Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection

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 noncoding RNAs and their proposed functions in fibre development of cotton (Gossypiumspp.)

(2015) Maojun Wang et al.   NEW PHYTOLOGIST

GREENC: a Wiki-based database of plant lncRNAs

(2015) Andreu Paytuví Gallart et al.   NUCLEIC ACIDS RESEARCH

PANTHER version 10: expanded protein families and functions, and analysis tools

(2015) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Long Non-coding RNAs and Their Biological Roles in Plants

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

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

RNA regulatory networks in animals and plants: a long noncoding RNA perspective

(2014) Y. Bai et al.   Briefings in Functional Genomics

Long Noncoding RNA Modulates Alternative Splicing Regulators in Arabidopsis

(2014) Florian Bardou et al.   DEVELOPMENTAL CELL

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

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

Identification of microRNAs in six solanaceous plants and their potential link with phosphate and mycorrhizal signaling

(2014) Mian Gu et al.   Journal of Integrative Plant Biology

PNRD: a plant non-coding RNA database

(2014) Xin Yi et al.   NUCLEIC ACIDS RESEARCH

Arabidopsis RRP6L1 and RRP6L2 Function in FLOWERING LOCUS C Silencing via Regulation of Antisense RNA Synthesis

(2014) Jun-Hye Shin et al.   PLoS Genetics

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

(2014) Lin Li et al.   GENOME BIOLOGY

Long non-coding RNA-dependent transcriptional regulation in neuronal development and disease

(2014) Brian S. Clark et al.   Frontiers in Genetics

Long noncoding RNAs: New regulators in plant development

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

PLncDB: plant long non-coding RNA database

(2013) J. Jin et al.   BIOINFORMATICS

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

Long noncoding RNAs responsive toFusarium oxysporuminfection inArabidopsis thaliana

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

Colonization Patterns of an mCherry-TaggedPectobacterium carotovorumsubsp.brasilienseStrain in Potato Plants

(2013) Gugulethu C. Kubheka et al.   PHYTOPATHOLOGY

Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing

(2013) Xin Qi et al.   PLANT MOLECULAR BIOLOGY

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

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

Identification and Characterization of miRNA Transcriptome in Potato by High-Throughput Sequencing

(2013) Runxuan Zhang et al.   PLoS One

On the classification of long non-coding RNAs

(2013) Lina Ma et al.   RNA Biology

Towards revealing the functions of all genes in plants

(2013) Seung Yon Rhee et al.   TRENDS IN PLANT SCIENCE

The role of long non-coding RNA in transcriptional gene silencing

(2012) Andrzej T Wierzbicki   CURRENT OPINION IN PLANT BIOLOGY

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

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

(2012) Susan Boerner et al.   PLoS One

MicroRNA regulation of plant innate immune receptors

(2012) F. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

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

psRNATarget: a plant small RNA target analysis server

(2011) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

Exploring long non-coding RNAs through sequencing

(2011) Sophie R. Atkinson et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Long noncoding RNA: unveiling hidden layer of gene regulatory networks

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Identification, characterization and expression analysis of MicroRNAs and their targets in the potato (Solanum tuberosum)

(2010) Fuliang Xie et al.   GENE

Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA

(2010) J. B. Heo et al.   SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Computational prediction of novel non-coding RNAs in Arabidopsis thaliana

(2009) Dandan Song et al.   BMC BIOINFORMATICS

Pectobacterium carotovorum subsp. brasiliensis causing blackleg on potatoes in South Africa

(2009) Johanna J. van der Merwe et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

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

(2009) Szymon Swiezewski et al.   NATURE

Long non-coding RNAs: insights into functions

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

Computational identification of 48 potato microRNAs and their targets

(2008) Wenwei Zhang et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

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

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

Decoding genes with coexpression networks and metabolomics – ‘majority report by precogs’

(2007) Kazuki Saito et al.   TRENDS IN PLANT SCIENCE