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

Accurate detection of differential RNA processing

(2013) Philipp Drewe et al.   NUCLEIC ACIDS RESEARCH

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data

(2012) A. M. Mezlini et al.   GENOME RESEARCH

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Modelling and simulating generic RNA-Seq experiments with the flux simulator

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes

(2012) Lisa M. Smith et al.   RNA Biology

Alternative Splicing of RNA Triplets Is Often Regulated and Accelerates Proteome Evolution

(2012) Robert K. Bradley et al.   PLOS BIOLOGY

NSMAP: A method for spliced isoforms identification and quantification from RNA-Seq

(2011) Zheng Xia et al.   BMC BIOINFORMATICS

The GENCODE exome: sequencing the complete human exome

(2011) Alison J Coffey et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing

(2011) J. H. Bahn et al.   GENOME RESEARCH

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Origins of theE. coliStrain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany

(2011) David A. Rasko et al.   NEW ENGLAND JOURNAL OF MEDICINE

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

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

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

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

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Transcript quantification with RNA-Seq data

(2009) Regina Bohnert et al.   BMC BIOINFORMATICS

mGene: Accurate SVM-based gene finding with an application to nematode genomes

(2009) G. Schweikert et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

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

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

Optimal spliced alignments of short sequence reads

(2008) F. De Bona et al.   BIOINFORMATICS

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

Annotating genomes with massive-scale RNA sequencing

(2008) France Denoeud et al.   GENOME BIOLOGY