Long noncoding RNAs in the model species Brachypodium distachyon

scientific article published on 12 September 2017

Long noncoding RNAs in the model species Brachypodium distachyon is …
instance of (P31):
scholarly articleQ13442814

External links are
P6179Dimensions Publication ID1091575814
P356DOI10.1038/S41598-017-11206-Z
P932PMC publication ID5595811
P698PubMed publication ID28900227

P50authorEdoardo BertoliniQ56056815
P2093author name stringMario Enrico Pè
Concetta De Quattro
P2860cites workMicrosatellites are preferentially associated with nonrepetitive DNA in plant genomesQ47319442
Discovery and annotation of long noncoding RNAsQ47573961
A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysisQ48068201
Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.).Q50589433
Widespread long noncoding RNAs as endogenous target mimics for microRNAs in plants.Q50758425
Interplay of SLIM1 and miR395 in the regulation of sulfate assimilation in Arabidopsis.Q54604638
Cutadapt removes adapter sequences from high-throughput sequencing readsQ55953584
miRNA Target Prediction in PlantsQ57822735
Primary transcripts of microRNAs encode regulatory peptidesQ59085442
Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolutionQ63640716
CACTA transposons in Triticeae. A diverse family of high-copy repetitive elementsQ73392630
An extensive evaluation of read trimming effects on Illumina NGS data analysisQ21559489
The rise of regulatory RNAQ22121998
The landscape of long noncoding RNAs in the human transcriptomeQ22122065
Genome sequencing and analysis of the model grass Brachypodium distachyonQ22122196
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expressionQ24608592
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and CufflinksQ24633890
TopHat: discovering splice junctions with RNA-SeqQ24655505
Rfam: an RNA family databaseQ24682045
Promoter features related to tissue specificity as measured by Shannon entropyQ24797793
Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNAQ25255243
Biogenesis, turnover, and mode of action of plant microRNAsQ26824566
RNA-Seq technology and its application in fish transcriptomicsQ26825688
A survey of the sorghum transcriptome using single-molecule long readsQ27315231
Genome regulation by long noncoding RNAs.Q27691812
edgeR: a Bioconductor package for differential expression analysis of digital gene expression dataQ27860819
Biogenesis of small RNAs in animalsQ27861013
The transcriptional landscape of the mammalian genomeQ27861110
Target mimicry provides a new mechanism for regulation of microRNA activityQ28237268
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolutionQ28241731
Pfam: the protein families databaseQ28660698
miRBase: annotating high confidence microRNAs using deep sequencing dataQ28660701
Clusters and superclusters of phased small RNAs in the developing inflorescence of riceQ28752065
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclassesQ29547647
VISTA: computational tools for comparative genomicsQ29547708
HTSeq--a Python framework to work with high-throughput sequencing dataQ29614489
CD-HIT: accelerated for clustering the next-generation sequencing dataQ29616664
A unified classification system for eukaryotic transposable elementsQ29617222
Molecular mechanisms of long noncoding RNAsQ29618027
sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification softwareQ30000664
Genome-wide identification and functional analysis of lincRNAs acting as miRNA targets or decoys in maizeQ30387313
Defining diversity, specialization, and gene specificity in transcriptomes through information theoryQ33349697
Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyonQ33481324
An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence dataQ33518463
Genome-wide discovery and characterization of maize long non-coding RNAs.Q33742695
The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAsQ33967993
The Sequence Read Archive: explosive growth of sequencing data.Q34051179
Discovery of Novel Leaf Rust Responsive microRNAs in Wheat and Prediction of Their Target GenesQ34087955
Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa.Q34089339
SQUAMOSA Promoter‐Binding Protein‐Like Transcription Factors: Star Players for Plant Growth and DevelopmentQ34145908
Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA.Q34153107
Functional interactions among microRNAs and long noncoding RNAsQ34175339
Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencingQ34202641
Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolutionQ34242790
Target mimics: an embedded layer of microRNA-involved gene regulatory networks in plantsQ34276382
Transcriptomics in the RNA-seq era.Q34320924
Computational identification and functional predictions of long noncoding RNA in Zea maysQ34391260
Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis.Q34470818
Addressing the role of microRNAs in reprogramming leaf growth during drought stress in Brachypodium distachyon.Q34522259
Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of riceQ34622310
Boron stress responsive microRNAs and their targets in barleyQ34651503
Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAsQ34699808
Software for computing and annotating genomic rangesQ34945230
Pervasive transcription of the eukaryotic genome: functional indices and conceptual implicationsQ35004344
Large-scale collection and analysis of full-length cDNAs from Brachypodium distachyon and integration with Pooideae sequence resourcesQ35018240
Pseudogene-derived lncRNAs: emerging regulators of gene expressionQ35048014
Translational dynamics revealed by genome-wide profiling of ribosome footprints in ArabidopsisQ35075061
Long non-coding RNAs as a source of new peptidesQ35176562
Spatiotemporally dynamic, cell-type-dependent premeiotic and meiotic phasiRNAs in maize anthers.Q35189973
A dynamic evolutionary and functional landscape of plant phased small interfering RNAs.Q35633301
A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid riceQ35787178
RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato fruit ripeningQ35867012
The many faces of long noncoding RNAsQ35903450
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.Q35914259
Rapid evolutionary turnover underlies conserved lncRNA-genome interactionsQ36480899
Transposable elements reveal a stem cell-specific class of long noncoding RNAsQ36633093
The biological effects of simple tandem repeats: lessons from the repeat expansion diseasesQ37204533
Genome-wide analysis of tandem repeats in plants and green algaeQ37460744
The long-distance signaling of mineral macronutrientsQ37501215
Identification of new stress-induced microRNA and their targets in wheat using computational approach.Q37529681
lincRNAs: genomics, evolution, and mechanismsQ37584905
Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in ArabidopsisQ37614942
Long noncoding RNA: unveiling hidden layer of gene regulatory networksQ37959132
Classification and comparison of small RNAs from plantsQ38075011
The four dimensions of noncoding RNA conservation.Q38194745
Long noncoding RNAs in spermatogenesis: insights from recent high-throughput transcriptome studiesQ38203075
Evolutionary dynamics of coding and non-coding transcriptomesQ38258263
Battles and hijacks: noncoding transcription in plants.Q38409814
Circular RNAs: Identification, biogenesis and function.Q38546674
The specificity of long noncoding RNA expressionQ38571483
Long non-coding RNAs and their functions in plants.Q38581513
Unique features of long non-coding RNA biogenesis and functionQ38668939
Salmon provides fast and bias-aware quantification of transcript expressionQ38926825
Evolution to the rescue: using comparative genomics to understand long non-coding RNAsQ38940313
Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural featuresQ38972100
Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines.Q39029280
Molecular and physiological analysis of growth-limiting drought stress in Brachypodium distachyon leavesQ39546662
Construction and analysis of cardiac hypertrophy-associated lncRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in cardiac hypertrophyQ40001300
Sequence-based estimation of minisatellite and microsatellite repeat variabilityQ40815198
Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species.Q40955031
Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon.Q41514063
Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencingQ41856334
A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in ArabidopsisQ42636436
The compact Brachypodium genome conserves centromeric regions of a common ancestor with wheat and riceQ42675374
Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb targetQ45101053
Correction: From Chemistry to Behavior. Molecular Structure and Bioactivity of Repellents against Ixodes ricinus TicksQ45849186
A miRNA involved in phosphate-starvation response in ArabidopsisQ46219280
P2507corrigendum / erratumPublisher Correction: Long noncoding RNAs in the model species Brachypodium distachyonQ96640135
P4510describes a project that usesedgeRQ113334690
P433issue1
P407language of work or nameEnglishQ1860
P921main subjectmodel organismQ213907
Brachypodium distachyonQ2352209
P304page(s)11252
P577publication date2017-09-12
P1433published inScientific ReportsQ2261792
P1476titleLong noncoding RNAs in the model species Brachypodium distachyon
P478volume7

Reverse relations

cites work (P2860)
Q92836887An Overview of Methodologies in Studying lncRNAs in the High-Throughput Era: When Acronyms ATTACK!
Q89474942Genome-wide identification and characterization of mRNAs and lncRNAs involved in cold stress in the wild banana (Musa itinerans)
Q90745769Long Non-coding RNA in Plants in the Era of Reference Sequences
Q92085561Prediction of regulatory long intergenic non-coding RNAs acting in trans through base-pairing interactions
Q97419158The regulatory landscape of early maize inflorescence development
Q64079551Transcriptome Analysis Suggests the Roles of Long Intergenic Non-coding RNAs in the Growth Performance of Weaned Piglets
Q92591365Transcriptome and Phytochemical Analyses Provide New Insights Into Long Non-Coding RNAs Modulating Characteristic Secondary Metabolites of Oolong Tea (Camellia sinensis) in Solar-Withering
Q55300097Transposon-Derived Non-coding RNAs and Their Function in Plants.

Search more.