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

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

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

Polyribosomal RNA-Seq Reveals the Decreased Complexity and Diversity of the Arabidopsis Translatome

(2015) Xingtan Zhang et al.   PLoS One

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

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

Defining a personal, allele-specific, and single-molecule long-read transcriptome

(2014) Hagen Tilgner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens

(2014) Hshin-Ping Wu et al.   GENOME BIOLOGY

Genome-Wide Landscape of Alternative Splicing Events in Brachypodium distachyon

(2013) B. Walters et al.   DNA RESEARCH

Regulation of the chloroplastic copper chaperone (CCS) and cuprozinc superoxide dismutase (CSD2) by alternative splicing and copper excess in Glycine max

(2013) Sara Sagasti et al.   FUNCTIONAL PLANT BIOLOGY

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

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

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Complexity of the Alternative Splicing Landscape in Plants

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

The Amborella Genome and the Evolution of Flowering Plants

(2013) et al.   SCIENCE

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

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

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Genome-Wide Identification and Mapping of NBS-Encoding Resistance Genes in Solanum tuberosum Group Phureja

(2012) Roberto Lozano et al.   PLoS One

Improving PacBio Long Read Accuracy by Short Read Alignment

(2012) Kin Fai Au et al.   PLoS One

Alternative splicing in plants – coming of age

(2012) Naeem H. Syed et al.   TRENDS IN PLANT SCIENCE

Extensive changes to alternative splicing patterns following allopolyploidy in natural and resynthesized polyploids

(2011) R. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes

(2011) J. P. Hamilton et al.   Database-The Journal of Biological Databases and Curation

Genome-wide analysis of alternative splicing in Caenorhabditis elegans

(2010) A. K. Ramani 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

Allopolyploidization reduces alternative splicing efficiency for transcripts of the wheat DREB2 homolog, WDREB2

(2009) Akihiro Terashima et al.   GENOME

Genome-Wide Identification of Alternative Splice Forms Down-Regulated by Nonsense-Mediated mRNA Decay in Drosophila

(2009) Kasper Daniel Hansen et al.   PLoS Genetics

Genome-wide analyses of alternative splicing in plants: Opportunities and challenges

(2008) W. B. Barbazuk et al.   GENOME RESEARCH

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

(2008) Qun Pan et al.   NATURE GENETICS

The Amborella genome: an evolutionary reference for plant biology

(2008) Douglas E Soltis et al.   GENOME BIOLOGY