Genome Wide Identification and Functional Prediction of Long Non-Coding RNAs Responsive to Sclerotinia sclerotiorum Infection in Brassica napus

A global study of transcriptome dynamics in canola (Brassica napus L.) responsive to Sclerotinia sclerotiorum infection using RNA-Seq

(2016) Raj Kumar Joshi et al.   GENE

iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data

(2016) Kun Sun et al.   BMC GENOMICS

Characterization of miRNAs associated with Botrytis cinerea infection of tomato leaves

(2015) Weibo Jin et al.   BMC PLANT BIOLOGY

Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits

(2015) Huan Wang et al.   PLANT JOURNAL

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

(2014) H. Wang et al.   GENOME RESEARCH

Natural Antisense Transcripts and Long Non-Coding RNA in Neurospora crassa

(2014) Yamini Arthanari et al.   PLoS One

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

(2014) Wei Zhang et al.   PLoS One

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

Contribution of Small RNA Pathway Components in Plant Immunity

(2013) Jang-Kyun Seo et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts

(2013) Sarah Geisler et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Long noncoding RNAs responsive toFusarium oxysporuminfection inArabidopsis thaliana

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

NONCODEv4: exploring the world of long non-coding RNA genes

(2013) Chaoyong Xie 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

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study

(2012) Lei Sun et al.   BMC BIOINFORMATICS

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

(2012) Tingting Lu et al.   BMC GENOMICS

Small RNAs in development – insights from plants

(2012) Xuemei Chen   CURRENT OPINION IN GENETICS & DEVELOPMENT

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Transcriptional analysis of the Arabidopsis ovule by massively parallel signature sequencing

(2012) Nidia Sánchez-León et al.   JOURNAL OF EXPERIMENTAL BOTANY

RNA Polymerase II Collision Interrupts Convergent Transcription

(2012) David J. Hobson et al.   MOLECULAR CELL

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat

(2012) Claudia Carrieri et al.   NATURE

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

(2012) Cole Trapnell et al.   Nature Protocols

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

(2012) J. Liu et al.   PLANT CELL

Functions of microRNAs in plant stress responses

(2012) Ramanjulu Sunkar et al.   TRENDS IN PLANT SCIENCE

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences

(2011) Yonggan Wu et al.   BMC BIOINFORMATICS

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

Genome-wide profiling of novel and conserved Populus microRNAs involved in pathogen stress response by deep sequencing

(2011) Lei Chen et al.   PLANTA

Long noncoding RNA: unveiling hidden layer of gene regulatory networks

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

Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

(2011) Joelle Amselem et al.   PLoS Genetics

Small RNAs are on the move

(2010) Daniel H. Chitwood et al.   NATURE

Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA

(2010) J. B. Heo et al.   SCIENCE

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Long noncoding RNAs: functional surprises from the RNA world

(2009) J. E. Wilusz et al.   GENES & DEVELOPMENT

Patterns of differential gene expression inBrassica napuscultivars infected withSclerotinia sclerotiorum

(2009) JIANWEI ZHAO et al.   MOLECULAR PLANT PATHOLOGY

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

(2009) Szymon Swiezewski et al.   NATURE

Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs

(2009)   NATURE

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

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

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

Proteome Changes in Leaves of Brassica napus L. as a Result of Sclerotinia sclerotiorum Challenge

(2008) Yue Liang et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Zm401, a short-open reading-frame mRNA or noncoding RNA, is essential for tapetum and microspore development and can regulate the floret formation in maize

(2008) Jinxia Ma et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS