated protein interaction datasets. PMID:19935838
Genetic resources for maize cell wall biology. PMID:19926802
Enriched partial correlations in genome-wide gene expression profiles of hybrids (A. thaliana): a systems biological approach towards the molecular basis of heterosis. PMID:19921139
The Arabidopsis B-box zinc finger family. PMID:19920209
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. PMID:19900971
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. PMID:19892828
PlnTFDB: updated content and new features of the plant transcription factor database. PMID:19858103
Martini: using literature keywords to compare gene sets. PMID:19858102
SALAD database: a motif-based database of protein annotations for plant comparative genomics. PMID:19854933
The Universal Protein Resource (UniProt) in 2010. PMID:19843607
STIFDB-Arabidopsis Stress Responsive Transcription Factor DataBase. PMID:19841686
Human capacitance to dosage imbalance: coping with inefficient selection. PMID:19819908
Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression. PMID:19767600
Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis. PMID:19620096
Identification and characterization of pseudogenes in the rice gene complement. PMID:19607679
Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment. PMID:19588101
Evidence-based gene predictions in plant genomes. PMID:19541913
HORMONOMETER: a tool for discerning transcript signatures of hormone action in the Arabidopsis transcriptome. PMID:19535475
Expansion mechanisms and functional annotations of hypothetical genes in the rice genome. PMID:19535473
PosMed-plus: an intelligent search engine that inferentially integrates cross-species information resources for molecular breeding of plants. PMID:19528193
PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction. PMID:19520768
ROOT UV-B SENSITIVE2 acts with ROOT UV-B SENSITIVE1 in a root ultraviolet B-sensing pathway. PMID:19515790
Internet Resources for Gene Expression Analysis in Arabidopsis thaliana. PMID:19506727
Phenome analysis in plant species using loss-of-function and gain-of-function mutants. PMID:19502383
PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning. PMID:19468046
A Survey of Chloroplast Protein Kinases and Phosphatases in Arabidopsis thaliana. PMID:19440515
Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs. PMID:19423640
Web-queryable large-scale data sets for hypothesis generation in plant biology. PMID:19401381
KIRMES: kernel-based identification of regulatory modules in euchromatic sequences. PMID:19389732
Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks. PMID:19357200
Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes. PMID:19321712
Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. PMID:19210792
Participation of leaky ribosome scanning in protein dual targeting by alternative translation initiation in higher plants. PMID:19182105
Literature-curated protein interaction datasets. PMID:19116613
Male reproductive development: gene expression profiling of maize anther and pollen ontogeny. PMID:19099579
The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program. PMID:19084081
Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process. PMID:19074628
KAGIANA: an excel-based tool for retrieving summary information on Arabidopsis genes. PMID:19043069
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. PMID:19036790
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis. PMID:19015126
QuantPrime--a flexible tool for reliable high-throughput primer design for quantitative PCR. PMID:18976492
ATTED-II provides coexpressed gene networks for Arabidopsis. PMID:18953027
Insights into corn genes derived from large-scale cDNA sequencing. PMID:18937034
Unique genes in plants: specificities and conserved features throughout evolution. PMID:18847470
AthaMap, integrating transcriptional and post-transcriptional data. PMID:18842622
The Universal Protein Resource (UniProt) 2009. PMID:18836194
GabiPD: the GABI primary database--a plant integrative 'omics' database. PMID:18812395
Longer first introns are a general property of eukaryotic gene structure. PMID:18769727
Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. PMID:18710561
At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. PMID:18613972
Comparative proteomics of chloroplast envelopes from C3 and C4 plants reveals specific adaptations of the plastid envelope to C4 photosynthesis and candidate proteins required for maintaining C4 metabolite fluxes. PMID:18599648
A genome-wide 20 K citrus microarray for gene expression analysis. PMID:18598343
A community-based annotation framework for linking solanaceae genomes with phenomes. PMID:18539779
Functional analysis of a predicted flavonol synthase gene family in Arabidopsis. PMID:18467451
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. PMID:18467421
The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome PubMed citations: 335.

335 articles citing: The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome

Characterization and analysis of the promoter region of monodehydroascorbate reductase 4 (CpMDAR4) in papaya. PMID:35920937
Translating the Arabidopsis thaliana Peroxisome Proteome Insights to Solanum lycopersicum: Consensus Versus Diversity. PMID:35912119
Interaction of Nitrate Assimilation and Photorespiration at Elevated CO2. PMID:35845694
Genome-Wide Identification and Structural Characterization of Growth-Regulating Factors (GRFs) in Actinida eriantha and Actinidia chinensis. PMID:35807582
NAC transcription factors ATAF1 and ANAC055 affect the heat stress response in Arabidopsis. PMID:35787631
The rolB-transgenic Nicotiana tabacum plants exhibit upregulated ARF7 and ARF19 gene expression. PMID:35774625
Bookend: precise transcript reconstruction with end-guided assembly. PMID:35768836
Inferring functional communities from partially observed biological networks exploiting geometric topology and side information. PMID:35760826
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba. PMID:35758513
Recombination landscape divergence between populations is marked by larger low-recombining regions in domesticated rye. PMID:35687854
Genome-Wide Identification and Functional Characterization of Auxin Response Factor (ARF) Genes in Eggplant. PMID:35682898
Developing a bioinformatics pipeline for comparative protein classification analysis. PMID:35668373
Dissecting the Genetic Architecture of Carbon Partitioning in Sorghum Using Multiscale Phenotypes. PMID:35665170
Image-Based Analysis Revealing the Molecular Mechanism of Peroxisome Dynamics in Plants. PMID:35592252
Role of LOC_Os01g68450, Containing DUF2358, in Salt Tolerance Is Mediated via Adaptation of Absorbed Light Energy Dissipation. PMID:35567234
Deciphering Pleiotropic Signatures of Regulatory SNPs in Zea mays L. Using Multi-Omics Data and Machine Learning Algorithms. PMID:35563516
Genome-Wide Association Study and Genomic Selection for Proteinogenic Methionine in Soybean Seeds. PMID:35557723
Exploring synergies between plant metabolic modelling and machine learning. PMID:35521559
Comparative Analysis of the Chalcone-Flavanone Isomerase Genes in Six Citrus Species and Their Expression Analysis in Sweet Orange (Citrus sinensis). PMID:35495138
The Arabidopsis gene co-expression network. PMID:35492683
Genome-wide mediation analysis: an empirical study to connect phenotype with genotype via intermediate transcriptomic data in maize. PMID:35460234
Solanum galapagense-derived purple tomato fruit color is conferred by novel alleles of the anthocyanin fruit and atroviolacium loci. PMID:35449754
Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy. PMID:35449401
An interolog-based barley interactome as an integration framework for immune signaling. PMID:35435213
TE Density: a tool to investigate the biology of transposable elements. PMID:35413944
Linnemannia elongata (Mortierellaceae) stimulates Arabidopsis thaliana aerial growth and responses to auxin, ethylene, and reactive oxygen species. PMID:35413060
The Sunflower WRINKLED1 Transcription Factor Regulates Fatty Acid Biosynthesis Genes through an AW Box Binding Sequence with a Particular Base Bias. PMID:35406952
Harmonizing model organism data in the Alliance of Genome Resources. PMID:35380658
SEED LIPID DROPLET PROTEIN1, SEED LIPID DROPLET PROTEIN2, and LIPID DROPLET PLASMA MEMBRANE ADAPTOR mediate lipid droplet-plasma membrane tethering. PMID:35348751
Tissue-Specific Expression of the Terpene Synthase Family Genes in Rosa chinensis and Effect of Abiotic Stress Conditions. PMID:35328100
Detection and Analysis of Syntenic Quantitative Trait Loci Controlling Cell Wall Quality in Angiosperms. PMID:35310628
Signaling Mechanisms by Arabidopsis Cryptochromes. PMID:35295637
Identification of Putative Markers of Non-infectious Bud Failure in Almond [Prunus dulcis (Mill.) D.A. Webb] Through Genome Wide DNA Methylation Profiling and Gene Expression Analysis in an Almond × Peach Hybrid Population. PMID:35237284
Antifungal activity of an artificial peptide aptamer SNP-D4 against Fusarium oxysporum. PMID:35223198
Comparative analysis of differential gene expression indicates divergence in ontogenetic strategies of leaves in two conifer genera. PMID:35222971
Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. PMID:35218346
An in-frame deletion mutation in the degron tail of auxin coreceptor IAA2 confers resistance to the herbicide 2,4-D in Sisymbrium orientale. PMID:35217601
Identification of the CesA Subfamily and Functional Analysis of GhMCesA35 in Gossypium hirsutum L. PMID:35205337
Systems scale characterization of circadian rhythm pathway in Camellia sinensis. PMID:35116135
The Grape Gene Reference Catalogue as a Standard Resource for Gene Selection and Genetic Improvement. PMID:35111182
SorghumBase: a web-based portal for sorghum genetic information and community advancement. PMID:35015132
NHX Gene Family in Camellia sinensis: In-silico Genome-Wide Identification, Expression Profiles, and Regulatory Network Analysis. PMID:34987532
Foster thy young: enhanced prediction of orphan genes in assembled genomes. PMID:34928390
qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE). PMID:34911434
Evidence for thermosensitivity of the cotton (Gossypium hirsutum L.) immature fiber (im) mutant via hypersensitive stomatal activity. PMID:34898615
Both Binding Strength and Evolutionary Accessibility Affect the Population Frequency of Transcription Factor Binding Sequences in Arabidopsis thaliana. PMID:34894231
Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection. PMID:34875081
Heterochromatin is a quantitative trait associated with spontaneous epiallele formation. PMID:34845222
Genomic Regions Associated with Fusarium Wilt Resistance in Flax. PMID:34830265
Successful intergeneric transfer of a major apple scab resistance gene (Rvi6) from apple to pear and precise comparison of the downstream molecular mechanisms of this resistance in both species. PMID:34802418
Primer Designing for Amplifying an AT-Rich Promoter from Arabidopsis thaliana. PMID:34773619
In-silico genome wide analysis of Mitogen activated protein kinase kinase kinase gene family in C. sinensis. PMID:34735479
PCMDB: a curated and comprehensive resource of plant cell markers. PMID:34718712
Arabidopsis thaliana PrimPol is a primase and lesion bypass DNA polymerase with the biochemical characteristics to cope with DNA damage in the nucleus, mitochondria, and chloroplast. PMID:34663822
Delayed Protein Changes During Seed Germination. PMID:34603360
Genome report: a draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics. PMID:34599816
RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation. PMID:34551440
Genomic impact of stress-induced transposable element mobility in Arabidopsis. PMID:34551439
The rice EP3 and OsFBK1 E3 ligases alter plant architecture and flower development, and affect transcript accumulation of microRNA pathway genes and their targets. PMID:34543503
Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives. PMID:34540375
Data Management and Modeling in Plant Biology. PMID:34539712
Genome-Wide Association Study of Seed Folate Content in Common Bean. PMID:34531882
Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements. PMID:34503979
Vision, challenges and opportunities for a Plant Cell Atlas. PMID:34491200
Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data. PMID:34484307
Crosstalk between the chloroplast protein import and SUMO systems revealed through genetic and molecular investigation in Arabidopsis. PMID:34473053
Dissection of Allelic Variation Underlying Floral and Fruit Traits in Flare Tree Peony (Paeonia rockii) Using Association Mapping. PMID:34456963
Pathway conversion enables a double-lock mechanism to maintain DNA methylation and genome stability. PMID:34453006
Finding differentially expressed sRNA-Seq regions with srnadiff. PMID:34415926
Extended mining of the oil biosynthesis pathway in biofuel plant Jatropha curcas by combined analysis of transcriptome and gene interactome data. PMID:34407772
A primary cell wall cellulose-dependent defense mechanism against vascular pathogens revealed by time-resolved dual transcriptomics. PMID:34404410
Comprehensive in silico Characterization of Universal Stress Proteins in Rice (Oryza sativa L.) With Insight Into Their Stress-Specific Transcriptional Modulation. PMID:34394169
Lipid Body Dynamics in Shoot Meristems: Production, Enlargement, and Putative Organellar Interactions and Plasmodesmal Targeting. PMID:34367200
The meristem-associated endosymbiont Methylorubrum extorquens DSM13060 reprograms development and stress responses of pine seedlings. PMID:34328183
Large-scale translatome profiling annotates the functional genome and reveals the key role of genic 3' untranslated regions in translatomic variation in plants. PMID:34327320
Genotype-Specific Expression and NLR Repertoire Contribute to Phenotypic Resistance Diversity in Plantago lanceolata. PMID:34322142
Functional Diversification of euANT/PLT Genes in Oryza sativa Panicle Architecture Determination. PMID:34305984
Multi-omics approach highlights differences between RLP classes in Arabidopsis thaliana. PMID:34284718
Dynamic Regulatory Event Mining by iDREM in Large-Scale Multi-omics Datasets During Biotic and Abiotic Stress in Plants. PMID:34251627
The Plastid-Localized AtFtsHi3 Pseudo-Protease of Arabidopsis thaliana Has an Impact on Plant Growth and Drought Tolerance. PMID:34249066
Loss of inner-envelope K+/H+ exchangers impairs plastid rRNA maturation and gene expression. PMID:34235544
Genome-Wide Investigation of N6-Methyladenosine Regulatory Genes and Their Roles in Tea (Camellia sinensis) Leaves During Withering Process. PMID:34211493
Network-based analysis of virulence factors for uncovering Aeromonas veronii pathogenesis. PMID:34162325
Extensive Variation in Drought-Induced Gene Expression Changes Between Loblolly Pine Genotypes. PMID:34140968
Transcriptomic Analysis of Resistant and Susceptible Responses in a New Model Root-Knot Nematode Infection System Using Solanum torvum and Meloidogyne arenaria. PMID:34122492
De novo activated transcription of inserted foreign coding sequences is inheritable in the plant genome. PMID:34111139
R2DT is a framework for predicting and visualising RNA secondary structure using templates. PMID:34108470
Origin and Evolution of the Cannabinoid Oxidocyclase Gene Family. PMID:34100927
From Microscopy to Nanoscopy: Defining an Arabidopsis thaliana Meiotic Atlas at the Nanometer Scale. PMID:34084178
noisyR: enhancing biological signal in sequencing datasets by characterizing random technical noise. PMID:34076236
Identification of cis-regulatory motifs in first introns and the prediction of intron-mediated enhancement of gene expression in Arabidopsis thaliana. PMID:34039279
Unravelling the molecular basis of the dominant negative effect of myosin XI tails on P-bodies. PMID:34038472
Gene Ontology Meta Annotator for Plants (GOMAP). PMID:34034755
TGIF-DB: terse genomics interface for developing botany. PMID:33985559
The amino acid permease (AAP) genes CsAAP2A and SlAAP5A/B are required for oomycete susceptibility in cucumber and tomato. PMID:33934492
Annotation and Molecular Characterisation of the TaIRO3 and TaHRZ Iron Homeostasis Genes in Bread Wheat (Triticum aestivum L.). PMID:33925484
Predictive Models of Genetic Redundancy in Arabidopsis thaliana. PMID:33871641
Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce. PMID:33846635
A multilayered cross-species analysis of GRAS transcription factors uncovered their functional networks in plant adaptation to the environment. PMID:33842016
The Candidate Photoperiod Gene MtFE Promotes Growth and Flowering in Medicago truncatula. PMID:33841463
Arabidopsis thaliana Genes Associated with Cucumber mosaic virus Virulence and Their Link to Virus Seed Transmission. PMID:33801693
Transcriptional Regulatory Networks Associate with Early Stages of Potato Virus X Infection of Solanum tuberosum. PMID:33799566
Genome-wide identification and functional characterization of the PheE2F/DP gene family in Moso bamboo. PMID:33781213
The Arabidopsis SMALL AUXIN UP RNA32 Protein Regulates ABA-Mediated Responses to Drought Stress. PMID:33777065
EORNA, a barley gene and transcript abundance database. PMID:33767193
Genome-wide identification of MIKC-type genes related to stamen and gynoecium development in Liriodendron. PMID:33753780
Genome-wide analysis of AP2/ERF superfamily in lotus (Nelumbo nucifera) and the association between NnADAP and rhizome morphology. PMID:33750315
Argonaute 5 family proteins play crucial roles in the defence against Cymbidium mosaic virus and Odontoglossum ringspot virus in Phalaenopsis aphrodite subsp. formosana. PMID:33749125
Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure. PMID:33690630
Gene expression for secondary metabolite biosynthesis in hop (Humulus lupulus L.) leaf lupulin glands exposed to heat and low-water stress. PMID:33664420
Genome-wide analysis of fluoride exporter genes in plants. PMID:33643759
Fine mapping of a thrips resistance QTL in Capsicum and the role of diterpene glycosides in the underlying mechanism. PMID:33609141
Genetic mechanisms associated with floral initiation and the repressive effect of fruit on flowering in apple (Malus x domestica Borkh). PMID:33606701
Mapping rRNA 2'-O-methylations and identification of C/D snoRNAs in Arabidopsis thaliana plants. PMID:33596769
Transcriptome analysis reveals major transcriptional changes during regrowth after mowing of red clover (Trifolium pratense). PMID:33588756
A Pipeline towards the Biochemical Characterization of the Arabidopsis GT14 Family. PMID:33572987
Genome-wide analysis of growth-regulating factors (GRFs) in Triticum aestivum. PMID:33552727
Multiscale plant modeling: from genome to phenome and beyond. PMID:33543231
Impact of Long-Term Organic and Mineral Fertilization on Rhizosphere Metabolites, Root-Microbial Interactions and Plant Health of Lettuce. PMID:33519736
Genome-wide characterization of the WAK gene family and expression analysis under plant hormone treatment in cotton. PMID:33509085
De Novo Mutation and Rapid Protein (Co-)evolution during Meiotic Adaptation in Arabidopsis arenosa. PMID:33502506
Analyzing the G3BP-like gene family of Arabidopsis thaliana in early turnip mosaic virus infection. PMID:33500425
Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance. PMID:33483627
Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana. PMID:33444439
A Comprehensive Transcriptional Profiling of Pepper Responses to Root-Knot Nematode. PMID:33333784
Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes in Arabidopsis thaliana. PMID:33322028
Computing on Phenotypic Descriptions for Candidate Gene Discovery and Crop Improvement. PMID:33313544
Dual targeting of DDX3 and eIF4A by the translation inhibitor rocaglamide A. PMID:33296667
Classification of Grain Amaranths Using Chromosome-Level Genome Assembly of Ramdana, A. hypochondriacus. PMID:33262776
Identification of the enzymes responsible for m2,2G and acp3U formation on cytosolic tRNA from insects and plants. PMID:33253256
Sugar Signaling and Post-transcriptional Regulation in Plants: An Overlooked or an Emerging Topic? PMID:33224165
Genome-Wide Analysis of the Five Phosphate Transporter Families in Camelina sativa and Their Expressions in Response to Low-P. PMID:33171866
Genome-Wide Identification and Functional Characterization of the Cation Proton Antiporter (CPA) Family Related to Salt Stress Response in Radish (Raphanus sativus L.). PMID:33158201
SATMF Suppresses the Premature Senescence Phenotype of the ATM Loss-of-Function Mutant and Improves Its Fertility in Arabidopsis. PMID:33143308
Determinants of correlated expression of transcription factors and their target genes. PMID:33104784
OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. PMID:33084874
From landrace to modern hybrid broccoli: the genomic and morphological domestication syndrome within a diverse B. oleracea collection. PMID:33082966
NAMS webserver: coding potential assessment and functional annotation of plant transcripts. PMID:33080021
Computational Identification and Comparative Analysis of Conserved miRNAs and Their Putative Target Genes in the Juglans regia and J. microcarpa Genomes. PMID:33050178
TERMINAL FLOWER 1-FD complex target genes and competition with FLOWERING LOCUS T. PMID:33046692
Genome-wide identification and characterization of ABA receptor PYL gene family in rice. PMID:32998689
A systematic comparison of chloroplast genome assembly tools. PMID:32988404
Genomic Prediction Informed by Biological Processes Expands Our Understanding of the Genetic Architecture Underlying Free Amino Acid Traits in Dry Arabidopsis Seeds. PMID:32978264
tRNA ADENOSINE DEAMINASE 3 is required for telomere maintenance in Arabidopsis thaliana. PMID:32959123
MAPK cascade gene family in Camellia sinensis: In-silico identification, expression profiles and regulatory network analysis. PMID:32894062
The Absence of C-5 DNA Methylation in Leishmania donovani Allows DNA Enrichment from Complex Samples. PMID:32824654
The Existence and Localization of Nuclear snoRNAs in Arabidopsis thaliana Revisited. PMID:32806552
Calcium Binding by Arabinogalactan Polysaccharides Is Important for Normal Plant Development. PMID:32769130
Contiguous and stochastic CHH methylation patterns of plant DRM2 and CMT2 revealed by single-read methylome analysis. PMID:32762764
Family-Specific Gains and Losses of Protein Domains in the Legume and Grass Plant Families. PMID:32694909
The oilseed rape developmental expression resource: a resource for the investigation of gene expression dynamics during the floral transition in oilseed rape. PMID:32693783
In vivo Reporters for Visualizing Alternative Splicing of Hormonal Genes. PMID:32650629
VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development. PMID:32646368
Computational analysis of microarray data of Arabidopsis thaliana challenged with Alternaria brassicicola for identification of key genes in Brassica. PMID:32607787
Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera). PMID:32601059
Network-guided search for genetic heterogeneity between gene pairs. PMID:32573681
Abundant expression of maternal siRNAs is a conserved feature of seed development. PMID:32541052
A two-tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae. PMID:32477841
mmannot: How to improve small-RNA annotation? PMID:32463818
Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe-microbe interaction networks in plant leaves. PMID:32405027
Identification and expression analysis of the DREB transcription factor family in pineapple (Ananas comosus (L.) Merr.). PMID:32377449
Loss of function of CRT1a (calreticulin) reduces plant susceptibility to Verticillium longisporum in both Arabidopsis thaliana and oilseed rape (Brassica napus). PMID:32358986
Genetic Architecture of Early Vigor Traits in Wild Soybean. PMID:32354037
Genetic controls of short- and long-term stomatal CO2 responses in Arabidopsis thaliana. PMID:32296835
Evolutionary and biochemical analyses reveal conservation of the Brassicaceae telomerase ribonucleoprotein complex. PMID:32271752
Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments. PMID:32265943
Using multiple reference genomes to identify and resolve annotation inconsistencies. PMID:32264824
Splicing conservation signals in plant long noncoding RNAs. PMID:32241834
The Position and Complex Genomic Architecture of Plant T-DNA Insertions Revealed by 4SEE. PMID:32235482
Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways. PMID:32213639
Lack of endoplasmic reticulum quality control (ERQC) promotes tonoplast (TP) targeting of KORRIGAN 1 (KOR1). PMID:32195619
Root Skewing-Associated Genes Impact the Spaceflight Response of Arabidopsis thaliana. PMID:32194611
Specific functions for Mediator complex subunits from different modules in the transcriptional response of Arabidopsis thaliana to abiotic stress. PMID:32193425
The beta Subunit of Nascent Polypeptide Associated Complex Plays A Role in Flowers and Siliques Development of Arabidopsis thaliana. PMID:32192231
Distinctive Gene Expression Patterns Define Endodormancy to Ecodormancy Transition in Apricot and Peach. PMID:32180783
Evaluation of Seven Different RNA-Seq Alignment Tools Based on Experimental Data from the Model Plant Arabidopsis thaliana. PMID:32138290
In the presence of population structure: From genomics to candidate genes underlying local adaptation. PMID:32128123
Arabidopsis RanBP2-Type Zinc Finger Proteins Related to Chloroplast RNA Editing Factor OZ1. PMID:32121603
Major Changes in Plastid Protein Import and the Origin of the Chloroplastida. PMID:32088393
Mitochondrial DNA Repair in an Arabidopsis thaliana Uracil N-Glycosylase Mutant. PMID:32085412
Natural variation in DNA methylation homeostasis and the emergence of epialleles. PMID:32071208
Genome-wide association and epistatic interactions of flowering time in soybean cultivar. PMID:31968016
PAREameters: a tool for computational inference of plant miRNA-mRNA targeting rules using small RNA and degradome sequencing data. PMID:31943065
Cyberinfrastructure and resources to enable an integrative approach to studying forest trees. PMID:31892954
Common alleles of CMT2 and NRPE1 are major determinants of CHH methylation variation in Arabidopsis thaliana. PMID:31887137
Local adaptation of a dominant coastal tree to freshwater availability and solar radiation suggested by genomic and ecophysiological approaches. PMID:31882752
GenFam: A web application and database for gene family-based classification and functional enrichment analysis. PMID:31844835
TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome. PMID:31831861
Investigations into a putative role for the novel BRASSIKIN pseudokinases in compatible pollen-stigma interactions in Arabidopsis thaliana. PMID:31829135
Leaf status and environmental signals jointly regulate proline metabolism in winter oilseed rape. PMID:31807778
Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts. PMID:31775622
Advances in Omics Approaches for Abiotic Stress Tolerance in Tomato. PMID:31775241
The effector GpRbp-1 of Globodera pallida targets a nuclear HECT E3 ubiquitin ligase to modulate gene expression in the host. PMID:31756029
Transcriptomic and evolutionary analysis of the mechanisms by which P. argentatum, a rubber producing perennial, responds to drought. PMID:31722667
The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response. PMID:31721759
The Acetate Pathway Supports Flavonoid and Lipid Biosynthesis in Arabidopsis. PMID:31719153
Further Elucidation of the Argonaute and Dicer Protein Families in the Model Grass Species Brachypodium distachyon. PMID:31708948
MaGenDB: a functional genomics hub for Malvaceae plants. PMID:31665439
Double triage to identify poorly annotated genes in maize: The missing link in community curation. PMID:31658277
Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.). PMID:31651257
Novel Informatic Tools to Support Functional Annotation of the Durum Wheat Genome. PMID:31649706
Spatially resolved transcriptomics reveals plant host responses to pathogens. PMID:31624491
Complex Horticultural Quality Traits in Broccoli Are Illuminated by Evaluation of the Immortal BolTBDH Mapping Population. PMID:31620146
Effect of Salt Stress on Cytosine Methylation within GL2, An Arabidopsis thaliana Gene Involved in Root Epidermal Cell Differentiation. Absence of Inheritance in the Unstressed Progeny. PMID:31509941
Critical Review of Plant Cell Wall Matrix Polysaccharide Glycosyltransferase Activities Verified by Heterologous Protein Expression. PMID:31379900
Comparative transcriptomics enables the identification of functional orthologous genes involved in early leaf growth. PMID:31361386
Genome-wide analysis of the NF-Y gene family in peach (Prunus persica L.). PMID:31349783
Isolation of Open Chromatin Identifies Regulators of Systemic Acquired Resistance. PMID:31337712
Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. PMID:31328773
Transcriptional Regulation of the Glucose-6-Phosphate/Phosphate Translocator 2 Is Related to Carbon Exchange Across the Chloroplast Envelope. PMID:31316533
CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis. PMID:31282937
Separating Golgi Proteins from Cis to Trans Reveals Underlying Properties of Cisternal Localization. PMID:31266899
artMAP: A user-friendly tool for mapping ethyl methanesulfonate-induced mutations in Arabidopsis. PMID:31245783
Waterlogging affects plant morphology and the expression of key genes in tef (Eragrostis tef). PMID:31245721
Maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER). PMID:31245718
Genome of the tropical plant Marchantia inflexa: implications for sex chromosome evolution and dehydration tolerance. PMID:31217536
Construction and analysis of an interologous protein-protein interaction network of Camellia sinensis leaf (TeaLIPIN) from RNA-Seq data sets. PMID:31197449
Loss of Wood Formation Genes in Monocot Genomes. PMID:31173081
Lateral Root Initiation in the Parental Root Meristem of Cucurbits: Old Players in a New Position. PMID:31110507
Cercis: A Non-polyploid Genomic Relic Within the Generally Polyploid Legume Family. PMID:31105714
Admixture mapping in interspecific Populus hybrids identifies classes of genomic architectures for phytochemical, morphological and growth traits. PMID:31104343
Identification of a role for an E6-like 1 gene in early pollen-stigma interactions in Arabidopsis thaliana. PMID:31069543
Lasy-Seq: a high-throughput library preparation method for RNA-Seq and its application in the analysis of plant responses to fluctuating temperatures. PMID:31068632
Effect of long-term organic and mineral fertilization strategies on rhizosphere microbiota assemblage and performance of lettuce. PMID:30990945
The auxin response factor gene family in allopolyploid Brassica napus. PMID:30958842
The unified rule of phyllotaxis explaining both spiral and non-spiral arrangements. PMID:30958198
A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. PMID:30940818
Tasselseed5 overexpresses a wound-inducible enzyme, ZmCYP94B1, that affects jasmonate catabolism, sex determination, and plant architecture in maize. PMID:30937397
Construction of the First SNP-Based Linkage Map Using Genotyping-by-Sequencing and Mapping of the Male-Sterility Gene in Leaf Chicory. PMID:30915092
Selection and validation of reference genes for quantitative Real-Time PCR in Arabis alpina. PMID:30830921
Transcriptomics Identifies Modules of Differentially Expressed Genes and Novel Cyclotides in Viola pubescens. PMID:30828342
Structural introspection of a putative fluoride transporter in plants. PMID:30800614
RNA-Seq reveals new DELLA targets and regulation in transgenic GA-insensitive grapevines. PMID:30777012
Development and validation of whole genome-wide and genic microsatellite markers in oil palm (Elaeis guineensis Jacq.): First microsatellite database (OpSatdb). PMID:30760842
Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs. PMID:30760640
Isoprene Acts as a Signaling Molecule in Gene Networks Important for Stress Responses and Plant Growth. PMID:30760638
A galling insect activates plant reproductive programs during gall development. PMID:30755671
Resistant and susceptible cacao genotypes exhibit defense gene polymorphism and unique early responses to Phytophthora megakarya inoculation. PMID:30739243
Genome wide analysis of W-box element in Arabidopsis thaliana reveals TGAC motif with genes down regulated by heat and salinity. PMID:30737427
First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.). PMID:30727959
Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry. PMID:30715294
A member of the CONSTANS-Like protein family is a putative regulator of reactive oxygen species homeostasis and spaceflight physiological adaptation. PMID:30705745
The Systems Architecture of Molecular Memory in Poplar after Abiotic Stress. PMID:30705134
Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds. PMID:30700268
Robust predictions of specialized metabolism genes through machine learning. PMID:30674669
Fine-mapping and validation of the genomic region underpinning pear red skin colour. PMID:30651990
Glycosyltransferase Family 61 in Liliopsida (Monocot): The Story of a Gene Family Expansion. PMID:30619412
Identification and characterisation of hypomethylated DNA loci controlling quantitative resistance in Arabidopsis. PMID:30608232
TCO, a Putative Transcriptional Regulator in Arabidopsis, Is a Target of the Protein Kinase CK2. PMID:30597831
Genome wide characterization of barley NAC transcription factors enables the identification of grain-specific transcription factors exclusive for the Poaceae family of monocotyledonous plants. PMID:30592743
Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map. PMID:30504416
Genome-Wide Analysis of LRR-RLK Gene Family in Four Gossypium Species and Expression Analysis during Cotton Development and Stress Responses. PMID:30501109
IRSOM, a reliable identifier of ncRNAs based on supervised self-organizing maps with rejection. PMID:30423081
Long-Read Annotation: Automated Eukaryotic Genome Annotation Based on Long-Read cDNA Sequencing. PMID:30401722
Global Analysis of WOX Transcription Factor Gene Family in Brassica napus Reveals Their Stress- and Hormone-Responsive Patterns. PMID:30400610
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. PMID:30395277
Genetic and transcriptional variations in NRAMP-2 and OPAQUE1 genes are associated with salt stress response in wheat. PMID:30392081
Overlapping Patterns of Gene Expression Between Gametophyte and Sporophyte Phases in the Fern Polypodium amorphum (Polypodiales). PMID:30356815
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
Mediator of tolerance to abiotic stress ERF6 regulates susceptibility of Arabidopsis to Meloidogyne incognita. PMID:30160354
RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of fully mycoheterotrophic plants. PMID:30092758
Comparative root transcriptome of wild Arachis reveals NBS-LRR genes related to nematode resistance. PMID:30081841
Short-Term Exposure to Nitrogen Dioxide Provides Basal Pathogen Resistance. PMID:30076223
GWAS with Heterogeneous Data: Estimating the Fraction of Phenotypic Variation Mediated by Gene Expression Data. PMID:30068524
Searching for best lower dimensional visualization angles for high dimensional RNA-Seq data. PMID:30013849
PAREsnip2: a tool for high-throughput prediction of small RNA targets from degradome sequencing data using configurable targeting rules. PMID:30007348
Spatio-temporal expression dynamics differ between homologues of flowering time genes in the allopolyploid Brassica napus. PMID:29989238
A comprehensive review of web-based resources of non-coding RNAs for plant science research. PMID:29989090
A genome-wide scan for correlated mutations detects macromolecular and chromatin interactions in Arabidopsis thaliana. PMID:29986106
Hub Protein Controversy: Taking a Closer Look at Plant Stress Response Hubs. PMID:29922309
Network biology discovers pathogen contact points in host protein-protein interactomes. PMID:29899369
Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant. PMID:29873777
Genetic differentiation in life history traits and thermal stress performance across a heterogeneous dune landscape in Arabidopsis lyrata. PMID:29846507
Robustness of Transposable Element Regulation but No Genomic Shock Observed in Interspecific Arabidopsis Hybrids. PMID:29788048
Enhanced Conjugation of Auxin by GH3 Enzymes Leads to Poor Adventitious Rooting in Carnation Stem Cuttings. PMID:29755501
The nonstop decay and the RNA silencing systems operate cooperatively in plants. PMID:29672715
Plant Glycine-Rich Proteins in Stress Response: An Emerging, Still Prospective Story. PMID:29568308
FERTILIZATION-INDEPENDENT SEED-Polycomb Repressive Complex 2 Plays a Dual Role in Regulating Type I MADS-Box Genes in Early Endosperm Development. PMID:29523711
Transcriptome analysis of response to Plasmodiophora brassicae infection in the Arabidopsis shoot and root. PMID:29304736
LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. PMID:29233850
Optimization of PCR conditions for amplifying an AT-rich amino acid transporter promoter sequence with high number of tandem repeats from Arabidopsis thaliana. PMID:29183338
Identification and Initial Characterization of the Effectors of an Anther Smut Fungus and Potential Host Target Proteins. PMID:29165363
Defense against Reactive Carbonyl Species Involves at Least Three Subcellular Compartments Where Individual Components of the System Respond to Cellular Sugar Status. PMID:29150548
Nucleotide patterns aiding in prediction of eukaryotic promoters. PMID:29141011
NONCODEV5: a comprehensive annotation database for long non-coding RNAs. PMID:29140524
A Role for the F-Box Protein HAWAIIAN SKIRT in Plant microRNA Function. PMID:29114080
Extreme Suppression of Lateral Floret Development by a Single Amino Acid Change in the VRS1 Transcription Factor. PMID:29101279
POTAGE: A Visualisation Tool for Speeding up Gene Discovery in Wheat. PMID:29085014
Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti. PMID:29078296
A sensitive short read homology search tool for paired-end read sequencing data. PMID:29072140
The transcriptome, extracellular proteome and active secretome of agroinfiltrated Nicotiana benthamiana uncover a large, diverse protease repertoire. PMID:29055088
Reference genome assessment from a population scale perspective: an accurate profile of variability and noise. PMID:28961772
Evidence-based gene models for structural and functional annotations of the oil palm genome. PMID:28886750
Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation. PMID:28814974
Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower. PMID:28814644
ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology. PMID:28808136
Global temporal dynamic landscape of pathogen-mediated subversion of Arabidopsis innate immunity. PMID:28798368
Identification of Conserved and Novel MicroRNAs in Blueberry. PMID:28713413
Relationships between drought, heat and air humidity responses revealed by transcriptome-metabolome co-analysis. PMID:28693422
Generation of a Collection of Mutant Tomato Lines Using Pooled CRISPR Libraries. PMID:28646085
Plant cell wall glycosyltransferases: High-throughput recombinant expression screening and general requirements for these challenging enzymes. PMID:28598995
Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species. PMID:28589392
Noncanonical Alternative Polyadenylation Contributes to Gene Regulation in Response to Hypoxia. PMID:28559476
Molecular dynamics simulations reveal the conformational dynamics of Arabidopsis thaliana BRI1 and BAK1 receptor-like kinases. PMID:28559283
Genome Wide Identification of Orthologous ZIP Genes Associated with Zinc and Iron Translocation in Setaria italica. PMID:28555148
The plant cell-wall enzyme AtXTH3 catalyses covalent cross-linking between cellulose and cello-oligosaccharide. PMID:28443615
ChloroKB: A Web Application for the Integration of Knowledge Related to Chloroplast Metabolic Network. PMID:28442501
HopBase: a unified resource for Humulus genomics. PMID:28415075
Improving transcriptome de novo assembly by using a reference genome of a related species: Translational genomics from oil palm to coconut. PMID:28334050
De novo computational identification of stress-related sequence motifs and microRNA target sites in untranslated regions of a plant translatome. PMID:28276452
Specific Caleosin/Peroxygenase and Lipoxygenase Activities Are Tissue-Differentially Expressed in Date Palm (Phoenix dactylifera L.) Seedlings and Are Further Induced Following Exposure to the Toxin 2,3,7,8-tetrachlorodibenzo-p-dioxin. PMID:28111588
TOMATOMICS: A Web Database for Integrated Omics Information in Tomato. PMID:28111364
Transcriptomic evidence for the control of soybean root isoflavonoid content by regulation of overlapping phenylpropanoid pathways. PMID:28077078
Evolution of protein N-glycosylation process in Golgi apparatus which shapes diversity of protein N-glycan structures in plants, animals and fungi. PMID:28074929
Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes. PMID:28069893
A Machine Learning Approach to Predict Gene Regulatory Networks in Seed Development in Arabidopsis. PMID:28066488
Plant genome and transcriptome annotations: from misconceptions to simple solutions. PMID:28062412
PPero, a Computational Model for Plant PTS1 Type Peroxisomal Protein Prediction. PMID:28045983
Atypical Protein Phosphatase 2A Gene Families Do Not Expand via Paleopolyploidization. PMID:28034953
Enhancing the GABI-Kat Arabidopsis thaliana T-DNA Insertion Mutant Database by Incorporating Araport11 Annotation. PMID:28013277
The BioGRID interaction database: 2017 update. PMID:27980099
Transcriptomic Effects of the Cell Cycle Regulator LGO in Arabidopsis Sepals. PMID:27920789
Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum. PMID:27917941
RNAcentral: a comprehensive database of non-coding RNA sequences. PMID:27794554
CoSpliceNet: a framework for co-splicing network inference from transcriptomics data. PMID:27793091
Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis. PMID:27791167
The state of play in higher eukaryote gene annotation. PMID:27773922
Importance of Translocon Subunit Tic56 for rRNA Processing and Chloroplast Ribosome Assembly. PMID:27733515
A De Novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny. PMID:27711162
Comparative analysis of Cucurbita pepo metabolism throughout fruit development in acorn squash and oilseed pumpkin. PMID:27688889
Telling plant species apart with DNA: from barcodes to genomes. PMID:27481790
MATH-Domain Family Shows Response toward Abiotic Stress in Arabidopsis and Rice. PMID:27446153
phRAIDER: Pattern-Hunter based Rapid Ab Initio Detection of Elementary Repeats. PMID:27307619
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model. PMID:26989150
WormBase 2016: expanding to enable helminth genomic research. PMID:26578572
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model PubMed citations: 19.

19 articles citing: Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model

New reasons for biologists to write with a formal language. PMID:35657112
System Principles Governing the Organization, Architecture, Dynamics, and Evolution of Gene Regulatory Networks. PMID:35646858
Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases. PMID:34251419
Identifying protein subcellular localisation in scientific literature using bidirectional deep recurrent neural network. PMID:33462256
Current status of the multinational Arabidopsis community. PMID:32775952
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. PMID:32652120
Wikidata as a knowledge graph for the life sciences. PMID:32180547
Ewé: a web-based ethnobotanical database for storing and analysing data. PMID:32052012
AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. PMID:31695717
Double triage to identify poorly annotated genes in maize: The missing link in community curation. PMID:31658277
Comparative Transcriptome Analysis of Pinus densiflora Following Inoculation with Pathogenic (Bursaphelenchus xylophilus) or Non-pathogenic Nematodes (B. thailandae). PMID:31434977
Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. PMID:31328773
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
Dynamic modeling of transcriptional gene regulatory network uncovers distinct pathways during the onset of Arabidopsis leaf senescence. PMID:30181903
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. PMID:28472432
ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium. PMID:28053168
Crowd-sourcing and author submission as alternatives to professional curation. PMID:28025340
AtPID: a genome-scale resource for genotype-phenotype associations in Arabidopsis. PMID:27899679
Prediction of Protein-Protein Interactions by Evidence Combining Methods. PMID:27879651
Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes PubMed citations: 17.

17 articles citing: Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes

GrainGenes: a data-rich repository for small grains genetics and genomics. PMID:35616118
GURFAP: A Platform for Gene Function Analysis in Glycyrrhiza Uralensis. PMID:35495163
ABI5 binding protein2 inhibits ABA responses during germination without ABA-INSENSITIVE5 degradation. PMID:35258597
The DUF221 domain-containing (DDP) genes identification and expression analysis in tomato under abiotic and phytohormone stress. PMID:34379048
Molecular Traits and Functional Analysis of the CLAVATA3/Endosperm Surrounding Region-Related Small Signaling Peptides in Three Species of Gossypium Genus. PMID:34149772
Building a successful international research community through data sharing: The case of the Wheat Information System (WheatIS). PMID:33763204
The prohibitins (PHB) gene family in tomato: Bioinformatic identification and expression analysis under abiotic and phytohormone stresses. PMID:33678114
GelFAP: Gene Functional Analysis Platform for Gastrodia elata. PMID:33193491
TaDrAp1 and TaDrAp2, Partner Genes of a Transcription Repressor, Coordinate Plant Development and Drought Tolerance in Spelt and Bread Wheat. PMID:33167455
A Genome-Wide Survey of MATE Transporters in Brassicaceae and Unveiling Their Expression Profiles under Abiotic Stress in Rapeseed. PMID:32825473
Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase. PMID:32185395
Unraveling candidate genes underlying biomass digestibility in elephant grass (Cenchrus purpureus). PMID:31822283
Transcription factor BnaA9.WRKY47 contributes to the adaptation of Brassica napus to low boron stress by up-regulating the boric acid channel gene BnaA3.NIP5;1. PMID:31705705
Plant Reactome: a knowledgebase and resource for comparative pathway analysis. PMID:31680153
An Undergraduate Research Project Utilizing CRISPR-Cas9 Gene Editing Technology to Study Gene Function in Arabidopsis thaliana. PMID:31316687
CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis. PMID:31282937
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679

Using the Arabidopsis information resource (TAIR) to find information about Arabidopsis genes PubMed citations: 15.

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More detailed information about this field from each metasource.

dna sequence data
metasource: Fairsharing.org
version: FAIRsharing.org: TAIR; The Arabidopsis Information Resource; DOI: https://doi.org/10.25504/FAIRsharing.4dqw0; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

gene
metasource: Fairsharing.org
version: FAIRsharing.org: TAIR; The Arabidopsis Information Resource; DOI: https://doi.org/10.25504/FAIRsharing.4dqw0; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

gene expression data
metasource: Fairsharing.org
version: FAIRsharing.org: TAIR; The Arabidopsis Information Resource; DOI: https://doi.org/10.25504/FAIRsharing.4dqw0; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

genetic map
metasource: Fairsharing.org
version: FAIRsharing.org: TAIR; The Arabidopsis Information Resource; DOI: https://doi.org/10.25504/FAIRsharing.4dqw0; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: re3data.org
version: re3data.org: The Arabidopsis Information Resource; editing status 2021-09-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QW21 last accessed: 2022-11-04

genome map
metasource: Fairsharing.org
version: FAIRsharing.org: TAIR; The Arabidopsis Information Resource; DOI: https://doi.org/10.25504/FAIRsharing.4dqw0; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

molecular structure
metasource: Fairsharing.org
version: FAIRsharing.org: TAIR; The Arabidopsis Information Resource; DOI: https://doi.org/10.25504/FAIRsharing.4dqw0; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

physical map
metasource: Fairsharing.org
version: FAIRsharing.org: TAIR; The Arabidopsis Information Resource; DOI: https://doi.org/10.25504/FAIRsharing.4dqw0; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: re3data.org
version: re3data.org: The Arabidopsis Information Resource; editing status 2021-09-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QW21 last accessed: 2022-11-04

publication
metasource: Fairsharing.org
version: FAIRsharing.org: TAIR; The Arabidopsis Information Resource; DOI: https://doi.org/10.25504/FAIRsharing.4dqw0; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

structure
metasource: Fairsharing.org
version: FAIRsharing.org: TAIR; The Arabidopsis Information Resource; DOI: https://doi.org/10.25504/FAIRsharing.4dqw0; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

bioinformatics
metasource: re3data.org
version: re3data.org: The Arabidopsis Information Resource; editing status 2021-09-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QW21 last accessed: 2022-11-04

clones
metasource: re3data.org
version: re3data.org: The Arabidopsis Information Resource; editing status 2021-09-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QW21 last accessed: 2022-11-04

data mining proteins
metasource: re3data.org
version: re3data.org: The Arabidopsis Information Resource; editing status 2021-09-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QW21 last accessed: 2022-11-04

gene expression
metasource: re3data.org
version: re3data.org: The Arabidopsis Information Resource; editing status 2021-09-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QW21 last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:56.409468

genetic markers
metasource: re3data.org
version: re3data.org: The Arabidopsis Information Resource; editing status 2021-09-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QW21 last accessed: 2022-11-04

genome sequence
metasource: re3data.org
version: re3data.org: The Arabidopsis Information Resource; editing status 2021-09-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QW21 last accessed: 2022-11-04

genomics
metasource: re3data.org
version: re3data.org: The Arabidopsis Information Resource; editing status 2021-09-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QW21 last accessed: 2022-11-04

germ plasm
metasource: re3data.org
version: re3data.org: The Arabidopsis Information Resource; editing status 2021-09-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QW21 last accessed: 2022-11-04

ontology
metasource: re3data.org
version: re3data.org: The Arabidopsis Information Resource; editing status 2021-09-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QW21 last accessed: 2022-11-04

taxonomy
metasource: re3data.org
version: re3data.org: The Arabidopsis Information Resource; editing status 2021-09-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QW21 last accessed: 2022-11-04

plant biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:56.409468

model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:56.409468

sequence assembly
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:56.409468

gene transcripts
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:56.409468

dna sequences gene gene expression genetic map genome map molecular structure physical map publication structure bioinformatics clones data mining proteins gene expression genetic markers genome sequence genomics germ plasm ontology taxonomy plant biology model organisms sequence assembly gene transcripts

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Arabidopsis Information Portal

TAIR annotation data Format

The Arabidopsis Gene Regulatory Information Server

Database of Arabidopsis Transcription Factors

Arabidopsis MPSS

Nottingham Arabidopsis Stock Centre Seeds Database

CATMA - Complete Arabidopsis Transcriptome MicroArray

AraPheno

Arabidopsis Mitochondrial Protein Database

RARGE - RIKEN Arabidopsis Genome Encyclopedia

NASCarrays (obsolete)

ASRP - Arabidopsis Small RNA Project

Arabidopsis Nucleolar Protein Database

Gene Product Information Format

AtPID

AthaMap

MAtDB2

Arabidopsis Hormone Database

SeedGenes

RIKEN Arabidopsis Genome Encyclopedia II