Related references
Note: Only part of the references are listed.Role of RNA silencing in plant-viroid interactions and in viroid pathogenesis
Francesco Di Serio et al.
VIRUS RESEARCH (2023)
Interpretation of network-based integration from multi-omics longitudinal data
Antoine Bodein et al.
NUCLEIC ACIDS RESEARCH (2022)
Insights into the Transcriptional Reprogramming in Tomato Response to PSTVd Variants Using Network Approaches
Katia Avina-Padilla et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)
Cytosine Methylation in Genomic DNA and Characterization of DNA Methylases and Demethylases and Their Expression Profiles in Viroid-Infected Hop Plants (Humulus lupulus Var. 'Celeia')
Andrej Secnik et al.
CELLS (2022)
Hop stunt viroid: A polyphagous pathogenic RNA that has shed light on viroid-host interactions
Joan Marquez-Molins et al.
MOLECULAR PLANT PATHOLOGY (2021)
Multi-omics network-based functional annotation of unknown Arabidopsis genes
Thomas Depuydt et al.
PLANT JOURNAL (2021)
MicroRNA expression dynamics reshape the cultivar-specific response of pepper (Capsicum annuum L.) to potato spindle tuber viroid (PSTVd) infection
E. Apostolova et al.
SCIENTIA HORTICULTURAE (2021)
sRNAanno-a database repository of uniformly annotated small RNAs in plants
Chengjie Chen et al.
HORTICULTURE RESEARCH (2021)
Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value
Tinashe Zenda et al.
FRONTIERS IN PLANT SCIENCE (2021)
Degradome Analysis of Tomato and Nicotiana benthamiana Plants Infected with Potato Spindle Tuber Viroid
Beatriz Navarro et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)
Next-Generation Sequencing Identification and Characterization of MicroRNAs in Dwarfed Citrus Trees Infected With Citrus Dwarfing Viroid in High-Density Plantings
Tyler Dang et al.
FRONTIERS IN MICROBIOLOGY (2021)
Viroids as a Tool to Study RNA-Directed DNA Methylation in Plants
Michael Wassenegger et al.
CELLS (2021)
Applications of Multi-Omics Technologies for Crop Improvement
Yaodong Yang et al.
FRONTIERS IN PLANT SCIENCE (2021)
Advances in Viroid-Host Interactions
Beatriz Navarro et al.
ANNUAL REVIEW OF VIROLOGY, VOL 8 (2021)
Current overview on viroid-host interactions
Charith Raj Adkar-Purushothama et al.
WILEY INTERDISCIPLINARY REVIEWS-RNA (2020)
Dynamic architecture and regulatory implications of the miRNA network underlying the response to stress in melon
Alejandro Sanz-Carbonell et al.
RNA BIOLOGY (2020)
Identification of MicroRNAs and Their Targets That Respond to Powdery Mildew Infection in Cucumber by Small RNA and Degradome Sequencing
Xuewen Xu et al.
FRONTIERS IN GENETICS (2020)
Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology
Ili Nadhirah Jamil et al.
FRONTIERS IN PLANT SCIENCE (2020)
Advances in Transcriptomics in the Response to Stress in Plants
Xiaojuan Wang et al.
GLOBAL MEDICAL GENETICS (2020)
Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon
Alejandro Sanz-Carbonell et al.
BMC PLANT BIOLOGY (2019)
Does co-transcriptional regulation of alternative splicing mediate plant stress responses?
Ibtissam Jabre et al.
NUCLEIC ACIDS RESEARCH (2019)
Epigenetics in the plant-virus interaction
Chenguang Wang et al.
PLANT CELL REPORTS (2019)
Evaluation of Disease Severity and Global Transcriptome Response Induced by Citrus bark cracking viroid, Hop latent viroid, and Their Co-Infection in Hop (Humulus lupulus L.)
Natasa Stajner et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2019)
Highly efficient construction of infectious viroid-derived clones
Joan Marquez-Molins et al.
PLANT METHODS (2019)
Small RNA sequencing identifies cucumber miRNA roles in waterlogging-triggered adventitious root primordia formation
Xuewen Xu et al.
MOLECULAR BIOLOGY REPORTS (2019)
Root Transcriptomic Analysis Reveals Global Changes Induced by Systemic Infection of Solanum lycopersicum with Mild and Severe Variants of Potato Spindle Tuber Viroid
Anna Gora-Sochacka et al.
VIRUSES-BASEL (2019)
RNAcentral: a hub of information for non-coding RNA sequences
Blake A. Sweeney et al.
NUCLEIC ACIDS RESEARCH (2019)
Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops
Yi Zheng et al.
