Genome-Wide Transcriptomic Analysis Reveals Insights into the Response to Citrus bark cracking viroid (CBCVd) in Hop (Humulus lupulus L.)

Transcriptome analysis reveals potential genes involved in flower pigmentation in a red-flowered mutant of white clover ( Trifolium repens L.)

(2018) Heshan Zhang et al.   GENOMICS

Time-Course Microarray Analysis Reveals Differences between Transcriptional Changes in Tomato Leaves Triggered by Mild and Severe Variants of Potato Spindle Tuber Viroid

(2018) Aneta Więsyk et al.   Viruses-Basel

Genome-wide transcriptome profiling of transgenic hop (Humulus lupulus L.) constitutively overexpressing HlWRKY1 and HlWDR1 transcription factors

(2018) Ajay Kumar Mishra et al.   BMC GENOMICS

Propagation and some physiological effects of Citrus bark cracking viroid and Apple fruit crinkle viroid in multiple infected hop ( Humulus lupulus L.)

(2017) J. Matoušek et al.   JOURNAL OF PLANT PHYSIOLOGY

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

(2017) Yi Zheng et al.   JOURNAL OF VIROLOGY

Chloroplast: the Trojan horse in plant-virus interaction

(2017) Dhriti Bhattacharyya et al.   MOLECULAR PLANT PATHOLOGY

Hop stunt viroid: Effect on Host (Humulus lupulus) Transcriptome and Its Interactions With Hop Powdery Mildew (Podospheara macularis)

(2017) Madhu Kappagantu et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Global Transcriptomic Changes Induced by Infection of Cucumber (Cucumis sativus L.) with Mild and Severe Variants of Hop Stunt Viroid

(2017) Changjian Xia et al.   Frontiers in Microbiology

Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing Approach for In-depth Understanding of Genes in Secondary Metabolism Pathways of Camellia sinensis

(2017) Qingshan Xu et al.   Frontiers in Plant Science

Development of hop transcriptome to support research into host-viroid interactions

(2017) Tine Pokorn et al.   PLoS One

Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity

(2016) Renesh Bedre et al.   BMC GENOMICS

Identification and characterization of microRNAs in Humulus lupulus using high-throughput sequencing and their response to Citrus bark cracking viroid (CBCVd) infection

(2016) Ajay Kumar Mishra et al.   BMC GENOMICS

Two Faces of One Seed: Hormonal Regulation of Dormancy and Germination

(2016) Kai Shu et al.   Molecular Plant

The “putative” role of transcription factors from HlWRKY family in the regulation of the final steps of prenylflavonid and bitter acids biosynthesis in hop (Humulus lupulus L.)

(2016) Jaroslav Matoušek et al.   PLANT MOLECULAR BIOLOGY

Reactive oxygen species, essential molecules, during plant–pathogen interactions

(2016) Daymi Camejo et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Plant Virus Infection and the Ubiquitin Proteasome Machinery: Arms Race along the Endoplasmic Reticulum

(2016) Jeanmarie Verchot   Viruses-Basel

The impact of phytohormones on virus infection and disease

(2016) Tamara D Collum et al.   Current Opinion in Virology

Citrus leprosis virus C Infection Results in Hypersensitive-Like Response, Suppression of the JA/ET Plant Defense Pathway and Promotion of the Colonization of Its Mite Vector

(2016) Gabriella D. Arena et al.   Frontiers in Plant Science

Insight on Genes Affecting Tuber Development in Potato upon Potato spindle tuber viroid (PSTVd) Infection

(2016) Konstantina Katsarou et al.   PLoS One

Salicylic Acid Is Involved in the Basal Resistance of Tomato Plants to Citrus Exocortis Viroid and Tomato Spotted Wilt Virus

(2016) M. Pilar López-Gresa et al.   PLoS One

Transcriptome Analysis of Nine Tissues to Discover Genes Involved in the Biosynthesis of Active Ingredients in Sophora flavescens

(2015) Rongchun Han et al.   BIOLOGICAL & PHARMACEUTICAL BULLETIN

Cucumber Necrosis Virus Recruits Cellular Heat Shock Protein 70 Homologs at Several Stages of Infection

(2015) Syed Benazir Alam et al.   JOURNAL OF VIROLOGY

NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data

(2015) Jianguo Xia et al.   Nature Protocols

Deep-sequencing revealedCitrus bark cracking viroid(CBCVd) as a highly aggressive pathogen on hop

(2015) J. Jakse et al.   PLANT PATHOLOGY

De novo and comparative transcriptome analysis of cultivated and wild spinach

(2015) Chenxi Xu et al.   Scientific Reports

Current status of viroid taxonomy

(2014) F. Di Serio et al.   ARCHIVES OF VIROLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A Metabolic Profiling Strategy for the Dissection of Plant Defense against Fungal Pathogens

(2014) Konstantinos A. Aliferis et al.   PLoS One

Advanced Heat Map and Clustering Analysis Using Heatmap3

(2014) Shilin Zhao et al.   Biomed Research International

The ER quality control and ER associated degradation machineries are vital for viral pathogenesis

(2014) Jeanmarie Verchot   Frontiers in Plant Science

Tombusvirus-yeast interactions identify conserved cell-intrinsic viral restriction factors

(2014) Zsuzsanna Sasvari et al.   Frontiers in Plant Science

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

A remarkable synergistic effect at the transcriptomic level in peach fruits doubly infected by prunus necrotic ringspot virus and peach latent mosaic viroid

(2013) Mari Herranz et al.   Virology Journal

Plant immune response to pathogens differs with changing temperatures

(2013) Cheng Cheng et al.   Nature Communications

Biological and molecular analysis of the pathogenic variant C3 of potato spindle tuber viroid (PSTVd) evolved during adaptation to chamomile (Matricaria chamomilla)

(2012) Jaroslav Matoušek et al.   BIOLOGICAL CHEMISTRY

Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells

(2012) Mingzhu Zhu et al.   BMC GENOMICS

Housekeeping Gene Selection for Real Time-PCR Normalization in Female Hop (Humulus lupulus L) Tissues

(2012) Lina Maloukh et al.   JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY

Involvement of the Chloroplastic Isoform of tRNA Ligase in the Replication of Viroids Belonging to the Family Avsunviroidae

(2012) M.-A. Nohales et al.   JOURNAL OF VIROLOGY

Microarray analysis of Etrog citron (Citrus medica L.) reveals changes in chloroplast, cell wall, peroxidase and symporter activities in response to viroid infection

(2012) SERENA RIZZA et al.   MOLECULAR PLANT PATHOLOGY

Global Analysis of Tomato Gene Expression DuringPotato spindle tuber viroidInfection Reveals a Complex Array of Changes Affecting Hormone Signaling

(2012) Robert A. Owens et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Small RNAs containing the pathogenic determinant of a chloroplast-replicating viroid guide the degradation of a host mRNA as predicted by RNA silencing

(2012) Beatriz Navarro et al.   PLANT JOURNAL

Flavonoids: biosynthesis, biological functions, and biotechnological applications

(2012) María L. Falcone Ferreyra et al.   Frontiers in Plant Science

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

High-throughput sequencing ofHop stunt viroid-derived small RNAs from cucumber leaves and phloem

(2010) GERMAN MARTINEZ et al.   MOLECULAR PLANT PATHOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

HSP70 and Its Cochaperone CPIP Promote Potyvirus Infection in Nicotiana benthamiana by Regulating Viral Coat Protein Functions

(2010) A. Hafren et al.   PLANT CELL

Viroids: self-replicating, mobile, and fast-evolving noncoding regulatory RNAs

(2010) Biao Ding   Wiley Interdisciplinary Reviews-RNA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

RNA-seq: from technology to biology

(2009) Samuel Marguerat et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments

(2009) S. A. Bustin et al.   CLINICAL CHEMISTRY

Hop (Humulus lupulus)-Derived Bitter Acids as Multipotent Bioactive Compounds

(2009) Marjan Van Cleemput et al.   JOURNAL OF NATURAL PRODUCTS

High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

(2008) Evandro Novaes et al.   BMC GENOMICS

Viroids

(2008) Efthimia Mina Tsagris et al.   CELLULAR MICROBIOLOGY

Pharmacognostic and pharmacological profile of Humulus lupulus L.

(2008) Paola Zanoli et al.   JOURNAL OF ETHNOPHARMACOLOGY

Analyzing real-time PCR data by the comparative CT method

(2008) Thomas D Schmittgen et al.   Nature Protocols

EST Analysis of Hop Glandular Trichomes Identifies an O-Methyltransferase That Catalyzes the Biosynthesis of Xanthohumol

(2008) J. Nagel et al.   PLANT CELL

Use, tolerance and avoidance of amplified RNA silencing by plants

(2008) Olivier Voinnet   TRENDS IN PLANT SCIENCE