Hybrid sequencing and map finding (HySeMaFi): optional strategies for extensively deciphering gene splicing and expression in organisms without reference genome

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

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

High-accuracyde novoassembly and SNP detection of chloroplast genomes using a SMRT circular consensus sequencing strategy

(2014) Qiushi Li et al.   NEW PHYTOLOGIST

Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing

(2014) Barbara Treutlein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional diversity during lineage commitment of human blood progenitors

(2014) L. Chen et al.   SCIENCE

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

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

Accurate Identification and Analysis of Human mRNA Isoforms Using Deep Long Read Sequencing

(2013) Hagen Tilgner et al.   G3-Genes Genomes Genetics

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

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

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

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

(2010) G. Zhang et al.   GENOME RESEARCH

Detection of splice junctions from paired-end RNA-seq data by SpliceMap

(2010) K. F. Au et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Statistical inferences for isoform expression in RNA-Seq

(2009) Hui Jiang et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

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

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

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

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

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE