Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant Transcriptomes

Detecting alternatively spliced transcript isoforms from single-molecule long-read sequences without a reference genome

(2017) Xiaoxian Liu et al.   Molecular Ecology Resources

The genome of Chenopodium quinoa

(2017) David E. Jarvis et al.   NATURE

A global survey of alternative splicing in allopolyploid cotton: landscape, complexity and regulation

(2017) Maojun Wang et al.   NEW PHYTOLOGIST

Global identification of alternative splicing via comparative analysis of SMRT- and Illumina-based RNA-seq in strawberry

(2017) Yongping Li et al.   PLANT JOURNAL

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

(2017) Taotao Wang et al.   PLANT JOURNAL

SOS1, HKT1;5, and NHX1 Synergistically Modulate Na+ Homeostasis in the Halophytic Grass Puccinellia tenuiflora

(2017) Wei-Dan Zhang et al.   Frontiers in Plant Science

A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize

(2017) Wenbin Mei et al.   Frontiers in Plant Science

Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts

(2017) Bing Cheng et al.   GigaScience

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

Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research

(2015) Lingli Dong et al.   BMC GENOMICS

Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing

(2015) Jason L. Weirather et al.   NUCLEIC ACIDS RESEARCH

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

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

(2015) Sean P. Gordon et al.   PLoS One

The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres

(2015) Daojun Yuan et al.   Scientific Reports

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

Detecting epigenetic motifs in low coverage and metagenomics settings

(2014) Noam D Beckmann et al.   BMC BIOINFORMATICS

PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme

(2014) Aimin Li et al.   BMC BIOINFORMATICS

Evolutionary Origins and Dynamics of Octoploid Strawberry Subgenomes Revealed by Dense Targeted Capture Linkage Maps

(2014) Jacob A. Tennessen et al.   Genome Biology and Evolution

Single-Nucleotide Resolution Mapping of the Gossypium raimondii Transcriptome Reveals a New Mechanism for Alternative Splicing of Introns

(2014) Qin Li et al.   Molecular Plant

Alternative cleavage and polyadenylation: extent, regulation and function

(2013) Ran Elkon et al.   NATURE REVIEWS GENETICS

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

(2012) Jianxing Feng et al.   BIOINFORMATICS

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Improving PacBio Long Read Accuracy by Short Read Alignment

(2012) Kin Fai Au et al.   PLoS One

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

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

(2011) Y. Shen et al.   GENOME RESEARCH

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

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

A flexible and efficient template format for circular consensus sequencing and SNP detection

(2010) K. J. Travers et al.   NUCLEIC ACIDS RESEARCH

Alternative polyadenylation and gene expression regulation in plants

(2010) Denghui Xing et al.   Wiley Interdisciplinary Reviews-RNA

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

(2009) F. Liu et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

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

(2008) Yingjia Shen et al.   NUCLEIC ACIDS RESEARCH

A Polyadenylation Factor Subunit Implicated in Regulating Oxidative Signaling in Arabidopsis thaliana

(2008) Jingxian Zhang et al.   PLoS One

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE