Genome-wide identification of novel long non-coding RNAs in Populus tomentosa tension wood, opposite wood and normal wood xylem by RNA-seq

Negative regulation of lncRNA GAS5 by miR-21

(2013) Z Zhang et al.   CELL DEATH AND DIFFERENTIATION

PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors

(2013) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

Systematic Transcriptome Wide Analysis of lncRNA-miRNA Interactions

(2013) Saakshi Jalali et al.   PLoS One

Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells

(2013) A. A. Sigova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa

(2013) S. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gibberellin is required for the formation of tension wood and stem gravitropism in Acacia mangium seedlings

(2012) Widyanto Dwi Nugroho et al.   ANNALS OF BOTANY

Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs

(2012) Saakshi Jalali et al.   Biology Direct

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

Posttranscriptional Gene Regulation by Long Noncoding RNA

(2012) Je-Hyun Yoon et al.   JOURNAL OF MOLECULAR BIOLOGY

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

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

(2012) Cole Trapnell et al.   Nature Protocols

Leaf-Induced Gibberellin Signaling Is Essential for Internode Elongation, Cambial Activity, and Fiber Differentiation in Tobacco Stems

(2012) J. Dayan et al.   PLANT CELL

Deep Annotation of Populus trichocarpa microRNAs from Diverse Tissue Sets

(2012) Joshua R. Puzey et al.   PLoS One

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

(2012) Susan Boerner et al.   PLoS One

A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice

(2012) J. Ding et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Arabidopsis CSLD1 and CSLD4 are required for cellulose deposition and normal growth of pollen tubes

(2011) Wei Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

MicroRNA-148b is frequently down-regulated in gastric cancer and acts as a tumor suppressor by inhibiting cell proliferation

(2011) Yong-Xi Song et al.   Molecular Cancer

psRNATarget: a plant small RNA target analysis server

(2011) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

The actin multigene family in Populus: organization, expression and phylogenetic analysis

(2010) Deqiang Zhang et al.   MOLECULAR GENETICS AND GENOMICS

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

Crystal Structures of aPopulus tomentosa4-Coumarate:CoA Ligase Shed Light on Its Enzymatic Mechanisms

(2010) Yonglin Hu et al.   PLANT CELL

The sucrose synthase gene family in Populus: structure, expression, and evolution

(2010) Deqiang Zhang et al.   Tree Genetics & Genomes

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Non-coding RNAs: regulators of disease

(2009) Ryan J Taft et al.   JOURNAL OF PATHOLOGY

Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry

(2009) Allison M Bond et al.   NATURE NEUROSCIENCE

Long non-coding RNAs: insights into functions

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

ThePopulusGenome Integrative Explorer (PopGenIE): a new resource for exploring thePopulusgenome

(2009) Andreas Sjödin et al.   NEW PHYTOLOGIST

RNAplex: a fast tool for RNA–RNA interaction search

(2008) Hakim Tafer et al.   BIOINFORMATICS

Wood cell walls: biosynthesis, developmental dynamics and their implications for wood properties

(2008) E MELLEROWICZ et al.   CURRENT OPINION IN PLANT BIOLOGY

Criteria for Annotation of Plant MicroRNAs

(2008) B. C. Meyers et al.   PLANT CELL

Stress-responsive microRNAs inPopulus

(2008) Shanfa Lu et al.   PLANT JOURNAL

Suppression of 4-Coumarate-CoA Ligase in the Coniferous Gymnosperm Pinus radiata

(2008) A. Wagner et al.   PLANT PHYSIOLOGY

Functional Analysis of the Cellulose Synthase-Like Genes CSLD1, CSLD2, and CSLD4 in Tip-Growing Arabidopsis Cells

(2008) A. J. Bernal et al.   PLANT PHYSIOLOGY

Real-time PCR quantification of precursor and mature microRNA

(2007) Thomas D. Schmittgen et al.   METHODS