NUCLEIC ACIDS RESEARCH (2019)
Stress response regulation by epigenetic mechanisms: changing of the guards
Maria Luz Annacondia et al.
PHYSIOLOGIA PLANTARUM (2018)
Pospiviroid Infection of Tomato Regulates the Expression of Genes Involved in Flower and Fruit Development
Katia Avina-Padilla et al.
VIRUSES-BASEL (2018)
Alternative Splicing in Plant Genes: A Means of Regulating the Environmental Fitness of Plants
Xudong Shang et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2017)
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
Yi Zheng et al.
JOURNAL OF VIROLOGY (2017)
Hop stunt viroid: Effect on Host (Humulus lupulus) Transcriptome and Its Interactions With Hop Powdery Mildew (Podospheara macularis)
Madhu Kappagantu et al.
MOLECULAR PLANT-MICROBE INTERACTIONS (2017)
Natural variation for gene expression responses to abiotic stress in maize
Amanda J. Waters et al.
PLANT JOURNAL (2017)
Global Transcriptomic Changes Induced by Infection of Cucumber (Cucumis sativus L.) with Mild and Severe Variants of Hop Stunt Viroid
Changjian Xia et al.
FRONTIERS IN MICROBIOLOGY (2017)
Editorial: Epigenetic Modifications Associated with Abiotic and Biotic Stresses in Plants: An Implication for Understanding Plant Evolution
Mahmoud W. Yaish
FRONTIERS IN PLANT SCIENCE (2017)
Genome-wide analysis of microRNA targeting impacted by SNPs in cucumber genome
Jian Ling et al.
BMC GENOMICS (2017)
DNA Methylation and Demethylation in Plant Immunity
A. Deleris et al.
ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 54 (2016)
Changes in the DNA methylation pattern of the host male gametophyte of viroid-infected cucumber plants
Mayte Castellano et al.
JOURNAL OF EXPERIMENTAL BOTANY (2016)
Epigenetic Mechanisms: An Emerging Player in Plant-Microbe Interactions
Qian-Hao Zhu et al.
MOLECULAR PLANT-MICROBE INTERACTIONS (2016)
A pathogenic long noncoding RNA redesigns the epigenetic landscape of the infected cells by subverting host Histone Deacetylase 6 activity
Mayte Castellano et al.
NEW PHYTOLOGIST (2016)
EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments
Olivia Wilkins et al.
PLANT CELL (2016)
Viroids, infectious long non-coding RNAs with autonomous replication
Selma Gago-Zachert
VIRUS RESEARCH (2016)
A nuclear-replicating viroid antagonizes infectivity and accumulation of a geminivirus by upregulating methylation-related genes and inducing hypermethylation of viral DNA
Enza Maria Torchetti et al.
SCIENTIFIC REPORTS (2016)
Insight on Genes Affecting Tuber Development in Potato upon Potato spindle tuber viroid (PSTVd) Infection
Konstantina Katsarou et al.
PLOS ONE (2016)
Replication of a pathogenic non-coding RNA increases DNA methylation in plants associated with a bromodomain-containing viroid-binding protein
Dian-Qiu Lv et al.
SCIENTIFIC REPORTS (2016)
Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions in Brachypodium distachyon
Kranthi K. Mandadi et al.
PLANT CELL (2015)
HTSeq-a Python framework to work with high-throughput sequencing data
Simon Anders et al.
BIOINFORMATICS (2015)
Changes in relative expression levels of viroid-specific small RNAs and microRNAs in tomato plants infected with severe and mild symptom-inducing isolates of Potato spindle tuber viroid
Daiki Tsushima et al.
JOURNAL OF GENERAL PLANT PATHOLOGY (2015)
NbClust: AnRPackage for Determining the Relevant Number of Clusters in a Data Set
Malika Charrad et al.
Journal of Statistical Software (2015)
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger et al.
BIOINFORMATICS (2014)
A pathogenic non-coding RNA induces changes in dynamic DNA methylation of ribosomal RNA genes in host plants
German Martinez et al.
NUCLEIC ACIDS RESEARCH (2014)
Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species
Adam Healey et al.
PLANT METHODS (2014)
Epigenetic Regulation in Plant Responses to the Environment
David C. Baulcombe et al.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2014)
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Michael I. Love et al.
GENOME BIOLOGY (2014)
Viroids: a light in the darkness of the lncRNA-directed regulatory networks in plants
Gustavo Gomez et al.
NEW PHYTOLOGIST (2013)
A remarkable synergistic effect at the transcriptomic level in peach fruits doubly infected by prunus necrotic ringspot virus and peach latent mosaic viroid
Mari Carmen Herranz et al.
VIROLOGY JOURNAL (2013)
Detecting differential usage of exons from RNA-seq data
Simon Anders et al.
GENOME RESEARCH (2012)
Microarray analysis of Etrog citron (Citrus medica L.) reveals changes in chloroplast, cell wall, peroxidase and symporter activities in response to viroid infection
Serena Rizza et al.
MOLECULAR PLANT PATHOLOGY (2012)
Global Analysis of Tomato Gene Expression During Potato spindle tuber viroid Infection Reveals a Complex Array of Changes Affecting Hormone Signaling
Robert A. Owens et al.
MOLECULAR PLANT-MICROBE INTERACTIONS (2012)
Epigenetics of Host-Pathogen Interactions: The Road Ahead and the Road Behind
Elena Gomez-Diaz et al.
PLOS PATHOGENS (2012)
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
Felix Krueger et al.
BIOINFORMATICS (2011)
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Manfred G. Grabherr et al.
NATURE BIOTECHNOLOGY (2011)
ggplot2
Hadley Wickham
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL STATISTICS (2011)
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
Mark D. Robinson et al.
BIOINFORMATICS (2010)
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan et al.
BIOINFORMATICS (2010)
Characterization of plant miRNAs and small RNAs derived from potato spindle tuber viroid (PSTVd) in infected tomato
Natalie Diermann et al.
BIOLOGICAL CHEMISTRY (2010)
Mechanisms of HDA6-mediated rRNA gene silencing: suppression of intergenic Pol II transcription and differential effects on maintenance versus siRNA-directed cytosine methylation
Keith W. Earley et al.
GENES & DEVELOPMENT (2010)
High-throughput sequencing of Hop stunt viroid-derived small RNAs from cucumber leaves and phloem
German Martinez et al.
MOLECULAR PLANT PATHOLOGY (2010)
The Biology of Viroid-Host Interactions
Biao Ding
Annual Review of Phytopathology (2009)
Deep Sequencing of the Small RNAs Derived from Two Symptomatic Variants of a Chloroplastic Viroid: Implications for Their Genesis and for Pathogenesis
Francesco Di Serio et al.
PLOS ONE (2009)
Deep Sequencing of Viroid-Derived Small RNAs from Grapevine Provides New Insights on the Role of RNA Silencing in Plant-Viroid Interaction
Beatriz Navarro et al.
PLOS ONE (2009)
Evolutionary Constraints to Viroid Evolution
Santiago F. Elena et al.
VIRUSES-BASEL (2009)
The post-transcriptional steps of eukaryotic ribosome biogenesis
A. K. Henras et al.
CELLULAR AND MOLECULAR LIFE SCIENCES (2008)
Characterization of small RNAs derived from Citrus exocortis viroid (CEVd) in infected tomato plants
Raquel Martin et al.
VIROLOGY (2007)
Mature monomeric forms of Hop stunt viroid resist RNA silencing in transgenic plants
G. Gomez et al.
PLANT JOURNAL (2007)
A structured viroid RNA serves as a substrate for dicer-like cleavage to produce biologically active small RNAs but is resistant to RNA-induced silencing complex-mediated degradation
Asuka Itaya et al.
JOURNAL OF VIROLOGY (2007)
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
TD Wu et al.
BIOINFORMATICS (2005)
A long-distance translocatable phloem protein from cucumber forms a ribonucleoprotein complex in vivo with Hop stunt viroid RNA
G Gómez et al.
JOURNAL OF VIROLOGY (2004)
Two chloroplastic viroids induce the accumulation of small RNAs associated with posttranscriptional gene silencing
AE Martínez de Alba et al.
JOURNAL OF VIROLOGY (2002)
Potato spindle tuber viroid strains of different pathogenicity induces and suppresses expression of common and unique genes in infected tomato
A Itaya et al.
MOLECULAR PLANT-MICROBE INTERACTIONS (2002)
Potato spindle tuber viroid as inducer of RNA silencing in infected tomato
A Itaya et al.
MOLECULAR PLANT-MICROBE INTERACTIONS (2001)
Identification of an in vitro ribonucleoprotein complex between a viroid RNA and a phloem protein from cucumber plants
G Gómez et al.
MOLECULAR PLANT-MICROBE INTERACTIONS (2001)
Replicating potato spindle tuber viroid RNA is accompanied by short RNA fragments that ave characteristic of post-transcriptional gene silencing
I Papaefthimiou et al.
NUCLEIC ACIDS RESEARCH (2001)