Accurate inference of isoforms from multiple sample RNA-Seq data

MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples

(2013) Jonas Behr et al.   BIOINFORMATICS

Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads

(2012) Wei Li et al.   BIOINFORMATICS

Ascaris suum draft genome

(2011) Aaron R. Jex et al.   NATURE

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation

(2011) J. J. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq

(2010) Zhengpeng Wu et al.   BIOINFORMATICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

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

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

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS