A survey of the sorghum transcriptome using single-molecule long reads

Regulation of Alternative Splicing Through Coupling with Transcription and Chromatin Structure

(2015) Shiran Naftelberg et al.   Annual Review of Biochemistry

Long non-coding RNAs and their functions in plants

(2015) Julia A Chekanova   CURRENT OPINION IN PLANT BIOLOGY

Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions inBrachypodium distachyon

(2015) Kranthi K. Mandadi et al.   PLANT CELL

Full-length transcriptome sequences and splice variants obtained by a combination of sequencing platforms applied to different root tissues ofSalvia miltiorrhizaand tanshinone biosynthesis

(2015) Zhichao Xu et al.   PLANT JOURNAL

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

(2014) Thomas Hackl et al.   BIOINFORMATICS

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

(2014) H. Wang et al.   GENOME RESEARCH

Poly(A)-tail profiling reveals an embryonic switch in translational control

(2014) Alexander O. Subtelny et al.   NATURE

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

Genome-Wide Analysis of Alternative Splicing in Zea mays: Landscape and Genetic Regulation

(2014) S. R. Thatcher et al.   PLANT CELL

A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing

(2014) Jeffrey A. Martin et al.   Scientific Reports

Genome-wide survey of Alternative Splicing in Sorghum Bicolor

(2014) Bahman Panahi et al.   PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS

Discovery and Expression Analysis of Alternative Splicing Events Conserved among Plant SR Proteins

(2013) Hypaitia B. Rauch et al.   MOLECULAR BIOLOGY AND EVOLUTION

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Alternative cleavage and polyadenylation: extent, regulation and function

(2013) Ran Elkon et al.   NATURE REVIEWS GENETICS

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Complexity of the Alternative Splicing Landscape in Plants

(2013) A. S. N. Reddy et al.   PLANT CELL

Characterization of the human ESC transcriptome by hybrid sequencing

(2013) K. F. Au et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data

(2012) Jianxing Feng et al.   BIOINFORMATICS

GuiTope: an application for mapping random-sequence peptides to protein sequences

(2012) Rebecca F Halperin et al.   BMC BIOINFORMATICS

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation

(2012) Alexander Sherstnev et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Identification of an intronic splicing regulatory element involved in auto-regulation of alternative splicing ofSCL33pre-mRNA

(2012) Julie Thomas et al.   PLANT JOURNAL

SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data

(2012) Mark F Rogers et al.   GENOME BIOLOGY

Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid

(2011) Diana V Dugas et al.   BMC GENOMICS

Sweet sorghum as a model system for bioenergy crops

(2011) Martín Calviño et al.   CURRENT OPINION IN BIOTECHNOLOGY

Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing

(2011) Y. Shen et al.   GENOME RESEARCH

Functional consequences of developmentally regulated alternative splicing

(2011) Auinash Kalsotra et al.   NATURE REVIEWS GENETICS

Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation

(2011) X. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of mRNA Translation and Stability by microRNAs

(2010) Marc Robert Fabian et al.   Annual Review of Biochemistry

miRBase: integrating microRNA annotation and deep-sequencing data

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

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

(2009) S. A. Filichkin et al.   GENOME RESEARCH

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Targeted 3' Processing of Antisense Transcripts Triggers Arabidopsis FLC Chromatin Silencing

(2009) F. Liu et al.   SCIENCE

Bio-Fuel Crops Research for Energy Security and Rural Development in Developing Countries

(2008) Belum V. S. Reddy et al.   BioEnergy Research

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation

(2008) Yingjia Shen et al.   NUCLEIC ACIDS RESEARCH