The interplay between microRNA and alternative splicing of linear and circular RNAs in eleven plant species

Identification of circular RNAs and their targets during tomato fruit ripening

(2018) Junliang Yin et al.   POSTHARVEST BIOLOGY AND TECHNOLOGY

Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching

(2018) Sergei A. Filichkin et al.   Frontiers in Plant Science

PlantcircBase: A Database for Plant Circular RNAs

(2017) Qinjie Chu et al.   Molecular Plant

Circular RNAs mediated by transposons are associated with transcriptomic and phenotypic variation in maize

(2017) Lu Chen et al.   NEW PHYTOLOGIST

Light Regulation of Alternative Pre-mRNA Splicing in Plants

(2017) Hangxiao Zhang et al.   PHOTOCHEMISTRY AND PHOTOBIOLOGY

Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis )

(2017) Taotao Wang et al.   PLANT JOURNAL

PlantCircNet: a database for plant circRNA–miRNA–mRNA regulatory networks

(2017) Peijing Zhang et al.   Database-The Journal of Biological Databases and Curation

Identifying and Characterizing the Circular RNAs during the Lifespan of Arabidopsis Leaves

(2017) Tengfei Liu et al.   Frontiers in Plant Science

Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean

(2017) Wei Zhao et al.   Scientific Reports

High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation

(2016) Song Li et al.   DEVELOPMENTAL CELL

Diverse alternative back-splicing and alternative splicing landscape of circular RNAs

(2016) Xiao-Ou Zhang et al.   GENOME RESEARCH

Genome-wide analysis of shoot growth-associated alternative splicing in moso bamboo

(2016) Long Li et al.   MOLECULAR GENETICS AND GENOMICS

Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice

(2016) Chu-Yu Ye et al.   RNA Biology

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

(2016) Salah E. Abdel-Ghany et al.   Nature Communications

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

(2016) Bo Wang et al.   Nature Communications

Intron Lariat RNA Inhibits MicroRNA Biogenesis by Sequestering the Dicing Complex in Arabidopsis

(2016) Ziwei Li et al.   PLoS Genetics

Spatiotemporal transcriptome provides insights into early fruit development of tomato (Solanum lycopersicum)

(2016) Shuaibin Zhang et al.   Scientific Reports

Daytime soybean transcriptome fluctuations during water deficit stress

(2015) Fabiana Aparecida Rodrigues et al.   BMC GENOMICS

Genome wide comparative analysis of the effects of PRMT5 and PRMT4/CARM1 arginine methyltransferases on the Arabidopsis thaliana transcriptome

(2015) Carlos E Hernando et al.   BMC GENOMICS

Transcriptome and hormone profiling reveals Eucalyptus grandis defence responses against Chrysoporthe austroafricana

(2015) Ronishree Mangwanda et al.   BMC GENOMICS

Widespread noncoding circular RNAs in plants

(2015) Chu-Yu Ye et al.   NEW PHYTOLOGIST

The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis

(2015) Tao Chen et al.   NUCLEIC ACIDS RESEARCH

The Transcriptome and Terpene Profile ofEucalyptus grandisReveals Mechanisms of Defense Against the Insect Pest,Leptocybe invasa

(2015) Caryn N. Oates et al.   PLANT AND CELL PHYSIOLOGY

Comprehensive Tissue-Specific Transcriptome Analysis Reveals Distinct Regulatory Programs during Early Tomato Fruit Development

(2015) Richard J. Pattison et al.   PLANT PHYSIOLOGY

Transcriptome-wide investigation of circular RNAs in rice

(2015) Tingting Lu et al.   RNA

The genome of Eucalyptus grandis

(2014) Alexander A. Myburg et al.   NATURE

sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software

(2014) Atul Kakrana et al.   NUCLEIC ACIDS RESEARCH

MOROKOSHI: Transcriptome Database in Sorghum bicolor

(2014) Yuko Makita et al.   PLANT AND CELL PHYSIOLOGY

Global Dissection of Alternative Splicing in Paleopolyploid Soybean

(2014) Yanting Shen et al.   PLANT CELL

Analysis of the Drought Stress-Responsive Transcriptome of Black Cottonwood (Populus trichocarpa) Using Deep RNA Sequencing

(2014) Sha Tang et al.   PLANT MOLECULAR BIOLOGY REPORTER

Intron-Mediated Alternative Splicing of WOOD-ASSOCIATED NAC TRANSCRIPTION FACTOR1B Regulates Cell Wall Thickening during Fiber Development in Populus Species

(2014) Y. Zhao et al.   PLANT PHYSIOLOGY

Comparative expression analysis of resistant and susceptible Populus clones inoculated with Septoria musiva

(2014) Haiying Liang et al.   PLANT SCIENCE

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs

(2014) Ricardo A. Chávez Montes et al.   Nature Communications

Genome-wide identification of non-coding RNAs interacted with microRNAs in soybean

(2014) Chu-Yu Ye et al.   Frontiers in Plant Science

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

(2014) Steve Hoffmann et al.   GENOME BIOLOGY

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

(2014) David B Neale et al.   GENOME BIOLOGY

HTQC: a fast quality control toolkit for Illumina sequencing data

(2013) Xi Yang et al.   BMC BIOINFORMATICS

The developing xylem transcriptome and genome-wide analysis of alternative splicing in Populus trichocarpa (black cottonwood) populations

(2013) Hua Bao et al.   BMC GENOMICS

Transcriptome analysis of rice root heterosis by RNA-Seq

(2013) Rongrong Zhai et al.   BMC GENOMICS

Identification of drought-responsive and novel Populus trichocarpa microRNAs by high-throughput sequencing and their targets using degradome analysis

(2013) Peng Shuai et al.   BMC GENOMICS

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

(2013) Zhenhua Peng et al.   NATURE GENETICS

Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles

(2013) Youko Oono et al.   PLANT MOLECULAR BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

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

(2012) Cole Trapnell et al.   Nature Protocols

PsRobot: a web-based plant small RNA meta-analysis toolbox

(2012) Hua-Jun Wu et al.   NUCLEIC ACIDS RESEARCH

Alternative mRNA processing increases the complexity of microRNA-based gene regulation in Arabidopsis

(2012) Xiaozeng Yang et al.   PLANT JOURNAL

Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types

(2012) Julia Salzman et al.   PLoS One

Improving PacBio Long Read Accuracy by Short Read Alignment

(2012) Kin Fai Au et al.   PLoS One

Circular RNAs are abundant, conserved, and associated with ALU repeats

(2012) W. R. Jeck et al.   RNA

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

Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing

(2011) Melissa ML Wong et al.   BMC GENOMICS

SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing

(2011) ARMANDO GERALDES et al.   Molecular Ecology Resources

MiRNA Control of Vegetative Phase Change in Trees

(2011) Jia-Wei Wang et al.   PLoS Genetics

Plant serine/arginine-rich proteins: roles in precursor messenger RNA splicing, plant development, and stress responses

(2011) Anireddy S. N. Reddy et al.   Wiley Interdisciplinary Reviews-RNA

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

(2011) Daehwan Kim et al.   GENOME BIOLOGY

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

(2010) T. Lu et al.   GENOME RESEARCH

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

(2010) G. Zhang et al.   GENOME RESEARCH

The developmental dynamics of the maize leaf transcriptome

(2010) Pinghua Li et al.   NATURE GENETICS

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

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

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

(2009) G. Ostlund et al.   NUCLEIC ACIDS RESEARCH

Alternative Splicing Studies of the Reactive Oxygen Species Gene Network in Populus Reveal Two Isoforms of High-Isoelectric-Point Superoxide Dismutase

(2009) V. Srivastava et al.   PLANT PHYSIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Sequencing sliced ends reveals microRNA targets

(2008) Ian R Henderson et al.   NATURE BIOTECHNOLOGY

Stress-responsive microRNAs inPopulus

(2008) Shanfa Lu et al.   PLANT JOURNAL

Characterization and comparison of intron structure and alternative splicing between Medicago truncatula, Populus trichocarpa, Arabidopsis and rice

(2008) Jong-Min Baek et al.   PLANT MOLECULAR BIOLOGY

Widespread Translational Inhibition by Plant miRNAs and siRNAs

(2008) P. Brodersen et al.   SCIENCE