Genome-wide identification and functional analysis of lincRNAs acting as miRNA targets or decoys in maize

High-throughput sequencing and degradome analysis reveal neutral evolution of Cercis gigantea microRNAs and their targets

(2015) Wenna Guo 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

Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing

(2014) Hongjun Liu et al.   BMC GENOMICS

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

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

Genome-wide identification and functional annotation of Plasmodium falciparum long noncoding RNAs from RNA-seq data

(2014) Qi Liao et al.   PARASITOLOGY RESEARCH

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

Competing endogenous RNAs (ceRNAs): new entrants to the intricacies of gene regulation

(2014) Reena V. Kartha et al.   Frontiers in Genetics

Combined small RNA and degradome sequencing reveals novel miRNAs and their targets in response to low nitrate availability in maize

(2013) Yongping Zhao et al.   ANNALS OF BOTANY

Potential roles of microRNAs in regulating long intergenic noncoding RNAs

(2013) Liran Juan et al.   BMC Medical Genomics

Emerging roles of microRNAs in the mediation of drought stress response in plants

(2013) Yanfei Ding et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

Systematic Transcriptome Wide Analysis of lncRNA-miRNA Interactions

(2013) Saakshi Jalali et al.   PLoS One

Nuclear microRNAs and their unconventional role in regulating non-coding RNAs

(2013) Hongwei Liang et al.   Protein & Cell

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Target mimics: an embedded layer of microRNA-involved gene regulatory networks in plants

(2012) Yijun Meng et al.   BMC GENOMICS

Unraveling the KNOTTED1 regulatory network in maize meristems

(2012) N. Bolduc et al.   GENES & DEVELOPMENT

Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents

(2012) A. Paschold et al.   GENOME RESEARCH

Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing

(2012) Tingting Li et al.   GENOMICS

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs

(2012) V. A. Moran et al.   NUCLEIC ACIDS RESEARCH

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

(2012) J. Liu et al.   PLANT CELL

Characterizing Regulatory and Functional Differentiation between Maize Mesophyll and Bundle Sheath Cells by Transcriptomic Analysis

(2012) Y.-M. Chang et al.   PLANT PHYSIOLOGY

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

(2012) Susan Boerner et al.   PLoS One

Molecular Functions of Long Non-Coding RNAs in Plants

(2012) Qian-Hao Zhu et al.   Genes

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 Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

(2011) Marcella Cesana et al.   CELL

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

(2011) Leonardo Salmena et al.   CELL

Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors

(2011) Shi-Yan Ng et al.   EMBO JOURNAL

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

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

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

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

Parent-of-Origin Effects on Gene Expression and DNA Methylation in the Maize Endosperm

(2011) A. J. Waters et al.   PLANT CELL

Regulation of Gene Expression in Plants through miRNA Inactivation

(2011) Sergey Ivashuta et al.   PLoS One

Utility of RNA Sequencing for Analysis of Maize Reproductive Transcriptomes

(2011) Rebecca M. Davidson et al.   Plant Genome

The developmental dynamics of the maize leaf transcriptome

(2010) Pinghua Li et al.   NATURE GENETICS

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-wide identification of microRNA targets in rice

(2010) Yong-Fang Li et al.   PLANT JOURNAL

A Collection of Target Mimics for Comprehensive Analysis of MicroRNA Function in Arabidopsis thaliana

(2010) Marco Todesco et al.   PLoS Genetics

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Redefining MicroRNA Targets

(2009) Hervé Seitz   CURRENT BIOLOGY

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Long non-coding RNAs: insights into functions

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

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets

(2008) C. Addo-Quaye et al.   BIOINFORMATICS

RNAplex: a fast tool for RNA–RNA interaction search

(2008) Hakim Tafer et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome

(2008) Charles Addo-Quaye et al.   CURRENT BIOLOGY