LncRNA expression profile and ceRNA analysis in tomato during flowering

Identification of Gossypium hirsutum long non-coding RNAs (lncRNAs) under salt stress

(2018) Fenni Deng et al.   BMC PLANT BIOLOGY

psRNATarget: a plant small RNA target analysis server (2017 release)

(2018) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

CRISPR/Cas9-mediated mutagenesis of lncRNA1459 alters tomato fruit ripening

(2018) Ran Li et al.   PLANT JOURNAL

Uncovering novel landscape of cardiovascular diseases and therapeutic targets for cardioprotection via long noncoding RNA–miRNA–mRNA axes

(2018) Liang He et al.   Epigenomics

Integrative analysis of genome-wide lncRNA and mRNA expression in newly synthesized Brassica hexaploids

(2018) Ruihua Wang et al.   Ecology and Evolution

Genome-wide analysis of long non-coding RNAs in Catalpa bungei and their potential function in floral transition using high-throughput sequencing

(2018) Zhi Wang et al.   BMC GENETICS

Conservation analysis of long non-coding RNAs in plants

(2017) Pingchuan Deng et al.   Science China-Life Sciences

Modular function of long noncoding RNA, COLDAIR, in the vernalization response

(2017) Dong-Hwan Kim et al.   PLoS Genetics

Functions of plants long non-coding RNAs

(2016) Sarfraz Shafiq et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Linking Long Noncoding RNA Localization and Function

(2016) Ling-Ling Chen   TRENDS IN BIOCHEMICAL SCIENCES

Computational Approaches for Functional Prediction and Characterisation of Long Noncoding RNAs

(2016) Bethany Signal et al.   TRENDS IN GENETICS

Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network

(2016) Xi-Wen Xu et al.   Scientific Reports

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

Long Non-coding RNAs and Their Biological Roles in Plants

(2015) Xue Liu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

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

(2015) Jinyan Wang et al.   Scientific Reports

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) H. Wang 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

Functional Consequences of Splicing of the Antisense Transcript COOLAIR on FLC Transcription

(2014) Sebastian Marquardt et al.   MOLECULAR CELL

Genomic Features and Regulatory Roles of Intermediate-Sized Non-Coding RNAs in Arabidopsis

(2014) Yuqiu Wang et al.   Molecular Plant

Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control

(2014) Jean-Marc Celton et al.   NEW PHYTOLOGIST

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

(2014) Chao Di et al.   PLANT JOURNAL

Identification of Maize Long Non-Coding RNAs Responsive to Drought Stress

(2014) Wei Zhang 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

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

(2014) Lin Li et al.   GENOME BIOLOGY

Long noncoding RNAs: New regulators in plant development

(2013) Yu-Chan Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Global analysis of cis-natural antisense transcripts and their heat-responsive nat-siRNAs in Brassica rapa

(2013) Xiang Yu et al.   BMC PLANT BIOLOGY

Epigenetic regulation by long noncoding RNAs in plants

(2013) Jae Bok Heo et al.   CHROMOSOME RESEARCH

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data

(2013) S. Li et al.   GENOME RESEARCH

Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice

(2012) Tingting Lu et al.   BMC GENOMICS

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

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

(2012) Susan Boerner et al.   PLoS One

Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing

(2011) Mingming Xin et al.   BMC PLANT BIOLOGY

ceRNAs: miRNA Target Mimic Mimics

(2011) Ignacio Rubio-Somoza et al.   CELL

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

(2011) John R Prensner et al.   NATURE BIOTECHNOLOGY

Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network

(2011) Qi Liao et al.   NUCLEIC ACIDS RESEARCH

Long noncoding RNA: unveiling hidden layer of gene regulatory networks

(2011) Eun-Deok Kim et al.   TRENDS IN PLANT SCIENCE

Unexpected Diversity of Chloroplast Noncoding RNAs as Revealed by Deep Sequencing of the Arabidopsis Transcriptome

(2011) Amber M. Hotto et al.   G3-Genes Genomes Genetics

Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA

(2010) J. B. Heo et al.   SCIENCE

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

Computational prediction of novel non-coding RNAs in Arabidopsis thaliana

(2009) Dandan Song et al.   BMC BIOINFORMATICS

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa

(2008) X. Zhou et al.   GENOME RESEARCH

Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses

(2008) B. Ben Amor et al.   GENOME RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS