Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.)

Genome-wide identification of long noncoding RNA genes and their potential association with fecundity and virulence in rice brown planthopper, Nilaparvata lugens

(2015) Huamei Xiao et al.   BMC GENOMICS

Plant nitrogen assimilation and its regulation: a complex puzzle with missing pieces

(2015) Anne Krapp   CURRENT OPINION IN PLANT BIOLOGY

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

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

(2014) H. Wang et al.   GENOME RESEARCH

Nitrogen-use efficiency in maize (Zea mays L.): from 'omics' studies to metabolic modelling

(2014) M. Simons et al.   JOURNAL OF EXPERIMENTAL BOTANY

PNRD: a plant non-coding RNA database

(2014) Xin Yi et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Chao Di et al.   PLANT JOURNAL

Genome-wide identification of housekeeping genes in maize

(2014) Feng Lin et al.   PLANT MOLECULAR BIOLOGY

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

Genome-wide expression profiling of maize in response to individual and combined water and nitrogen stresses

(2013) Sabrina Humbert et al.   BMC GENOMICS

Adaptation of maize source leaf metabolism to stress related disturbances in carbon, nitrogen and phosphorus balance

(2013) Urte Schlüter et al.   BMC GENOMICS

Arabidopsis Non-Coding RNA Regulation in Abiotic Stress Responses

(2013) Akihiro Matsui et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Long non-coding RNAs: new players in cell differentiation and development

(2013) Alessandro Fatica et al.   NATURE REVIEWS GENETICS

Structure and function of long noncoding RNAs in epigenetic regulation

(2013) Tim R Mercer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Plant Nitrogen Assimilation and Use Efficiency

(2012) Guohua Xu et al.   Annual Review of Plant Biology

Transcriptome response to nitrogen starvation in rice

(2012) Hongmei Cai et al.   JOURNAL OF BIOSCIENCES

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

(2012) Cole Trapnell et al.   Nature Protocols

Cis-acting noncoding RNAs: friends and foes

(2012) Sònia Guil et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2012) J. Liu et al.   PLANT CELL

Non-coding RNAs in the plant response to abiotic stress

(2012) Cecilia Contreras-Cubas et al.   PLANTA

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

(2012) Susan Boerner et al.   PLoS One

Polyadenylation-Dependent Control of Long Noncoding RNA Expression by the Poly(A)-Binding Protein Nuclear 1

(2012) Yves B. Beaulieu et al.   PLoS Genetics

Genome-wide views of long non-coding RNAs

(2011) Mary Muers   NATURE REVIEWS GENETICS

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

Gene Expression Biomarkers Provide Sensitive Indicators of in Planta Nitrogen Status in Maize

(2011) X. S. Yang et al.   PLANT PHYSIOLOGY

Global food demand and the sustainable intensification of agriculture

(2011) D. Tilman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural genetic variation in plant photosynthesis

(2011) Pádraic J. Flood et al.   TRENDS IN PLANT SCIENCE

Genomewide characterization of non-polyadenylated RNAs

(2011) Li Yang et al.   GENOME BIOLOGY

Nitrogen uptake, assimilation and remobilization in plants: challenges for sustainable and productive agriculture

(2010) Céline Masclaux-Daubresse et al.   ANNALS OF BOTANY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

A general co-expression network-based approach to gene expression analysis: comparison and applications

(2010) Jianhua Ruan et al.   BMC Systems Biology

Understanding plant response to nitrogen limitation for the improvement of crop nitrogen use efficiency

(2010) S. Kant et al.   JOURNAL OF EXPERIMENTAL BOTANY

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

Breeding Technologies to Increase Crop Production in a Changing World

(2010) M. Tester et al.   SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Deep sequencing analysis of the Methanosarcina mazei Go1 transcriptome in response to nitrogen availability

(2009) D. Jager et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni 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

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS