Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection

Genome-wide analysis of bHLH transcription factor and involvement in the infection by yellow leaf curl virus in tomato (Solanum lycopersicum)

(2015) Jinyan Wang et al.   BMC GENOMICS

RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato fruit ripening

(2015) Benzhong Zhu et al.   JOURNAL OF EXPERIMENTAL BOTANY

High-throughput sequencing reveals differential expression of miRNAs in tomato inoculated with Phytophthora infestans

(2015) Yushi Luan et al.   PLANTA

Small RNA and degradome sequencing reveals microRNAs and their targets involved in tomato pedicel abscission

(2015) Tao Xu et al.   PLANTA

Genome-Wide Identification, Characterization and Evolutionary Analysis of Long Intergenic Noncoding RNAs in Cucumber

(2015) Zhiqiang Hao et al.   PLoS One

Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis

(2014) H. Wang et al.   GENOME RESEARCH

Detection of Pol IV/RDR2-dependent transcripts at the genomic scale inArabidopsisreveals features and regulation of siRNA biogenesis

(2014) Shaofang Li et al.   GENOME RESEARCH

Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa

(2014) Peng Shuai et al.   JOURNAL OF EXPERIMENTAL BOTANY

Editorial

(2014) Henry Daniell   PLANT BIOTECHNOLOGY JOURNAL

Sly-miR166 and Sly-miR319 are components of the cold stress response in Solanum lycopersicum

(2014) Ehsan Valiollahi et al.   Plant Biotechnology Reports

Characterization of stress-responsive lncRNAs inArabidopsis thalianaby integrating expression, epigenetic and structural features

(2014) Chao Di et al.   PLANT JOURNAL

Genome-Wide Analysis of Soybean HD-Zip Gene Family and Expression Profiling under Salinity and Drought Treatments

(2014) Xue Chen et al.   PLoS One

AntisenseCOOLAIRmediates the coordinated switching of chromatin states atFLCduring vernalization

(2014) Tibor Csorba et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tomato yellow leaf curl virus resistance by Ty-1 involves increased cytosine methylation of viral genomes and is compromised by cucumber mosaic virus infection

(2014) P. Butterbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unconventionally secreted effectors of two filamentous pathogens target plant salicylate biosynthesis

(2014) Tingli Liu et al.   Nature Communications

Genome-wide discovery and characterization of maize long non-coding RNAs

(2014) Lin Li et al.   GENOME BIOLOGY

Long noncoding RNAs and the genetics of cancer

(2013) S W Cheetham et al.   BRITISH JOURNAL OF CANCER

Novel Long Noncoding RNAs Are Regulated by Angiotensin II in Vascular Smooth Muscle Cells

(2013) Amy Leung et al.   CIRCULATION RESEARCH

The Long Noncoding RNA RMST Interacts with SOX2 to Regulate Neurogenesis

(2013) Shi-Yan Ng et al.   MOLECULAR CELL

Long noncoding RNAs responsive toFusarium oxysporuminfection inArabidopsis thaliana

(2013) Qian-Hao Zhu et al.   NEW PHYTOLOGIST

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts

(2013) Liang Sun et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Widespread Long Noncoding RNAs as Endogenous Target Mimics for MicroRNAs in Plants

(2013) H.-J. Wu et al.   PLANT PHYSIOLOGY

Comparative Transcriptome Profiling of a Resistant vs. Susceptible Tomato (Solanum lycopersicum) Cultivar in Response to Infection by Tomato Yellow Leaf Curl Virus

(2013) Tianzi Chen et al.   PLoS One

The Tomato Yellow Leaf Curl Virus Resistance Genes Ty-1 and Ty-3 Are Allelic and Code for DFDGD-Class RNA–Dependent RNA Polymerases

(2013) Maarten G. Verlaan et al.   PLoS Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Small RNAs in development – insights from plants

(2012) Xuemei Chen   CURRENT OPINION IN GENETICS & DEVELOPMENT

Long noncoding RNAs in C. elegans

(2012) J.-W. Nam et al.   GENOME RESEARCH

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

PsRobot: a web-based plant small RNA meta-analysis toolbox

(2012) Hua-Jun Wu et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

(2012) J. Liu et al.   PLANT CELL

Involvement of microRNA-Mediated Gene Expression Regulation in the Pathological Development of Stem Canker Disease in Populus trichocarpa

(2012) Jia-Ping Zhao et al.   PLoS One

Computational Identification and Functional Predictions of Long Noncoding RNA in Zea mays

(2012) Susan Boerner et al.   PLoS One

miR165/166 and the development of land plants

(2011) Jun Sakaguchi et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

Top 10 plant viruses in molecular plant pathology

(2011) KAREN-BETH G. SCHOLTHOF et al.   MOLECULAR PLANT PATHOLOGY

Evolution and Functional Diversification ofMIRNAGenes

(2011) Josh T. Cuperus et al.   PLANT CELL

Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.)

(2010) Mingming Xin et al.   BMC PLANT BIOLOGY

miRNA expression patterns of Triticum dicoccoides in response to shock drought stress

(2010) Melda Kantar et al.   PLANTA

Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA

(2010) J. B. Heo et al.   SCIENCE

The long and the short of noncoding RNAs

(2009) Christopher A Brosnan et al.   CURRENT OPINION IN CELL BIOLOGY

Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target

(2009) Szymon Swiezewski et al.   NATURE

Molecular characterization and pathogenicity of tomato yellow leaf curl virus in China

(2009) Hui Zhang et al.   VIRUS GENES

MicroRNA166 controls root and nodule development in Medicago truncatula

(2008) Adnane Boualem et al.   PLANT JOURNAL

Developmental Role and Auxin Responsiveness of Class III Homeodomain Leucine Zipper Gene Family Members in Rice

(2008) J.-I. Itoh et al.   PLANT PHYSIOLOGY

Diamonds in the rough: mRNA-like non-coding RNAs

(2008) Linda A. Rymarquis et al.   TRENDS IN PLANT SCIENCE