Transcriptome analysis of nitrogen-starvation-responsive genes in rice

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

(2013) Sabrina Humbert et al.   BMC GENOMICS

Analysis of the early-flowering mechanisms and generation of T-DNA tagging lines in Kitaake, a model rice cultivar

(2013) Song Lim Kim et al.   JOURNAL OF EXPERIMENTAL BOTANY

Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics

(2013) Hiroaki Sakai et al.   PLANT AND CELL PHYSIOLOGY

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

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

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

Genome-Wide Identification of MicroRNAs in Response to Low Nitrate Availability in Maize Leaves and Roots

(2011) Zhenhua Xu et al.   PLoS One

Nitrogen stress response of a hybrid species: a gene expression study

(2010) Larry C. Brouillette et al.   ANNALS OF BOTANY

RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

(2010) Andrew J Severin et al.   BMC PLANT BIOLOGY

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

(2010) G. Zhang et al.   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Effects of AOX1a Deficiency on Plant Growth, Gene Expression of Respiratory Components and Metabolic Profile Under Low-Nitrogen Stress in Arabidopsis thaliana

(2010) Chihiro K. Watanabe et al.   PLANT AND CELL PHYSIOLOGY

Transcriptome analysis of nitrogen-efficient rice over-expressing alanine aminotransferase

(2009) Perrin H. Beatty et al.   PLANT BIOTECHNOLOGY JOURNAL

Increased nitrogen-use efficiency in transgenic rice plants over-expressing a nitrogen-responsive early nodulin gene identified from rice expression profiling

(2009) YONG-MEI BI et al.   PLANT CELL AND ENVIRONMENT

R2R3-type MYB transcription factor, CmMYB1, is a central nitrogen assimilation regulator in Cyanidioschyzon merolae

(2009) S. Imamura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

AmiGO: online access to ontology and annotation data

(2008) Seth Carbon et al.   BIOINFORMATICS

The search for alternative splicing regulators: new approaches offer a path to a splicing code

(2008) C. J. David et al.   GENES & DEVELOPMENT

Adaptation of Arabidopsis to nitrogen limitation involves induction of anthocyanin synthesis which is controlled by the NLA gene

(2008) M. Peng et al.   JOURNAL OF EXPERIMENTAL BOTANY

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Genetic engineering of improved nitrogen use efficiency in rice by the tissue-specific expression ofalanine aminotransferase

(2008) Ashok K. Shrawat et al.   PLANT BIOTECHNOLOGY JOURNAL

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE